From 8e255b425a24981be611c27e7a93620255254889 Mon Sep 17 00:00:00 2001 From: Oreoluwa Akinola <101526668+dear-ore@users.noreply.github.com> Date: Tue, 18 Oct 2022 13:33:19 +0100 Subject: [PATCH 01/49] Update command to install graphviz (#307) The command to install graphviz should be "sudo apt-get install graphviz" not "sudo apt get install graphviz". Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com> --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 0646b614..63bdc9d3 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -106,7 +106,7 @@ The `dot` program from Graphviz is needed to render some of the diagrams. * For Debian/Ubuntu users: ```bash -sudo apt get install graphviz +sudo apt-get install graphviz ``` * For non-Debian/Ubuntu users, follow the directions at [the GraphViz download site](https://graphviz.org/download). ```bash From 828f41caaacb47325f35933d8af5cf2a7c2ce351 Mon Sep 17 00:00:00 2001 From: Ngumih Fien <72187339+Fienne@users.noreply.github.com> Date: Tue, 18 Oct 2022 14:12:48 +0100 Subject: [PATCH 02/49] YAML collection require a space after the colon (#301) --- src/topics/yaml-guide.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/topics/yaml-guide.md b/src/topics/yaml-guide.md index 6d05c6ed..6d12538e 100644 --- a/src/topics/yaml-guide.md +++ b/src/topics/yaml-guide.md @@ -25,7 +25,7 @@ You can skip this section if you are already comfortable with YAML. Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, -where whitespace after the `:` is optional. +where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - We use [_camelCase_][camelCase] for multi-word key names that have special meaning in the CWL specification From 2ee768c13c9ad66f626888545db3ea7d7a271c57 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 18 Oct 2022 17:26:32 +0200 Subject: [PATCH 03/49] add attribution for Bamiwo Aluko --- .zenodo.json | 2 +- AUTHORS.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index b36b3818..634d5e79 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -12,7 +12,7 @@ "name": "Andrew Jesaitis" }, { - "name": "bamiwoaluko" + "name": "Bamiwo Aluko" }, { "orcid": "https://orcid.org/0000-0002-6206-4638", diff --git a/AUTHORS.md b/AUTHORS.md index 49ca6978..ed256bfc 100644 --- a/AUTHORS.md +++ b/AUTHORS.md @@ -1,7 +1,7 @@ Thank you to the following contributors (in alphabetical order by user name): * Alain Domissy (@alaindomissy) * Andrew Jesaitis (@andrewjesaitis) -* @bamiwoaluko +* Bamiwo Alukoi (@bamiwoaluko) * Benjamin Carr (@BenjaminHCCarr) * Michele Mastropietro (@elehcim) * Emannuel Fernandes de Oliveira Carvalho (@emannuelOC) From f9e63daf90cb84fb23e5df678592528b451263e0 Mon Sep 17 00:00:00 2001 From: Oreoluwa Akinola <101526668+dear-ore@users.noreply.github.com> Date: Tue, 18 Oct 2022 16:29:25 +0100 Subject: [PATCH 04/49] It should be stated that comments start with # (#300) --- src/introduction/quick-start.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/introduction/quick-start.md b/src/introduction/quick-start.md index 98476fcf..2448de88 100644 --- a/src/introduction/quick-start.md +++ b/src/introduction/quick-start.md @@ -11,7 +11,7 @@ must be comfortable following instructions for the command-line. CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated -with comments: +with comments. Note that comments start with `#`: ```{literalinclude} /_includes/cwl/hello_world.cwl :language: cwl From 864f866dbd21b77acdff6ca8627606c18677717c Mon Sep 17 00:00:00 2001 From: Oreoluwa Akinola <101526668+dear-ore@users.noreply.github.com> Date: Wed, 19 Oct 2022 09:24:25 +0100 Subject: [PATCH 05/49] Changing command to create a virtual environment (#311) `python3 -m venv venv` instead of `python -m venv venv` --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 63bdc9d3..0d38ea9a 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -111,7 +111,7 @@ sudo apt-get install graphviz * For non-Debian/Ubuntu users, follow the directions at [the GraphViz download site](https://graphviz.org/download). ```bash # Create and activate a virtual environment -python -m venv venv +python3 -m venv venv source venv/bin/activate # update the version of pip, setuptools, and wheel (venv) pip install -U pip setuptools wheel From 3b0e1a6502ad0f23b74a7206805d8244e0df21a0 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Wed, 19 Oct 2022 15:32:39 +0200 Subject: [PATCH 06/49] fix typo --- AUTHORS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AUTHORS.md b/AUTHORS.md index ed256bfc..c5c4d8e6 100644 --- a/AUTHORS.md +++ b/AUTHORS.md @@ -1,7 +1,7 @@ Thank you to the following contributors (in alphabetical order by user name): * Alain Domissy (@alaindomissy) * Andrew Jesaitis (@andrewjesaitis) -* Bamiwo Alukoi (@bamiwoaluko) +* Bamiwo Aluko (@bamiwoaluko) * Benjamin Carr (@BenjaminHCCarr) * Michele Mastropietro (@elehcim) * Emannuel Fernandes de Oliveira Carvalho (@emannuelOC) From 676582f58295fb99786c5804cc18c70a7f049f17 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Levai=20Mackenzie=20=C3=81gb=C3=A0r=C3=A0?= <97461848+Mackenzie-OO7@users.noreply.github.com> Date: Wed, 19 Oct 2022 14:42:02 +0100 Subject: [PATCH 07/49] Made modifications to pages (#299) * modified quick-start.md * Update prerequisites.md * Update basic-concepts.md * Update faq.md * Update yaml-guide.md Co-authored-by: Peter Amstutz --- src/faq.md | 67 +++++++++++++++++++++++++++--- src/introduction/basic-concepts.md | 25 +++++------ src/introduction/prerequisites.md | 41 +++++++++--------- src/topics/yaml-guide.md | 24 +++++------ 4 files changed, 106 insertions(+), 51 deletions(-) diff --git a/src/faq.md b/src/faq.md index 8e7f41a2..1b4419bb 100644 --- a/src/faq.md +++ b/src/faq.md @@ -40,10 +40,10 @@ outputs: ## Rename an input file -This example shows how you can change the name of an input file +This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another -step in a workflow and don't want to work with the default names that these +step in a workflow, and don't want to work with the default names that these files were given when they were created. ```yaml @@ -58,7 +58,7 @@ requirements: ## Rename an output file -This example shows how you can change the name of an output file +This example demonstrates how to change the name of an output file from the default name given to it by a tool: ```yaml @@ -79,6 +79,61 @@ outputs: outputEval: ${self[0].basename=inputs.otu_table_name; return self;} ``` +## Referencing a local script + +There are two ways to reference a local script: + +The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script without using `sh` or `bash` commands. + +Start with adding a _shebang_ at the top of your file: + +```{code-block} +#!/bin/bash +``` + +After that, make the script executable with the command `chmod +x scriptname.sh` + +Finally, modify your `PATH` to add the directory where your script is located. +(It is good practice to use `$HOME/bin` for storing your own scripts). + +```bash +export PATH=$PATH:/appropriate/directory +``` + +Now you can use `baseCommand: scriptname.sh` to run the script directly. + +```cwl +#!/bin/bash +cwlVersion: v1.0 +class: CommandLineTool +baseCommand: scriptname.sh +``` + +When you wish to share your work later, you can place your script in a software container in the Docker format. + +The second method involves including an input of `type: File` in the script itself: + +```cwl +class: CommandLineTool + +inputs: + my_script: + type: File + inputBinding: + position: 0 + + + # other inputs go here + +baseCommand: sh + +outputs: [] +``` + +```{note} +In CWL, everything must be directly stated. +``` + ## Setting `self`-based input bindings for optional inputs Currently, `cwltool` can't cope with missing optional inputs if their @@ -108,8 +163,8 @@ outputs: [] ## Model a "one-or-the-other" parameter -Below is an example of how -you can specify different strings to be added to a command line +Below is an example showing how +to specify different strings to be added to a command line, based on the value given to a Boolean parameter. ```yaml @@ -265,7 +320,7 @@ For command-line flags that are either **mutually exclusive** or **dependent**, ``` ## Setting Mutually Exclusive Parameters -In order to properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline javascript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value. +To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value. ```yaml steps: diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index 30459c8a..1c81fde7 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -1,10 +1,10 @@ # Basic Concepts -This section describes the basic concepts for users to get started working with +This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar -with workflow managers, YAML, and comfortable following instructions for the -command-line. The other sections of the user guide cover the same concepts but -in more detail. If you are already familiar with CWL or looking for more advanced +with workflow managers, YAML, and comfortable with following instructions for the +command-line. The other sections of the user guide cover the same concepts, but +in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section. ## The CWL specification @@ -24,7 +24,7 @@ is the {{ cwl_version }}. The specification version can have up to three numbers separated by `.`'s (dots). The first number is the major release, used for backward-incompatible changes like -the removal of deprecated features. The second is the minor release number, +the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification. @@ -37,7 +37,7 @@ the end of this section to [learn more](#learn-more) about it. ## Implementations An implementation of the CWL specification is any software written following -what is defined in a version of the specification document. Implementations may +what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses. @@ -47,6 +47,7 @@ in parallel across many nodes. % TODO: add a link to the Core Concepts -> Requirements section below? + ```{graphviz} :name: specification-and-implementations-graph :caption: CWL specification, implementations, and other tools. @@ -125,13 +126,13 @@ takes inputs and produces outputs like a command-line tool. The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. -The inputs of a workflow can be passed to any of its steps, and +The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow. Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation -not so commonly used. It is discussed in another section. +not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide. The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. @@ -149,12 +150,12 @@ runners. Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained -in detail in another section. +in detail in the [Requirements](../topics/requirements-and-hints.md) section. ## FAIR workflows > The FAIR principles have laid a foundation for sharing and publishing -> digital assets and, in particular, data. The FAIR principles emphasize +> digital assets, and in particular, data. The FAIR principles emphasize > machine accessibility and that all digital assets should be Findable, > Accessible, Interoperable, and Reusable. Workflows encode the methods > by which the scientific process is conducted and via which data are @@ -164,11 +165,11 @@ in detail in another section. > Workflows Community Initiative. CWL has roots in "make" and many similar tools that determine order of -execution based on dependencies between tasks. However, unlike "make", CWL +execution, based on dependencies between tasks. However, unlike "make", CWL tasks are isolated, and you must be explicit about your inputs and outputs. The benefit of explicitness and isolation are flexibility, portability, and -scalability: tools and workflows described with CWL can transparently leverage +scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors. diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index f739add6..20a654a4 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -1,18 +1,18 @@ # Prerequisites -% This page supersedes the old setup.md. We used that page as reference while +% This page supersedes the old setup page: setup.md. We used that page as a reference while % writing this documentation. The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, -`cwltool`. You can use another CWL compatible runner or workflow systems but the results and +`cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical). ```{admonition} CWL Implementations -There are many implementations of the CWL standards. Some are complete CWL runners, -others are plug-ins or extensions to workflow engines. We have a better +There are many implementations of the CWL standards. Some are complete CWL runners, while +others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section. ``` @@ -26,7 +26,7 @@ of the following options for your operating system: - Windows ```{note} -If you are using Windows, you will have to install the Windows Subsystem for Linux 2. +If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+). @@ -59,7 +59,7 @@ $ (venv) pip install cwltool ``` ```{note} -You can find the `cwl-runner` source code [here](https://github.com/common-workflow-language/cwltool/tree/main/cwlref-runner). +You can find the `cwl-runner` [source code](https://github.com/common-workflow-language/cwltool/tree/main/cwlref-runner) in the `cwltool` repository. Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`. ``` @@ -71,10 +71,10 @@ Let's use a simple CWl tool description `true.cwl` with `cwltool`. :name: true.cwl ``` -The `cwltool` command has an option to validate CWL tool and workflow descriptionss. It will parse the -CWL document, look for syntax errors, and verify that the descriptions are compliant -with the CWL standards, without running it. To validate CWL workflows (or even a -standalone command line tool description like above) pass the `--validate` option +The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the +CWL document, look for syntax errors, and verify that the workflow descriptions are compliant +with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a +standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command: ```{runcmd} cwltool --validate true.cwl @@ -91,7 +91,7 @@ You can run the CWL tool description by omitting the `--validate` option: ### cwl-runner Python module -`cwl-runner` is an implementation-agnostic alias for CWL Runners. +`cwl-runner` is an implementation-agnostic alias for CWL Runners. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` alias command then chooses the correct CWL runner. This is convenient for environments with multiple CWL runners. @@ -106,7 +106,7 @@ an alias for `cwltool` under the name `cwl-runner` $ pip install cwlref-runner ``` -Now you can validate and run your workflow with `cwl-runner` executable, +Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section. @@ -120,9 +120,9 @@ as in the previous section. :caption: Running `true.cwl` with `cwl-runner`. ``` -Another way to execute `cwl-runner` is invoking the file directly. For that, -the first thing you need to copy `true.cwl` workflow into a new file -`true_shebang.cwl` and include a special first line, a *shebang*: +Another way to execute `cwl-runner` is by invoking the file directly. For that, +the first thing you need to do is copy `true.cwl` workflow into a new file: +`true_shebang.cwl`, and include a special first line, a *shebang*: ```{literalinclude} /_includes/cwl/true_shebang.cwl :language: cwl @@ -139,7 +139,7 @@ Now you can make the file `true_shebang.cwl` executable with `chmod u+x`. $ chmod u+x true.cwl ``` -And finally you can execute it directly in the command-line and the program +And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file. @@ -152,9 +152,8 @@ rest of the file. The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is -considered a good practice to use `/usr/bin/env ` since it -looks for the `` program in the system `PATH`, instead of -using a hard-coded location. +considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` +looks for the `` program in the system `PATH`, ``` ## Text Editor @@ -164,7 +163,7 @@ an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs. There are extensions for Visual Studio Code and WebStorm that provide -integration with CWL, with customized syntax highlighting and better +integration with CWL, and features such as customized syntax highlighting and better auto-complete: - Visual Studio Code with the Benten (CWL) plugin - @@ -182,7 +181,7 @@ Follow the instructions in the Docker documentation to install it for your operating system: . You do not need to know how to write and build Docker containers. In the -rest of the user guide we will use existing Docker images for running +rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers. diff --git a/src/topics/yaml-guide.md b/src/topics/yaml-guide.md index 6d12538e..9475f83a 100644 --- a/src/topics/yaml-guide.md +++ b/src/topics/yaml-guide.md @@ -5,7 +5,7 @@ [YAML][yaml] is a file format designed to be readable by both computers and humans. -This guide introduces the features of YAML +This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files. ```{note} @@ -27,7 +27,7 @@ Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - -We use [_camelCase_][camelCase] for multi-word key names +[_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example: @@ -48,7 +48,7 @@ numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below). -Values may be wrapped in quotation marks +Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `"1234"` will be treated as a character string , while `1234` will be treated as an integer. @@ -80,7 +80,7 @@ be sure to add at least one space before the `#`! When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. -Called _maps_, +Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as "children") are written @@ -101,7 +101,7 @@ inputs: # this key has an object value prefix: -f ``` -The YAML above illustrates how you can build up complex nested object +The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, @@ -126,7 +126,7 @@ graph TD ## Arrays -In certain circumstances it is necessary to provide +In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. @@ -166,8 +166,8 @@ exclusive_parameters: ## JSON Style -YAML is based on [JavaScript Object Notation (JSON)][json] -and maps and arrays can also be defined in YAML using the native JSON syntax. +YAML is based on [JavaScript Object Notation (JSON)][json]. +Maps and arrays can also be defined in YAML using the native JSON syntax. For example: ```yaml @@ -182,13 +182,13 @@ inputs: {example_flag: {type: boolean, inputBinding: {position: 1, prefix: -f}}} ``` Native JSON can be useful -to indicate where a field is being left intentionally empty +in indicating where a field is intentionally left empty (such as `[]` for an empty array), -and where it makes more sense +as well as where it makes more sense for the values to be located on the same line -(such as when providing option flags and their values in a shell command). +(For example, when providing option flags and their values in a shell command). However, as the second example above shows, -it can severely affect the readability of a YAML file +it can severely affect the readability of a YAML file, and should be used sparingly. ## Reference From c6daa45ca6e871c73f665d87c98ee8f44d173e10 Mon Sep 17 00:00:00 2001 From: Oreoluwa Akinola <101526668+dear-ore@users.noreply.github.com> Date: Wed, 19 Oct 2022 14:59:50 +0100 Subject: [PATCH 08/49] Update prerequisites.md (#312) --- src/introduction/prerequisites.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index 20a654a4..d4ef8993 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -52,7 +52,7 @@ environment: :name: installing-cwltool-with-pip-and-venv :caption: Installing `cwltool` with `pip` and `venv`. -$ python -m venv venv +$ python3 -m venv venv $ source venv/bin/activate $ (venv) pip install -U pip setuptools wheel $ (venv) pip install cwltool From 8b5809d87c54120ea67799bc1e0f7aa1b76d61dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Levai=20Mackenzie=20=C3=81gb=C3=A0r=C3=A0?= <97461848+Mackenzie-OO7@users.noreply.github.com> Date: Wed, 19 Oct 2022 15:09:09 +0100 Subject: [PATCH 09/49] fixed typos (#314) * fixed typos and punctuation errors * Update best-practices.md * Update best-practices.md Co-authored-by: Peter Amstutz --- src/topics/best-practices.md | 24 ++++++++++++------------ src/topics/operations.md | 6 +++--- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/src/topics/best-practices.md b/src/topics/best-practices.md index fe0d663f..4c2e18ab 100644 --- a/src/topics/best-practices.md +++ b/src/topics/best-practices.md @@ -1,8 +1,8 @@ # Best Practices -Below are a set of recommended good practices to keep in mind when writing a +The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines -are presented for consideration on a scale of usefulness: more is better, not +are presented for consideration on a scale of usefulness: although more is better, not all are required. - No `type: string` parameters for names of input or reference @@ -10,15 +10,15 @@ all are required. - A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this - document. For example if the workflow is shared publicly, licensing terms have to be clear so that - a future user can understand under what conditions they can run the workflow, modify it and/or - combine it with other workflows. For this reason please consider including a license field in the + document. For example, if the workflow is shared publicly, licensing terms must be clear so that + a future user understands under what conditions they can run the workflow, modify it and/or + combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]. If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. - Construct the metadata field for the licence by providing a URL of the form + Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license. @@ -38,7 +38,7 @@ all are required. [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md). - Include [attribution information][license-example] for the author(s) of - the CWL tool or workflow description. Use unambiguous identifiers like + the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]. - In tool descriptions, list dependencies using short name(s) under @@ -60,7 +60,7 @@ all are required. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: "https://www.iana.org/assignments/media-types/" }`. [Full IANA media type list][iana-types] (also known as MIME types). For - non-bioinformatics tools use or build an appropriate ontology/controlled + non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it. - Mark all input and output `File`s that are read from or written to in a @@ -68,15 +68,15 @@ all are required. - Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your - tool descriptions with options that you don't need/use. + tool descriptions with options that you don't need or use. - Custom types should be defined with one external YAML per type definition for re-use. -- Include a top level short `label` summarising the tool/workflow. +- Include a top-level short `label` summarising the tool/workflow. -- If useful, include a top level `doc` as well. This should provide a - longer, more detailed description than was provided in the top level `label` +- If useful, include a top-level `doc` as well. This should provide a + longer, more detailed description than was provided in the top-level `label` (see above). - Use `type: enum` instead of `type: string` for elements with a fixed diff --git a/src/topics/operations.md b/src/topics/operations.md index 19f8c817..b6afca2a 100644 --- a/src/topics/operations.md +++ b/src/topics/operations.md @@ -1,6 +1,6 @@ # Operations -Operation is a type of CWL process just like a workflow, a command line tool, or +An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed. @@ -14,7 +14,7 @@ you are ready to submit the workflow to a CWL runner: ``` The `uppercase` step of the workflow is an operation. It can be used like -use a command line tool or an expression. You can also plot it with the +a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`: ```{runcmd} cwltool --print-dot operations.cwl @@ -52,7 +52,7 @@ style=dashed; } ``` -If you try running it with `cwltool` the command will fail, since `cwltool` +If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it: ```{runcmd} cwltool operations.cwl --message Hello From d269169899cd7dfa6d915494bf9f3417b2861593 Mon Sep 17 00:00:00 2001 From: Smyja Date: Wed, 19 Oct 2022 16:11:59 +0100 Subject: [PATCH 10/49] Docker Clarity (#313) * docker clarity * typo fix Co-authored-by: Peter Amstutz --- src/faq.md | 4 ++-- src/topics/using-containers.md | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/faq.md b/src/faq.md index 1b4419bb..fb50e9ad 100644 --- a/src/faq.md +++ b/src/faq.md @@ -246,7 +246,7 @@ inputs: ## Enum Inputs ⚜️ -For command-line flags that require a specific input as the argument, an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.** +For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.** ```yaml Format: @@ -266,7 +266,7 @@ Format: ## Record Inputs 📀 -For command-line flags that are either **mutually exclusive** or **dependent**, a special record type can be defined. You can also specify null here to create optional inputs. +For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs. ```yaml #Using record inputs to create mutually exclusive inputs diff --git a/src/topics/using-containers.md b/src/topics/using-containers.md index 903e6fdc..90a3f0bb 100644 --- a/src/topics/using-containers.md +++ b/src/topics/using-containers.md @@ -41,7 +41,7 @@ hints: dockerPull: node:slim ``` -`baseCommand: node` tells CWL that we will be running this command in a container. We +`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, @@ -49,7 +49,7 @@ the name of the container image (you can even specify the tag, which is good ide best practices when using containers for reproducible research). In this case we have used a container called `node:slim`. -Provide a "hello.js" and invoke `cwltool` providing the tool description and the +Create a Javascript file named "hello.js" and invoke `cwltool` providing the tool description and the input object on the command line: ```{literalinclude} /_includes/cwl/using-containers/hello.js From e24e362a8662314cca337c1ff7ac28401df899c4 Mon Sep 17 00:00:00 2001 From: Ngumih Fien <72187339+Fienne@users.noreply.github.com> Date: Wed, 19 Oct 2022 18:49:44 +0100 Subject: [PATCH 11/49] format the arrangement of the license terms (#317) Co-authored-by: Peter Amstutz --- LICENSE.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/LICENSE.md b/LICENSE.md index d3eb47a0..4345a729 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -28,16 +28,14 @@ Under the following terms: so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. -**No additional restrictions**---You may not apply legal terms or +* **No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that: -Notices: - -* You do not have to comply with the license for elements of the + * You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation. -* No warranties are given. The license may not give you all of the + * No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material. From debd2948da10f9cc9eda88679b22e113910b60fc Mon Sep 17 00:00:00 2001 From: khaiyra <44167602+khaiyra@users.noreply.github.com> Date: Thu, 20 Oct 2022 14:41:17 +0100 Subject: [PATCH 12/49] Update prerequisites.md (#320) --- src/introduction/prerequisites.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index d4ef8993..481caade 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -63,7 +63,7 @@ You can find the `cwl-runner` [source code](https://github.com/common-workflow-l Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`. ``` -Let's use a simple CWl tool description `true.cwl` with `cwltool`. +Let's use a simple CWL tool description `true.cwl` with `cwltool`. ```{literalinclude} /_includes/cwl/true.cwl :language: yaml From aaef4452d3ea296cafd72c9bf79d178a52caeef3 Mon Sep 17 00:00:00 2001 From: Ngumih Fien <72187339+Fienne@users.noreply.github.com> Date: Thu, 20 Oct 2022 20:04:21 +0100 Subject: [PATCH 13/49] edit hd5 to hdf5 and fix broken link (#323) --- src/topics/custom-types.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/topics/custom-types.md b/src/topics/custom-types.md index f0b59caf..e4c47a59 100644 --- a/src/topics/custom-types.md +++ b/src/topics/custom-types.md @@ -7,7 +7,7 @@ customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly. The example below is a CWL description of the [biom convert format][biom] tool for -converting a standard biom table file to hd5 format. +converting a standard biom table file to hdf5 format. ```{literalinclude} /_includes/cwl/custom-types/custom-types.cwl :language: cwl @@ -21,7 +21,7 @@ converting a standard biom table file to hd5 format. :name: custom-types.yml ``` -___Note:___ To follow the example below, you need to [download the example input file](https://raw.githubusercontent.com/common-workflow-language/user_guide/main/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`: +___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`: ```{code-block} console $ wget https://github.com/common-workflow-language/user_guide/raw/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom @@ -48,7 +48,7 @@ the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that -tells the tool to create an OTU table in hd5 format. +tells the tool to create an OTU table in hdf5 format. The contents of the YAML file describing the custom type are given below: From 8b034bb170a0d7424189fb7a3360ce42fadc5e86 Mon Sep 17 00:00:00 2001 From: MARVEBUKA <109809277+MARVEBUKA@users.noreply.github.com> Date: Mon, 24 Oct 2022 18:39:26 +0100 Subject: [PATCH 14/49] updated visualization command (#326) --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 0d38ea9a..3db281a4 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -119,7 +119,7 @@ source venv/bin/activate (venv) pip install ".[all]" # Create the HTML to visualize locally (venv) make html -(venv) open _build/index.html +(venv) open _build/html/index.html # Or you can start a serve that watches for local file changes (venv) make watch # Open in your browser From 8e9dee1316bc5dbf33980b5513791563aa0d810d Mon Sep 17 00:00:00 2001 From: bamiwoaluko <115556244+bamiwoaluko@users.noreply.github.com> Date: Mon, 24 Oct 2022 18:53:00 +0100 Subject: [PATCH 15/49] Update basic-concepts.md (#319) corrected typos, corrected punctuations, rephrased sentences, added a link where required Co-authored-by: Peter Amstutz --- src/introduction/basic-concepts.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index 1c81fde7..a7169c43 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -22,7 +22,7 @@ The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}. -The specification version can have up to three numbers separated by `.`'s (dots). +The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number @@ -109,10 +109,10 @@ behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}: -- A command-line tool; -- An expression tool; -- An operation; -- And a workflow. +- A command-line tool. +- An expression tool. +- An operation. +- A workflow. {{ CWL_PROCESSING_UNITS_GRAPH }} @@ -121,7 +121,7 @@ A command-line tool is a wrapper for a command-line utility like `echo`, An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common -parts of a workflow execution into reusable JavaScript code, that +parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool. The workflow is a process that contains steps. Steps can be other @@ -138,9 +138,9 @@ The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance: -- `InlineJavascriptWorkflow`, enables JavaScript in expressions. -- `SubworkflowFeatureRequirement`, enables nested workflows. -- `InitialWorkDirRequirement`, controls staging files in the input directory. +- `InlineJavascriptWorkflow` - enables JavaScript in expressions. +- `SubworkflowFeatureRequirement` - enables nested workflows. +- `InitialWorkDirRequirement` - controls staging files in the input directory. Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the @@ -159,8 +159,8 @@ in detail in the [Requirements](../topics/requirements-and-hints.md) section. > machine accessibility and that all digital assets should be Findable, > Accessible, Interoperable, and Reusable. Workflows encode the methods > by which the scientific process is conducted and via which data are -> created. It is thus important that workflows both support the creation -> of FAIR data and themselves adhere to the FAIR principles. +> created. It is thus important that workflows support the creation +> of FAIR data and adhere to the FAIR principles. > — [FAIR Computational Workflows](https://workflows.community/groups/fair/), > Workflows Community Initiative. From 217d7d8713c633a43da17fc27d0d520164af9dbc Mon Sep 17 00:00:00 2001 From: khaiyra <44167602+khaiyra@users.noreply.github.com> Date: Mon, 24 Oct 2022 19:28:29 +0100 Subject: [PATCH 16/49] Update basic-concepts.md (#324) Co-authored-by: Peter Amstutz --- src/introduction/basic-concepts.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index a7169c43..086f8c11 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -124,16 +124,16 @@ be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool. +Operation is an abstract process that also takes inputs, produces +outputs, and can be used in a workflow. But it is a special operation +not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide. + The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow. -Operation is an abstract process that also takes inputs, produces -outputs, and can be used in a workflow. But it is a special operation -not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide. - The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance: From 0b55dc767ecd8b288d3ffa3e6f24afbf59864f5f Mon Sep 17 00:00:00 2001 From: MARVEBUKA <109809277+MARVEBUKA@users.noreply.github.com> Date: Mon, 24 Oct 2022 21:48:26 +0100 Subject: [PATCH 17/49] Updated titles to use consistent capitalization (#330) Co-authored-by: Peter Amstutz --- CONTRIBUTING.md | 2 +- src/faq.md | 20 ++++++++++---------- src/introduction/basic-concepts.md | 6 +++--- src/introduction/prerequisites.md | 6 +++--- src/introduction/quick-start.md | 4 ++-- src/topics/expressions.md | 2 +- 6 files changed, 20 insertions(+), 20 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3db281a4..7298c7de 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -148,7 +148,7 @@ are still working after the change. Use “tool description” not “tool wrapper” for describing the first argument given to the `cwl-runner` or `cwltool` commands. -### Code examples +### Code Examples To include code into a Markdown file you have two options. For external files use the following command: diff --git a/src/faq.md b/src/faq.md index fb50e9ad..6da7efa5 100644 --- a/src/faq.md +++ b/src/faq.md @@ -8,7 +8,7 @@ :backlinks: "top" ``` -## Non "`File`" types using `evalFrom` +## Non "`File`" Types Using `evalFrom` ```yaml cwlVersion: v1.0 # or v1.1 @@ -38,7 +38,7 @@ outputs: outputEval: $(self[0].contents) ``` -## Rename an input file +## Rename an Input File This example demonstrates how to change the name of an input file as part of a tool description. @@ -56,7 +56,7 @@ requirements: entryName: $(inputs.src1.basename)_custom_extension ``` -## Rename an output file +## Rename an Output File This example demonstrates how to change the name of an output file from the default name given to it by a tool: @@ -79,7 +79,7 @@ outputs: outputEval: ${self[0].basename=inputs.otu_table_name; return self;} ``` -## Referencing a local script +## Referencing a Local Script There are two ways to reference a local script: @@ -134,7 +134,7 @@ outputs: [] In CWL, everything must be directly stated. ``` -## Setting `self`-based input bindings for optional inputs +## Setting `self`-based Input Bindings for Optional Inputs Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. @@ -161,7 +161,7 @@ baseCommand: echo outputs: [] ``` -## Model a "one-or-the-other" parameter +## Model a "one-or-the-other" Parameter Below is an example showing how to specify different strings to be added to a command line, @@ -184,7 +184,7 @@ baseCommand: echo outputs: [] ``` -## Connect a solo value to an input that expects an array of that type +## Connect a Solo Value to an Input that Expects an Array of that Type Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with @@ -355,7 +355,7 @@ input: My String: $(input.stringvalue) ``` -## `cwltool` errors due to filenames with space characters inside +## `cwltool` Errors due to Filenames with Space Characters Inside `cwltool` does not allow some characters in filenames by default. @@ -369,7 +369,7 @@ Invalid filename: 'a space is here.txt' contains illegal characters If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`. -## CWL Parameter Reference error due to hyphen in input identifier +## CWL Parameter Reference Error due to Hyphen in Input Identifier If `cwltool --validate` returns valid @@ -446,7 +446,7 @@ The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards. -## Debug JavaScript expressions +## Debug JavaScript Expressions You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index 086f8c11..33f1ced7 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -7,7 +7,7 @@ command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section. -## The CWL specification +## The CWL Specification ```{include} /_includes/what-is-cwl.md ``` @@ -152,7 +152,7 @@ Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section. -## FAIR workflows +## FAIR Workflows > The FAIR principles have laid a foundation for sharing and publishing > digital assets, and in particular, data. The FAIR principles emphasize @@ -175,7 +175,7 @@ vendors. `cwltool` also uses the PROV-O standard ontology for data provenance. -## Learn more +## Learn More - Semantic Versioning - - The CWL Specification page in the CWL website: diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index 481caade..94908733 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -32,7 +32,7 @@ for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+). ``` -## CWL runner +## CWL Runner % https://github.com/common-workflow-language/user_guide/issues/166 % https://github.com/common-workflow-language/user_guide/issues/64 @@ -89,7 +89,7 @@ You can run the CWL tool description by omitting the `--validate` option: :caption: Running `true.cwl` with `cwltool`. ``` -### cwl-runner Python module +### Cwl-runner Python Module `cwl-runner` is an implementation-agnostic alias for CWL Runners. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` @@ -191,7 +191,7 @@ Singularity. You can also use alternative container registries for pulling images. ``` -## Learn more +## Learn More - The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts. - The Python `venv` module: diff --git a/src/introduction/quick-start.md b/src/introduction/quick-start.md index 2448de88..84d52dc9 100644 --- a/src/introduction/quick-start.md +++ b/src/introduction/quick-start.md @@ -29,7 +29,7 @@ for the sake of simplicity, we are using the term “workflow” here. You will more about this in the [basic concepts](basic-concepts.md) section. ``` -## Installing a CWL runner +## Installing a CWL Runner `cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the @@ -91,7 +91,7 @@ a requirement. You can choose any name for your workflows and Inputs Object files. ``` -## Learn more +## Learn More Continue reading the next sections of this User Guide! - [List of CWL Implementations](https://www.commonwl.org/implementations). diff --git a/src/topics/expressions.md b/src/topics/expressions.md index eebc027b..4c034a7f 100644 --- a/src/topics/expressions.md +++ b/src/topics/expressions.md @@ -113,7 +113,7 @@ only in certain fields. These are: [file-prop]: https://www.commonwl.org/v1.0/CommandLineTool.html#File -## Using external libraries and inline JavaScript code with `expressionLib` +## Using External Libraries and Inline JavaScript Code with `expressionLib` The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript From 7b71012f6d286fbea44e052a54a1d5977eb9f3ca Mon Sep 17 00:00:00 2001 From: khaiyra <44167602+khaiyra@users.noreply.github.com> Date: Fri, 28 Oct 2022 16:16:00 +0100 Subject: [PATCH 18/49] Network Access documentation (#335) * Update basic-concepts.md * Update command-line-tool.md --- src/topics/command-line-tool.md | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/src/topics/command-line-tool.md b/src/topics/command-line-tool.md index 2977e3a1..1aea6311 100644 --- a/src/topics/command-line-tool.md +++ b/src/topics/command-line-tool.md @@ -63,3 +63,23 @@ and in the [Outputs](../topics/outputs.md) sections. % % - Spaces in commands https://github.com/common-workflow-language/user_guide/issues/39 % - Arguments (tell the reader the different use cases for arguments and inputs, tell them there is a section about inputs) + + +## Network Access +This indicates whether a process requires outgoing IPv4/IPv6 network access. +If a command-line tool is written manually in CWL v1.1+, there is a need to +specify when network access is required. + +```cwl +cwlVersion: v1.2 +class: CommandLineTool + +requirements: + NetworkAccess: + networkAccess: true +``` + +```{note} +CWL v1.0 command-line tools that are upgraded to v1.1 +or v1.2 get Network Access automatically. +``` From ea6ba8e271e85613f4aff849f3c959128dadfdb4 Mon Sep 17 00:00:00 2001 From: "lgtm-com[bot]" <43144390+lgtm-com[bot]@users.noreply.github.com> Date: Wed, 16 Nov 2022 15:20:56 +0100 Subject: [PATCH 19/49] Add CodeQL workflow for GitHub code scanning (#345) Co-authored-by: LGTM Migrator --- .github/workflows/codeql.yml | 42 ++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 .github/workflows/codeql.yml diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml new file mode 100644 index 00000000..c880dca1 --- /dev/null +++ b/.github/workflows/codeql.yml @@ -0,0 +1,42 @@ +name: "CodeQL" + +on: + push: + branches: [ "main", "gh-pages", "release" ] + pull_request: + branches: [ "main" ] + schedule: + - cron: "59 14 * * 5" + +jobs: + analyze: + name: Analyze + runs-on: ubuntu-latest + permissions: + actions: read + contents: read + security-events: write + + strategy: + fail-fast: false + matrix: + language: [ javascript, python ] + + steps: + - name: Checkout + uses: actions/checkout@v3 + + - name: Initialize CodeQL + uses: github/codeql-action/init@v2 + with: + languages: ${{ matrix.language }} + queries: +security-and-quality + + - name: Autobuild + uses: github/codeql-action/autobuild@v2 + if: ${{ matrix.language == 'javascript' || matrix.language == 'python' }} + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v2 + with: + category: "/language:${{ matrix.language }}" From c90de3221f290b56a7102d94e8851c0cf5cdbf1e Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Sun, 13 Nov 2022 09:01:09 +0100 Subject: [PATCH 20/49] Copy fonts style from commonwl.org --- src/_static/css/custom.css | 10 ++++++++++ src/conf.py | 4 ++++ 2 files changed, 14 insertions(+) create mode 100644 src/_static/css/custom.css diff --git a/src/_static/css/custom.css b/src/_static/css/custom.css new file mode 100644 index 00000000..9f53adff --- /dev/null +++ b/src/_static/css/custom.css @@ -0,0 +1,10 @@ +body { + /* + * These settings are copied from the https://commonwl.org website style + * for consistency. + */ + font-family: system-ui, -apple-system, "Segoe UI", Roboto, "Helvetica Neue", Arial, "Noto Sans", "Liberation Sans", sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji"; + font-size: 16px; + line-height: 24px; + color: rgb(33, 37, 41); +} diff --git a/src/conf.py b/src/conf.py index c893d8a5..df703367 100644 --- a/src/conf.py +++ b/src/conf.py @@ -157,6 +157,10 @@ # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] +html_css_files = [ + 'css/custom.css', +] + html_logo = '_static/images/logos/cwl/CWL-Logo-HD-cropped2.png' html_favicon = '_static/images/favicons/cwl/favicon.ico' From e5e47e0cc3834e0490aa08fde95ef21204fe32a8 Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Sun, 13 Nov 2022 09:07:12 +0100 Subject: [PATCH 21/49] Update template from pydata sphinx theme --- src/_templates/sidebar-nav-bs.html | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/src/_templates/sidebar-nav-bs.html b/src/_templates/sidebar-nav-bs.html index 73c66bee..a559969d 100644 --- a/src/_templates/sidebar-nav-bs.html +++ b/src/_templates/sidebar-nav-bs.html @@ -1,11 +1,8 @@ From 385340e4bc6f586b868e750bf46bd30358acbcd5 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 22 Nov 2022 17:45:53 +0100 Subject: [PATCH 22/49] clarify CWL runner --- src/introduction/prerequisites.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index 94908733..afd26dd1 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -59,7 +59,6 @@ $ (venv) pip install cwltool ``` ```{note} -You can find the `cwl-runner` [source code](https://github.com/common-workflow-language/cwltool/tree/main/cwlref-runner) in the `cwltool` repository. Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`. ``` @@ -91,9 +90,12 @@ You can run the CWL tool description by omitting the `--validate` option: ### Cwl-runner Python Module -`cwl-runner` is an implementation-agnostic alias for CWL Runners. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner. +`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means +that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular +CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` -directly. The `cwl-runner` alias command then chooses the correct CWL runner. +directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred +CWL implementation. This is convenient for environments with multiple CWL runners. The CWL community publishes a Python package with the name `cwlref-runner` that installs @@ -153,7 +155,7 @@ The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` -looks for the `` program in the system `PATH`, +looks for the `` program in the system `PATH`, ``` ## Text Editor From ec5285f8feb1d83eff4a08b498f9406a8e7eae0f Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 22 Nov 2022 17:48:56 +0100 Subject: [PATCH 23/49] clarify local script running --- src/faq.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/faq.md b/src/faq.md index 6da7efa5..50843d6a 100644 --- a/src/faq.md +++ b/src/faq.md @@ -83,7 +83,8 @@ outputs: There are two ways to reference a local script: -The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script without using `sh` or `bash` commands. +The first method involves adding the folder containing your scripts to the `PATH` environment variable. +This allows you to run the shell script directly without using `sh` or `bash` commands. Start with adding a _shebang_ at the top of your file: @@ -97,7 +98,7 @@ Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts). ```bash -export PATH=$PATH:/appropriate/directory +export PATH=$PATH:$HOME/bin ``` Now you can use `baseCommand: scriptname.sh` to run the script directly. From c46b733d36ae7dc1b2f609a78378dc2f039c96a5 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 22 Nov 2022 19:01:18 +0100 Subject: [PATCH 24/49] use CWL version 1.2 everywhere --- CONTRIBUTING.md | 3 +++ .../cwl/additional-arguments-and-parameters/arguments.cwl | 3 +-- src/_includes/cwl/creating-files-at-runtime/createfile.cwl | 3 ++- src/_includes/cwl/custom-types/custom-types.cwl | 2 +- src/_includes/cwl/environment-variables/env.cwl | 3 +-- src/_includes/cwl/expressions/expression.cwl | 3 +-- src/_includes/cwl/file-formats/metadata_example.cwl | 2 +- src/_includes/cwl/inputs/array-inputs.cwl | 3 +-- src/_includes/cwl/inputs/inp.cwl | 3 +-- src/_includes/cwl/inputs/record.cwl | 3 +-- .../cwl/metadata-and-authorship/metadata_example2.cwl | 2 +- .../cwl/metadata-and-authorship/metadata_example3.cwl | 2 +- src/_includes/cwl/outputs/array-outputs.cwl | 3 +-- src/_includes/cwl/outputs/stdout.cwl | 3 +-- src/_includes/cwl/outputs/tar.cwl | 3 +-- src/_includes/cwl/parameter-references/tar-param.cwl | 3 +-- .../cwl/specifying-software-requirements/custom-types.cwl | 3 ++- src/_includes/cwl/staging-input-files/linkfile.cwl | 3 +-- src/_includes/cwl/using-containers/docker.cwl | 3 +-- src/_includes/cwl/workflows/1st-workflow.cwl | 3 +-- src/_includes/cwl/workflows/arguments.cwl | 3 +-- src/_includes/cwl/workflows/hello_world.cwl | 3 +-- src/_includes/cwl/workflows/hello_world_to_stdout.cwl | 3 +-- src/_includes/cwl/workflows/nestedworkflows.cwl | 3 +-- src/_includes/cwl/workflows/scatter-nested-workflow.cwl | 3 +-- src/_includes/cwl/workflows/scatter-two-steps.cwl | 3 +-- src/_includes/cwl/workflows/scatter-workflow.cwl | 3 +-- src/_includes/cwl/workflows/tar-param.cwl | 3 +-- src/_includes/cwl/workflows/wc-tool.cwl | 3 +-- 29 files changed, 33 insertions(+), 50 deletions(-) mode change 100644 => 100755 src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl mode change 100644 => 100755 src/_includes/cwl/creating-files-at-runtime/createfile.cwl mode change 100644 => 100755 src/_includes/cwl/custom-types/custom-types.cwl mode change 100644 => 100755 src/_includes/cwl/expressions/expression.cwl mode change 100644 => 100755 src/_includes/cwl/file-formats/metadata_example.cwl mode change 100644 => 100755 src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl mode change 100644 => 100755 src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl mode change 100644 => 100755 src/_includes/cwl/outputs/tar.cwl mode change 100644 => 100755 src/_includes/cwl/specifying-software-requirements/custom-types.cwl mode change 100644 => 100755 src/_includes/cwl/staging-input-files/linkfile.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/1st-workflow.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/arguments.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/nestedworkflows.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/scatter-nested-workflow.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/scatter-two-steps.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/scatter-workflow.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/tar-param.cwl diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7298c7de..7b954969 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -148,8 +148,11 @@ are still working after the change. Use “tool description” not “tool wrapper” for describing the first argument given to the `cwl-runner` or `cwltool` commands. + ### Code Examples +All CWL documents should be version 1.2 unless there is a very good reason otherwise. + To include code into a Markdown file you have two options. For external files use the following command: diff --git a/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl b/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl old mode 100644 new mode 100755 index 3a2e4538..a6f7287c --- a/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl +++ b/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: Example trivial wrapper for Java 9 compiler hints: diff --git a/src/_includes/cwl/creating-files-at-runtime/createfile.cwl b/src/_includes/cwl/creating-files-at-runtime/createfile.cwl old mode 100644 new mode 100755 index 5e39a36f..d5694aab --- a/src/_includes/cwl/creating-files-at-runtime/createfile.cwl +++ b/src/_includes/cwl/creating-files-at-runtime/createfile.cwl @@ -1,5 +1,6 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.2 class: CommandLineTool -cwlVersion: v1.0 baseCommand: ["sh", "example.sh"] requirements: diff --git a/src/_includes/cwl/custom-types/custom-types.cwl b/src/_includes/cwl/custom-types/custom-types.cwl old mode 100644 new mode 100755 index 707d5c2a..d60e6e92 --- a/src/_includes/cwl/custom-types/custom-types.cwl +++ b/src/_includes/cwl/custom-types/custom-types.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool requirements: diff --git a/src/_includes/cwl/environment-variables/env.cwl b/src/_includes/cwl/environment-variables/env.cwl index 7e4d4087..6162a04c 100755 --- a/src/_includes/cwl/environment-variables/env.cwl +++ b/src/_includes/cwl/environment-variables/env.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: env requirements: diff --git a/src/_includes/cwl/expressions/expression.cwl b/src/_includes/cwl/expressions/expression.cwl old mode 100644 new mode 100755 index da1e75dc..a04695bb --- a/src/_includes/cwl/expressions/expression.cwl +++ b/src/_includes/cwl/expressions/expression.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo diff --git a/src/_includes/cwl/file-formats/metadata_example.cwl b/src/_includes/cwl/file-formats/metadata_example.cwl old mode 100644 new mode 100755 index 9485522b..bcaaff70 --- a/src/_includes/cwl/file-formats/metadata_example.cwl +++ b/src/_includes/cwl/file-formats/metadata_example.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: An example tool demonstrating metadata. diff --git a/src/_includes/cwl/inputs/array-inputs.cwl b/src/_includes/cwl/inputs/array-inputs.cwl index bef63538..0e5d6e44 100755 --- a/src/_includes/cwl/inputs/array-inputs.cwl +++ b/src/_includes/cwl/inputs/array-inputs.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool inputs: filesA: diff --git a/src/_includes/cwl/inputs/inp.cwl b/src/_includes/cwl/inputs/inp.cwl index 576c16da..20ac1d79 100755 --- a/src/_includes/cwl/inputs/inp.cwl +++ b/src/_includes/cwl/inputs/inp.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo inputs: diff --git a/src/_includes/cwl/inputs/record.cwl b/src/_includes/cwl/inputs/record.cwl index e33cb44a..e69a1ac9 100755 --- a/src/_includes/cwl/inputs/record.cwl +++ b/src/_includes/cwl/inputs/record.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool inputs: dependent_parameters: diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl old mode 100644 new mode 100755 index 745c1779..ca2b59bd --- a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl +++ b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: An example tool demonstrating metadata. diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl old mode 100644 new mode 100755 index 09d31e4a..e30a3c64 --- a/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl +++ b/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: An example tool demonstrating metadata. diff --git a/src/_includes/cwl/outputs/array-outputs.cwl b/src/_includes/cwl/outputs/array-outputs.cwl index 2d6654ea..9d7d8022 100755 --- a/src/_includes/cwl/outputs/array-outputs.cwl +++ b/src/_includes/cwl/outputs/array-outputs.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: touch inputs: diff --git a/src/_includes/cwl/outputs/stdout.cwl b/src/_includes/cwl/outputs/stdout.cwl index 5908f88f..53e2db0e 100755 --- a/src/_includes/cwl/outputs/stdout.cwl +++ b/src/_includes/cwl/outputs/stdout.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo stdout: output.txt diff --git a/src/_includes/cwl/outputs/tar.cwl b/src/_includes/cwl/outputs/tar.cwl old mode 100644 new mode 100755 index f1b45964..187fe05f --- a/src/_includes/cwl/outputs/tar.cwl +++ b/src/_includes/cwl/outputs/tar.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: [tar, --extract] inputs: diff --git a/src/_includes/cwl/parameter-references/tar-param.cwl b/src/_includes/cwl/parameter-references/tar-param.cwl index 87ad9e0f..913b7fdd 100644 --- a/src/_includes/cwl/parameter-references/tar-param.cwl +++ b/src/_includes/cwl/parameter-references/tar-param.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: [tar, --extract] inputs: diff --git a/src/_includes/cwl/specifying-software-requirements/custom-types.cwl b/src/_includes/cwl/specifying-software-requirements/custom-types.cwl old mode 100644 new mode 100755 index 044db0bf..70cb9dee --- a/src/_includes/cwl/specifying-software-requirements/custom-types.cwl +++ b/src/_includes/cwl/specifying-software-requirements/custom-types.cwl @@ -1,4 +1,5 @@ -cwlVersion: v1.0 +#!/usr/bin/env cwl-runner +cwlVersion: v1.2 class: CommandLineTool label: "InterProScan: protein sequence classifier" diff --git a/src/_includes/cwl/staging-input-files/linkfile.cwl b/src/_includes/cwl/staging-input-files/linkfile.cwl old mode 100644 new mode 100755 index ffeb6996..43cf79bc --- a/src/_includes/cwl/staging-input-files/linkfile.cwl +++ b/src/_includes/cwl/staging-input-files/linkfile.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool hints: DockerRequirement: diff --git a/src/_includes/cwl/using-containers/docker.cwl b/src/_includes/cwl/using-containers/docker.cwl index 9f6090a1..35c5e842 100755 --- a/src/_includes/cwl/using-containers/docker.cwl +++ b/src/_includes/cwl/using-containers/docker.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: node hints: diff --git a/src/_includes/cwl/workflows/1st-workflow.cwl b/src/_includes/cwl/workflows/1st-workflow.cwl old mode 100644 new mode 100755 index 24b19bd2..4da55143 --- a/src/_includes/cwl/workflows/1st-workflow.cwl +++ b/src/_includes/cwl/workflows/1st-workflow.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow inputs: tarball: File diff --git a/src/_includes/cwl/workflows/arguments.cwl b/src/_includes/cwl/workflows/arguments.cwl old mode 100644 new mode 100755 index c26d2642..ff80076a --- a/src/_includes/cwl/workflows/arguments.cwl +++ b/src/_includes/cwl/workflows/arguments.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: Example trivial wrapper for Java 9 compiler hints: diff --git a/src/_includes/cwl/workflows/hello_world.cwl b/src/_includes/cwl/workflows/hello_world.cwl index 48e2f792..1c39bca4 100755 --- a/src/_includes/cwl/workflows/hello_world.cwl +++ b/src/_includes/cwl/workflows/hello_world.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo inputs: diff --git a/src/_includes/cwl/workflows/hello_world_to_stdout.cwl b/src/_includes/cwl/workflows/hello_world_to_stdout.cwl index 1d550fc2..39e8e2d4 100755 --- a/src/_includes/cwl/workflows/hello_world_to_stdout.cwl +++ b/src/_includes/cwl/workflows/hello_world_to_stdout.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo inputs: diff --git a/src/_includes/cwl/workflows/nestedworkflows.cwl b/src/_includes/cwl/workflows/nestedworkflows.cwl old mode 100644 new mode 100755 index 75a4f00a..c43e5096 --- a/src/_includes/cwl/workflows/nestedworkflows.cwl +++ b/src/_includes/cwl/workflows/nestedworkflows.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow inputs: [] diff --git a/src/_includes/cwl/workflows/scatter-nested-workflow.cwl b/src/_includes/cwl/workflows/scatter-nested-workflow.cwl old mode 100644 new mode 100755 index 9b2f6aa6..7bc6c1d7 --- a/src/_includes/cwl/workflows/scatter-nested-workflow.cwl +++ b/src/_includes/cwl/workflows/scatter-nested-workflow.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/src/_includes/cwl/workflows/scatter-two-steps.cwl b/src/_includes/cwl/workflows/scatter-two-steps.cwl old mode 100644 new mode 100755 index 57b9ca2e..c2963cfc --- a/src/_includes/cwl/workflows/scatter-two-steps.cwl +++ b/src/_includes/cwl/workflows/scatter-two-steps.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/src/_includes/cwl/workflows/scatter-workflow.cwl b/src/_includes/cwl/workflows/scatter-workflow.cwl old mode 100644 new mode 100755 index 80a334f3..954e1660 --- a/src/_includes/cwl/workflows/scatter-workflow.cwl +++ b/src/_includes/cwl/workflows/scatter-workflow.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/src/_includes/cwl/workflows/tar-param.cwl b/src/_includes/cwl/workflows/tar-param.cwl old mode 100644 new mode 100755 index 87ad9e0f..913b7fdd --- a/src/_includes/cwl/workflows/tar-param.cwl +++ b/src/_includes/cwl/workflows/tar-param.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: [tar, --extract] inputs: diff --git a/src/_includes/cwl/workflows/wc-tool.cwl b/src/_includes/cwl/workflows/wc-tool.cwl index c3064634..397df77e 100755 --- a/src/_includes/cwl/workflows/wc-tool.cwl +++ b/src/_includes/cwl/workflows/wc-tool.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: wc arguments: ["-c"] From 1e5d8074fad65eb835953d728b1a8c1adf5ac42d Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 22 Nov 2022 19:36:06 +0100 Subject: [PATCH 25/49] rename CWL tests file --- Makefile | 2 +- src/_includes/cwl/{conformance-test.yml => cwl_tests.yml} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename src/_includes/cwl/{conformance-test.yml => cwl_tests.yml} (100%) diff --git a/Makefile b/Makefile index 9f6459ec..81bc3c77 100644 --- a/Makefile +++ b/Makefile @@ -33,7 +33,7 @@ watch: clean ## unittest-examples : unittest-examples: - cd src/_includes/cwl; cwltest --test=conformance-test.yml --tool=${RUNNER} + cd src/_includes/cwl; cwltest --test=cwl_tests.yml --tool=${RUNNER} ## check-json : check-json: diff --git a/src/_includes/cwl/conformance-test.yml b/src/_includes/cwl/cwl_tests.yml similarity index 100% rename from src/_includes/cwl/conformance-test.yml rename to src/_includes/cwl/cwl_tests.yml From 288d912899c6359652cc8544f2186ea4ac3e026d Mon Sep 17 00:00:00 2001 From: XiongJF <624188314@qq.com> Date: Tue, 3 Jan 2023 14:42:19 +0800 Subject: [PATCH 26/49] add exclude_cache_cmd domain for CMDCache --- cwl/sphinx/runcmd.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/cwl/sphinx/runcmd.py b/cwl/sphinx/runcmd.py index ff8bb245..b4ea08de 100644 --- a/cwl/sphinx/runcmd.py +++ b/cwl/sphinx/runcmd.py @@ -40,10 +40,13 @@ class Singleton(_Singleton("SingletonMeta", (object,), {})): class CMDCache(Singleton): cache = {} + exclude_cache_cmd = {hash("cat output.txt")} def get(self, cmd, working_directory): h = hash(cmd) - if h in self.cache: + if h in self.exclude_cache_cmd: + return run_command(cmd, working_directory) + elif h in self.cache: return self.cache[h] else: result = run_command(cmd, working_directory) From a2e4fedd427efcd5c87510c9018093172845597c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Levai=20Mackenzie=20=C3=81gb=C3=A0r=C3=A0?= <97461848+Mackenzie-OO7@users.noreply.github.com> Date: Tue, 3 Jan 2023 17:22:30 +0100 Subject: [PATCH 27/49] add community link to the navbar (#356) --- src/conf.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/conf.py b/src/conf.py index df703367..bcba3134 100644 --- a/src/conf.py +++ b/src/conf.py @@ -171,6 +171,10 @@ ] html_theme_options = { + "external_links": [ + {"name": "Community", "url": "https://www.commonwl.org/community/"}, + ], + "header_links_before_dropdown": 6, "icon_links": [ { "name": "GitHub", From e87eaa2f3927a17b9415c9deaf25a9d337781df3 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Tue, 24 Jan 2023 17:36:11 +0100 Subject: [PATCH 28/49] add PO file for English (#359) --- locales/en/LC_MESSAGES/LICENSE.po | 120 +++++ .../en/LC_MESSAGES/_includes/what-is-cwl.po | 28 + locales/en/LC_MESSAGES/episodes.po | 31 ++ locales/en/LC_MESSAGES/faq.po | 307 +++++++++++ locales/en/LC_MESSAGES/index.po | 68 +++ .../introduction/basic-concepts.po | 270 ++++++++++ locales/en/LC_MESSAGES/introduction/index.po | 31 ++ .../LC_MESSAGES/introduction/prerequisites.po | 298 +++++++++++ .../LC_MESSAGES/introduction/quick-start.po | 191 +++++++ locales/en/LC_MESSAGES/setup.po | 31 ++ locales/en/LC_MESSAGES/sphinx.po | 28 + .../additional-arguments-and-parameters.po | 84 +++ .../en/LC_MESSAGES/topics/best-practices.po | 191 +++++++ .../LC_MESSAGES/topics/command-line-tool.po | 71 +++ .../topics/creating-files-at-runtime.po | 104 ++++ locales/en/LC_MESSAGES/topics/custom-types.po | 99 ++++ .../topics/environment-variables.po | 45 ++ .../en/LC_MESSAGES/topics/expression-tool.po | 53 ++ locales/en/LC_MESSAGES/topics/expressions.po | 383 +++++++++++++ locales/en/LC_MESSAGES/topics/file-formats.po | 93 ++++ locales/en/LC_MESSAGES/topics/index.po | 24 + locales/en/LC_MESSAGES/topics/inputs.po | 313 +++++++++++ .../topics/metadata-and-authorship.po | 70 +++ locales/en/LC_MESSAGES/topics/operations.po | 73 +++ locales/en/LC_MESSAGES/topics/outputs.po | 147 +++++ .../topics/parameter-references.po | 279 ++++++++++ .../topics/requirements-and-hints.po | 24 + .../specifying-software-requirements.po | 68 +++ .../LC_MESSAGES/topics/staging-input-files.po | 48 ++ .../en/LC_MESSAGES/topics/troubleshooting.po | 101 ++++ .../en/LC_MESSAGES/topics/using-containers.po | 106 ++++ locales/en/LC_MESSAGES/topics/workflows.po | 504 ++++++++++++++++++ locales/en/LC_MESSAGES/topics/yaml-guide.po | 193 +++++++ locales/en/LC_MESSAGES/tutorials.po | 58 ++ setup.cfg | 2 + src/conf.py | 4 + 36 files changed, 4540 insertions(+) create mode 100644 locales/en/LC_MESSAGES/LICENSE.po create mode 100644 locales/en/LC_MESSAGES/_includes/what-is-cwl.po create mode 100644 locales/en/LC_MESSAGES/episodes.po create mode 100644 locales/en/LC_MESSAGES/faq.po create mode 100644 locales/en/LC_MESSAGES/index.po create mode 100644 locales/en/LC_MESSAGES/introduction/basic-concepts.po create mode 100644 locales/en/LC_MESSAGES/introduction/index.po create mode 100644 locales/en/LC_MESSAGES/introduction/prerequisites.po create mode 100644 locales/en/LC_MESSAGES/introduction/quick-start.po create mode 100644 locales/en/LC_MESSAGES/setup.po create mode 100644 locales/en/LC_MESSAGES/sphinx.po create mode 100644 locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po create mode 100644 locales/en/LC_MESSAGES/topics/best-practices.po create mode 100644 locales/en/LC_MESSAGES/topics/command-line-tool.po create mode 100644 locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po create mode 100644 locales/en/LC_MESSAGES/topics/custom-types.po create mode 100644 locales/en/LC_MESSAGES/topics/environment-variables.po create mode 100644 locales/en/LC_MESSAGES/topics/expression-tool.po create mode 100644 locales/en/LC_MESSAGES/topics/expressions.po create mode 100644 locales/en/LC_MESSAGES/topics/file-formats.po create mode 100644 locales/en/LC_MESSAGES/topics/index.po create mode 100644 locales/en/LC_MESSAGES/topics/inputs.po create mode 100644 locales/en/LC_MESSAGES/topics/metadata-and-authorship.po create mode 100644 locales/en/LC_MESSAGES/topics/operations.po create mode 100644 locales/en/LC_MESSAGES/topics/outputs.po create mode 100644 locales/en/LC_MESSAGES/topics/parameter-references.po create mode 100644 locales/en/LC_MESSAGES/topics/requirements-and-hints.po create mode 100644 locales/en/LC_MESSAGES/topics/specifying-software-requirements.po create mode 100644 locales/en/LC_MESSAGES/topics/staging-input-files.po create mode 100644 locales/en/LC_MESSAGES/topics/troubleshooting.po create mode 100644 locales/en/LC_MESSAGES/topics/using-containers.po create mode 100644 locales/en/LC_MESSAGES/topics/workflows.po create mode 100644 locales/en/LC_MESSAGES/topics/yaml-guide.po create mode 100644 locales/en/LC_MESSAGES/tutorials.po diff --git a/locales/en/LC_MESSAGES/LICENSE.po b/locales/en/LC_MESSAGES/LICENSE.po new file mode 100644 index 00000000..29b53dd1 --- /dev/null +++ b/locales/en/LC_MESSAGES/LICENSE.po @@ -0,0 +1,120 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../../LICENSE.md:2 f0c9a54a904e42249441ee22e39d6f3a +msgid "Licenses" +msgstr "" + +#: ../../../LICENSE.md:4 6c99230ebe4d48689e09e2da1484abc9 +msgid "Instructional Material" +msgstr "" + +#: ../../../LICENSE.md:6 327a6405608b4df488fc6aee756f94b7 +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." +msgstr "" + +#: ../../../LICENSE.md:12 91d85fe9673942658f5d17e286ac6b69 +msgid "You are free:" +msgstr "" + +#: ../../../LICENSE.md:14 c010a0b9145e4532896b114d4e0c7768 +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../../LICENSE.md:15 8e7d2d9301a8452994e4b33edb3c7ea0 +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../../LICENSE.md:17 0fdc0b2074bc4cfd8cd020d51a3d4f3b +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../../LICENSE.md:19 220eba84dd874fb59ac0d4f7a95695fc +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms." +msgstr "" + +#: ../../../LICENSE.md:22 c21178abaf374ca5ae83fb9b94761e7e +msgid "Under the following terms:" +msgstr "" + +#: ../../../LICENSE.md:24 90e30b28cfdb4c8fb6bf2e2687ac47c3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" + +#: ../../../LICENSE.md:32 c40a837670f84762bffc0cc8d697d45d +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" +msgstr "" + +#: ../../../LICENSE.md:36 233edb183ff44c7293756df599b2a130 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." +msgstr "" + +#: ../../../LICENSE.md:39 027339c3a92747e8948b11671ace4145 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." +msgstr "" + +#: ../../../LICENSE.md:44 89dcc55f3d5d445b97912648ee5dba03 +msgid "Software" +msgstr "" + +#: ../../../LICENSE.md:46 070952c76313480d92f0b78321a6a1e2 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../../LICENSE.md:51 3279f7573aa44853af83dbf9dd9748a9 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." +msgstr "" + +#: ../../../LICENSE.md:57 979969ab3c3f4080b6c7e879efe9f351 +msgid "Trademark" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/_includes/what-is-cwl.po b/locales/en/LC_MESSAGES/_includes/what-is-cwl.po new file mode 100644 index 00000000..bc854eb9 --- /dev/null +++ b/locales/en/LC_MESSAGES/_includes/what-is-cwl.po @@ -0,0 +1,28 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../_includes/what-is-cwl.md:1 ffc6d3382e944f22a8b13062eb1badc4 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/episodes.po b/locales/en/LC_MESSAGES/episodes.po new file mode 100644 index 00000000..ed5b10aa --- /dev/null +++ b/locales/en/LC_MESSAGES/episodes.po @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../episodes.md:5 0c99dd9365d14d26b9b3bb5e88f33570 +msgid "This page has moved" +msgstr "" + +#: ../../episodes.md:9 2718a75eccf84a1fa22356367d3b772e +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/faq.po b/locales/en/LC_MESSAGES/faq.po new file mode 100644 index 00000000..c74aeb6e --- /dev/null +++ b/locales/en/LC_MESSAGES/faq.po @@ -0,0 +1,307 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../faq.md:1 1479ffe379ea483290f2c16ddc8d6358 +msgid "FAQ" +msgstr "" + +#: ../../faq.md:11 b6cd88863b754a7d8467948ea72063ac +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../faq.md:41 29876633f61f4befa1ba764a8e14909a +msgid "Rename an Input File" +msgstr "" + +#: ../../faq.md:43 c523a45d4fff4ac5b451b8c9e947a0c1 +msgid "" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "" + +#: ../../faq.md:59 6761f620fae44513ba675bb845dad5af +msgid "Rename an Output File" +msgstr "" + +#: ../../faq.md:61 83312f5876ea492c9a881b8d1d8ec232 +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" +msgstr "" + +#: ../../faq.md:82 da3f295db7584f2ab5532fb915c8ada7 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../faq.md:84 e4aec7bca9bf4ef0a3d709fd0771d886 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../faq.md:86 f6fcb55812944ad98053fee5243125fb +msgid "" +"The first method involves adding the folder containing your scripts to " +"the `PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../faq.md:89 7a83b32f4124408ab1f0dc3303d5d640 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../faq.md:95 c59ec88c1d1545699fd0c00f6173dccc +msgid "" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" +msgstr "" + +#: ../../faq.md:97 dbd4fb58d2e34ccbb9544f2106ee56e5 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "" + +#: ../../faq.md:104 9fb24ecdc09b438bb46e8107880e77a0 +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../faq.md:113 b8624be7349d472b9b86409bd5b786cd +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." +msgstr "" + +#: ../../faq.md:115 fdcc23c875974ee58a4e5ae702eaac67 +msgid "" +"The second method involves including an input of `type: File` in the " +"script itself:" +msgstr "" + +#: ../../faq.md:135 da2ee2848dbc4dff8663c1fbf00c863f +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../faq.md:138 782152c8aab84a12bb04375096f492b6 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../faq.md:140 da2600292146447aa527f24c69cfb776 +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." +msgstr "" + +#: ../../faq.md:165 dc07a65c25854ef6b21cb4a43bee4d31 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../faq.md:167 76bfb57ea05647748b60e36712a8b100 +msgid "" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../faq.md:188 be450f9113f3451691eea5f0d30c3c74 +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../faq.md:190 a328ad7be4e44194b8a1fb5a436d1265 +msgid "" +"Using " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../faq.md:194 d86e24a5d27b418ba29e5439b34a5c13 +msgid "merge_nested" +msgstr "" + +#: ../../faq.md:196 f9b6d21ce7f3405da57fa7443e623b8a +msgid "" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../faq.md:199 1ac676ef33bb45c4b7fc371e7bd84f07 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../faq.md:201 75cef09a92cc44c397a18f81840743b2 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." +msgstr "" + +#: ../../faq.md:229 5bd33a98001148e7b8e83b9bb83b62ee +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../faq.md:231 70651f1b65fd4e20b0f1719c3b8ea3f8 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." +msgstr "" + +#: ../../faq.md:247 cb3f5cae1479448c9669e2751fd34460 +msgid "" +msgstr "" + +#: ../../faq.md:248 74eafea819d6405b8f573da4ec712445 +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../faq.md:250 4955ef4f959143b096125f95ec32c1e2 +msgid "" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" +msgstr "" + +#: ../../faq.md:267 bdf0e5bf3c754f639fbb4ad24076bc4a +msgid "" +msgstr "" + +#: ../../faq.md:268 64c7ae1eaf6b4b0cb4a5fc23feb6349e +msgid "Record Inputs 📀" +msgstr "" + +#: ../../faq.md:270 ad83e44a7f914cfbb46aa191a17d4c85 +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." +msgstr "" + +#: ../../faq.md:322 68e228ecf0be4753832a31ceb933fc19 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../faq.md:324 e2f19825601845b59d5cbeeeb0024622 +msgid "" +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." +msgstr "" + +#: ../../faq.md:342 0824a9e1f5684da481163cd16fed94b9 +msgid "Setting Booleans" +msgstr "" + +#: ../../faq.md:344 192e416a398845838d55bdb71190bb70 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../faq.md:349 eb6a00b2ff3a4ec384a0308f00dd8c4c +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../faq.md:351 9a7df9d0f389421298e6d456822e52a4 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../faq.md:359 9cab760a07114447a817f63ff61ff346 +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../faq.md:361 9ccf1286db084b67a37b2217a9764584 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../faq.md:363 33ea1db2582f4fe78436fb1a8f431b15 +msgid "" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "" + +#: ../../faq.md:371 0f8a3fc6e622464fae1366a053baa78c +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "" + +#: ../../faq.md:373 6a3ba881461642aa8d7654dad772ccd3 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../faq.md:375 253cbea8229743b8a064d4d2fac24f12 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../faq.md:384 63190f04254b4459880b1ee84886bbab +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../faq.md:396 61d3a0026a274eafa31b02220bc4bd0e +msgid "The file is here" +msgstr "" + +#: ../../faq.md:410 2a99b8770636429693ff44563f0ac148 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../faq.md:423 a0d1eff495924aeaaad2ed92010e92f4 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../faq.md:436 a901e5d22e644dcc848d347bcf87d59b +msgid "" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../faq.md:442 5baccb1d1e604c849cce7b27223b1f9f +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../faq.md:445 b8421426848c470db2324fde8ae8f05d +msgid "" +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." +msgstr "" + +#: ../../faq.md:450 1a3fecc9eb7a4dcdaf577983c505ba13 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../faq.md:452 b17460fcb17e40da879383df593f2a93 +msgid "" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/index.po b/locales/en/LC_MESSAGES/index.po new file mode 100644 index 00000000..2437acd8 --- /dev/null +++ b/locales/en/LC_MESSAGES/index.po @@ -0,0 +1,68 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../index.md:1 618bf3fb1f364be791cc5f2bf77667d5 +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../index.md:3 67f4f01edc5b4261a70e4efc3d792f64 +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../index.md:7 284c0f5ead3142649c3c6d4f04da4851 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../index.md:9 75a3c6a67c2e4593a098c839483ae47f +msgid "" +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." +msgstr "" + +#: ../../index.md:16 6061795c74ce415eb3e4f1ca3ed91de6 +msgid "Navigating the User Guide" +msgstr "" + +#: ../../index.md:18 c74efbca9bcd4fda9c4e94d774caa91c +msgid "" +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." +msgstr "" + +#: ../../index.md:23 f2bc70925dea4573ab177c5d2f2b5dcb +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../index.md:28 3e4e62c52c5547c6a4e77131ab1dee39 +msgid "Table of Contents" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/introduction/basic-concepts.po b/locales/en/LC_MESSAGES/introduction/basic-concepts.po new file mode 100644 index 00000000..3fe5662f --- /dev/null +++ b/locales/en/LC_MESSAGES/introduction/basic-concepts.po @@ -0,0 +1,270 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../introduction/basic-concepts.md:1 5f43861a84a2494b8e1bc973ac85b3d0 +msgid "Basic Concepts" +msgstr "" + +#: ../../introduction/basic-concepts.md:3 90cc7b0ef1404f72ae0f5b17f6f2a966 +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." +msgstr "" + +#: ../../introduction/basic-concepts.md:10 1685ddf11a014fe28df75dedb7c39e07 +msgid "The CWL Specification" +msgstr "" + +#: ../../_includes/what-is-cwl.md:2 9cb90a376bfe4058922b1c91ea4ce184 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../introduction/basic-concepts.md:21 cc05f8193ee6403daca03d2d19ccfcd7 +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../introduction/basic-concepts.md:25 f5a0ba9dfc1f49ab937e8122fe4761e0 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." +msgstr "" + +#: ../../introduction/basic-concepts.md:33 8100683970154870993d19d7a5a6bd22 +msgid "" +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." +msgstr "" + +#: ../../introduction/basic-concepts.md:37 cc5c29f65655465db44dd4eed8f11c7b +msgid "Implementations" +msgstr "" + +#: ../../introduction/basic-concepts.md:39 c07822e70e774ea2bb3da2cfd69aa360 +msgid "" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." +msgstr "" + +#: ../../introduction/basic-concepts.md:44 6735911046aa466aa2a371ffff22a9fe +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." +msgstr "" + +#: ../../introduction/basic-concepts.md:51 795e23a746c749deacb68a18d9a3333b +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../introduction/basic-concepts.md:105 e7c0b2155a024860b8d3fd7c9ef75f38 +msgid "Processes and Requirements" +msgstr "" + +#: ../../introduction/basic-concepts.md:107 cf57f60e189e40c09e946f56a1fdf0b8 +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" +msgstr "" + +#: ../../introduction/basic-concepts.md:112 6201ed50ccf944c2aaf7795d411e236d +msgid "A command-line tool." +msgstr "" + +#: ../../introduction/basic-concepts.md:113 a6f9f66dec354e09bd1778d2bf71a7ef +msgid "An expression tool." +msgstr "" + +#: ../../introduction/basic-concepts.md:114 43927a824e584c3c8914119bcdfdffbc +msgid "An operation." +msgstr "" + +#: ../../introduction/basic-concepts.md:115 98f30716f9154c51bcf95a9a26613c6e +msgid "A workflow." +msgstr "" + +#: ../../introduction/basic-concepts.md:118 07807b77a0a444568348e8c20e540296 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../introduction/basic-concepts.md:119 f7dd65df72be46e88ad933e85d2cfe32 +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../introduction/basic-concepts.md:122 7c12205b897c4d6ea918fc8b371ba329 +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." +msgstr "" + +#: ../../introduction/basic-concepts.md:127 965bd0c3dedc43d188c9c7b5db33b1f5 +msgid "" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../introduction/basic-concepts.md:131 7299dcb09d2b4967a9d46d3b433d439e +msgid "" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." +msgstr "" + +#: ../../introduction/basic-concepts.md:137 ea9d197aab4c41788a4a0e3d48c1c168 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" +msgstr "" + +#: ../../introduction/basic-concepts.md:141 592f212970f84365a86a69cfb8c26369 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../introduction/basic-concepts.md:142 57e5ad64e68545a788b43e4e921bb23f +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../introduction/basic-concepts.md:143 397171706bf349feb2c9bee5a993ea1e +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input " +"directory." +msgstr "" + +#: ../../introduction/basic-concepts.md:145 fa9d473ae58b4053981a45a888470655 +msgid "" +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." +msgstr "" + +#: ../../introduction/basic-concepts.md:151 b9cc1fd288764bd78eda4703a2700a02 +msgid "" +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." +msgstr "" + +#: ../../introduction/basic-concepts.md:155 cf12d86b4e7c48c892d6be8233ea2bc9 +msgid "FAIR Workflows" +msgstr "" + +#: ../../introduction/basic-concepts.md:157 a83ecf7c5eaa4af3a676060d12ec7e7e +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows support the creation of FAIR data " +"and adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." +msgstr "" + +#: ../../introduction/basic-concepts.md:167 7451c042271941d6b283bf6d54b76acb +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." +msgstr "" + +#: ../../introduction/basic-concepts.md:171 d356140962c244d78b4a2c888bf03963 +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." +msgstr "" + +#: ../../introduction/basic-concepts.md:176 8fee6b5cd95144e1bced764b112a9d3f +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../introduction/basic-concepts.md:178 38ce1ceb880b4421b9ea2ee52e1153da +msgid "Learn More" +msgstr "" + +#: ../../introduction/basic-concepts.md:180 9a631f69c9504527bcd02a8f40f21c3f +msgid "Semantic Versioning - " +msgstr "" + +#: ../../introduction/basic-concepts.md:181 6141f823850e411691c2ef7047c9ecab +msgid "" +"The CWL Specification page in the CWL website: " +"" +msgstr "" + +#: ../../introduction/basic-concepts.md:182 6a07a8b45dc54851b5b78597891be763 +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../introduction/basic-concepts.md:183 f246c41bb0f946c590736c40713af684 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "" + +#: ../../introduction/basic-concepts.md:184 d9d8d29e5c0e427299f696073dfbfc1b +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../introduction/basic-concepts.md:185 581a427aed9e483489b6123ee1879d80 +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/introduction/index.po b/locales/en/LC_MESSAGES/introduction/index.po new file mode 100644 index 00000000..3b6add35 --- /dev/null +++ b/locales/en/LC_MESSAGES/introduction/index.po @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../introduction/index.md:1 b93db93ee9a24f03805cc032d22ca212 +msgid "Introduction" +msgstr "" + +#: ../../introduction/index.md:3 f77b8595af564c688c37097c43e04c86 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/introduction/prerequisites.po b/locales/en/LC_MESSAGES/introduction/prerequisites.po new file mode 100644 index 00000000..f8f47a94 --- /dev/null +++ b/locales/en/LC_MESSAGES/introduction/prerequisites.po @@ -0,0 +1,298 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../introduction/prerequisites.md:1 7bbfeec267824100866390bfcfa6cec9 +msgid "Prerequisites" +msgstr "" + +#: ../../introduction/prerequisites.md:6 aa8e8b6a8dfa499f99598f30dca4074f +msgid "" +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../introduction/prerequisites.md:12 cf4757d4aef2456397017d2ff13499ba +msgid "CWL Implementations" +msgstr "" + +#: ../../introduction/prerequisites.md:14 502c3afa077249b98a51051b23698a6d +msgid "" +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." +msgstr "" + +#: ../../introduction/prerequisites.md:19 9a788e46f9d64d30aeff30a86182884c +msgid "Operating System" +msgstr "" + +#: ../../introduction/prerequisites.md:21 cc76660874a944369f69207bb1e0e856 +msgid "" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" +msgstr "" + +#: ../../introduction/prerequisites.md:24 77c62d947e894088afc8520451c79ac1 +msgid "Linux" +msgstr "" + +#: ../../introduction/prerequisites.md:25 32cd53abe1744596b3b33835cd8d1eb1 +msgid "macOS" +msgstr "" + +#: ../../introduction/prerequisites.md:26 1a7b4392aec64e3e9c053288362f342a +msgid "Windows" +msgstr "" + +#: ../../introduction/prerequisites.md:29 dcea6593d35c40bc9c0d39d4a788fbc1 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem" +" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " +"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" +"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " +"details on installing WSL2. Your operating system also needs internet " +"access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../introduction/prerequisites.md:35 45bde9e20d0d45eb93427f5b6a3634dd +msgid "CWL Runner" +msgstr "" + +#: ../../introduction/prerequisites.md:41 998f8c45ed8f4075a577d4e6af1eda5b +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../introduction/prerequisites.md:46 813a16e6431744b1aad3bc11a2402e44 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create " +"and activate a Python virtual environment using the `venv` module, and " +"install `cwltool` in that environment:" +msgstr "" + +#: ../../introduction/prerequisites.md:51 297d141896a84499a91f312a0016547f +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../introduction/prerequisites.md:62 ad7893d4a87d441c8aedbf168d3ca9ad +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` " +"and `conda`." +msgstr "" + +#: ../../introduction/prerequisites.md:65 5dbc4e8a1c544a258d5b2d965db08be2 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../introduction/prerequisites.md:67 380bf05c4a754d008499fa6206e86e90 +msgid "`true.cwl`" +msgstr "" + +#: ../../introduction/prerequisites.md:73 6d772529b43746a9bbb7c3bd2fb033a2 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" +msgstr "" + +#: ../../introduction/prerequisites.md:79 d48c1d5aab4d4b78b610a6a8cecbac3f +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../introduction/prerequisites.md:84 50a41a581e2045fd9fcd7149162d1b43 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../introduction/prerequisites.md:86 35183394d2db4b0797e6a5533cf91eed +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../introduction/prerequisites.md:91 b59575e71904478e8833c13b38d53c91 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../introduction/prerequisites.md:93 c784985a2d3d4d5c9583fe8d76037a90 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../introduction/prerequisites.md:101 1fa903efc96d46c79a00a49b9ed778ee +msgid "" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../introduction/prerequisites.md:104 ebecb9c15b7549c1bf82cbc381721378 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../introduction/prerequisites.md:111 4290343102b746a6987d45a33fb75e8f +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." +msgstr "" + +#: ../../introduction/prerequisites.md:115 95dd822409aa414d848cf74a0882f12d +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../introduction/prerequisites.md:120 be41ce025e294eef8015ac9ffaecd31d +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../introduction/prerequisites.md:125 6ff60669f1ec486e9c80cd32f2f0b8da +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" +msgstr "" + +#: ../../introduction/prerequisites.md:129 284249ed02604c479e8a7f9ae098a936 +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../introduction/prerequisites.md:135 2830ba8ada494febaa3cab175aae5c96 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../introduction/prerequisites.md:137 b4a5c084f47a4524b4bbc783481ddb80 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../introduction/prerequisites.md:144 09daa94a2e764c588ed9bdf05686195c +msgid "" +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." +msgstr "" + +#: ../../introduction/prerequisites.md:148 16b2246ddcde4bd4bab4c9b85a3245cd +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../introduction/prerequisites.md:154 8e5ac54df4264041a8766f683a530806 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env ` rather than" +" using a hard-coded location, since `/usr/bin/env ` looks for" +" the `` program in the system `PATH`," +msgstr "" + +#: ../../introduction/prerequisites.md:161 98043798d4f04488b47f65f6a3d0cbdf +msgid "Text Editor" +msgstr "" + +#: ../../introduction/prerequisites.md:163 dd5138ef1899479eb6a8419834dc94d4 +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../introduction/prerequisites.md:167 2c49302420ca4ef58824a611f6e21631 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" +msgstr "" + +#: ../../introduction/prerequisites.md:171 121e8e64431f49159424ed4ffad079e0 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +"" +msgstr "" + +#: ../../introduction/prerequisites.md:172 786d0c2fb6c44f5c8ddb42ad714b43cc +msgid "" +"cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../introduction/prerequisites.md:174 0a7322840cc64223985de5eaf3f6e5ef +msgid "" +"The CWL community also maintains a list of editors and viewers: " +"" +msgstr "" + +#: ../../introduction/prerequisites.md:177 adf7801f93e54841935427ad5fa76ee1 +msgid "Docker" +msgstr "" + +#: ../../introduction/prerequisites.md:181 2d5c42927e8347efa27e75882e59f27d +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: " +"." +msgstr "" + +#: ../../introduction/prerequisites.md:185 58f717b8eb5546459d0e97cf3f4eef0a +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models " +"with and without containers." +msgstr "" + +#: ../../introduction/prerequisites.md:191 2c0ad9dee73c4e278ef0ad7f731c4931 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for " +"pulling images." +msgstr "" + +#: ../../introduction/prerequisites.md:196 a80ae1bdfdb04e1598f06d5115d624eb +msgid "Learn More" +msgstr "" + +#: ../../introduction/prerequisites.md:198 baf0ff9fd9314b5884cf6f2110d964b3 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." +msgstr "" + +#: ../../introduction/prerequisites.md:199 958ac076e60a420b8b8d790cd49f6da8 +msgid "The Python `venv` module: " +msgstr "" + diff --git a/locales/en/LC_MESSAGES/introduction/quick-start.po b/locales/en/LC_MESSAGES/introduction/quick-start.po new file mode 100644 index 00000000..077b542d --- /dev/null +++ b/locales/en/LC_MESSAGES/introduction/quick-start.po @@ -0,0 +1,191 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../introduction/quick-start.md:1 47ace6396c93455bb9b8cb8a70be0679 +msgid "Quick Start" +msgstr "" + +#: ../../introduction/quick-start.md:3 17131fb92d5a46d99b7665d0c2890a46 +msgid "" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../introduction/quick-start.md:7 ad577f43c1ec4d79b9cbe4cd5125a31a +msgid "“Hello World”" +msgstr "" + +#: ../../_includes/what-is-cwl.md:2 4d26ec28a1fa419bb9a1f536e4168925 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../introduction/quick-start.md:12 12247e5c020e4eabaddc0a62364c45e2 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../introduction/quick-start.md:16 60c57d9de0e449bbb1ec517663e9047f +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../introduction/quick-start.md:22 0a89aaf525d349349bb23ecf11f00a1e +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../introduction/quick-start.md:27 f33aad86b3194d92b87e51b8551de335 +msgid "" +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." +msgstr "" + +#: ../../introduction/quick-start.md:32 bba033bcce684da99d8561c644a288b9 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../introduction/quick-start.md:34 74c2a60629734132baf21f950f51a2a8 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" +msgstr "" + +#: ../../introduction/quick-start.md:39 688e1f06579d44b8975c3db85d5969f6 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../introduction/quick-start.md:47 77a52c31fce14347bbb47d80f59489e7 +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." +msgstr "" + +#: ../../introduction/quick-start.md:51 235356675f8b492b86a59fe345d67184 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../introduction/quick-start.md:53 4caaccb9352a46678835a5bfb413803b +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../introduction/quick-start.md:57 ccbc60f4811e4a479530094958219224 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../introduction/quick-start.md:62 3b3cd61bd0fe4dddbab7ce4fabc16421 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../introduction/quick-start.md:65 71f096c461ef47f8a920339e164bf314 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../introduction/quick-start.md:70 cbaa83776dc041dd963ce47a67b3b405 +msgid "" +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" +msgstr "" + +#: ../../introduction/quick-start.md:74 04e272f684be44be911dc6e50ac1660b +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../introduction/quick-start.md:80 5d1ebc06dc2d44439135ee1e75cc714a +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" +msgstr "" + +#: ../../introduction/quick-start.md:82 6ad6b44a644b482382cec3bfda23e4ac +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../introduction/quick-start.md:88 bf7a0bd183f64f6883ecee1dae23607a +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." +msgstr "" + +#: ../../introduction/quick-start.md:94 002680b62d5d4d8fbf8d730e38ef154a +msgid "Learn More" +msgstr "" + +#: ../../introduction/quick-start.md:96 716e6ec03d974ee9ac59a055fcdabe41 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../introduction/quick-start.md:97 a098326c57f34af5972578ebb580d6a2 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../introduction/quick-start.md:98 cba27320bbe844fc8bfbad0ba2aa9c01 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." +msgstr "" + +#: ../../introduction/quick-start.md:99 e377948d6db94e1aa5c3b28c44a9707c +msgid "" +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../introduction/quick-start.md:100 b554f9e0572e4b02a5cc1cb817c70539 +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../introduction/quick-start.md:101 a2ce57a5a0a24bb0bb858e076df51e6c +msgid "" +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." +msgstr "" + +#: ../../introduction/quick-start.md:102 edb34dacc1674731a7b5fa510c81d38b +msgid "" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/setup.po b/locales/en/LC_MESSAGES/setup.po new file mode 100644 index 00000000..15bfffe9 --- /dev/null +++ b/locales/en/LC_MESSAGES/setup.po @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../setup.md:5 27e5c491bbd4441d96d85f6d8f66181e +msgid "This page has moved" +msgstr "" + +#: ../../setup.md:9 4b442c302c2d4c84a462c1fa1781b35d +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/sphinx.po b/locales/en/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..d097c6cb --- /dev/null +++ b/locales/en/LC_MESSAGES/sphinx.po @@ -0,0 +1,28 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../_templates/sidebar-nav-bs.html:1 94578a793f824c289114eb8091fcbb83 +msgid "Main navigation" +msgstr "" + +#: ../../_templates/sidebar-nav-bs.html:3 0004714627914a26a46506c14c85806d +msgid "Section Navigation" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po b/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po new file mode 100644 index 00000000..0adab36c --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po @@ -0,0 +1,84 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/additional-arguments-and-parameters.md:1 +#: 245426859a1e4d2db7facb0504eb028c +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:3 +#: 6be40170e1d14af08a2b49daecae8df7 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:6 +#: a3f17f29d2ab4ad2993696400f7be61b +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:13 +#: 77443a85f1a14fef94fc4d6d4add43ca +msgid "`arguments.cwl`" +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:19 +#: 42d3138cc25d4570ada1a25ac13fb8bc +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:24 +#: 1a7130850048412fa12f6fcec745e4ee +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:30 +#: f4fcf30ed13c42d3a93817dc29651686 +msgid "" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:36 +#: c470ae16de004280a2bd2b0a99f391b3 +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:43 +#: a31eeefe78ab4442bcfea3e1106cf8a9 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/best-practices.po b/locales/en/LC_MESSAGES/topics/best-practices.po new file mode 100644 index 00000000..30c7c72e --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/best-practices.po @@ -0,0 +1,191 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/best-practices.md:1 400480770c074343aae662a25b257a31 +msgid "Best Practices" +msgstr "" + +#: ../../topics/best-practices.md:3 fe9e19076d74462cab67b4a3cb340724 +msgid "" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." +msgstr "" + +#: ../../topics/best-practices.md:8 caab132559d84593ac23530e36ec6c21 +msgid "" +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../topics/best-practices.md:11 e15eb191624846c4b1d3e3e96731a8ff +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." +msgstr "" + +#: ../../topics/best-practices.md:20 d5c2b325d05f4afca4008f4733d92100 +msgid "" +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../topics/best-practices.md:26 99b89f6ce812463093ee0da9255178bb +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" +msgstr "" + +#: ../../topics/best-practices.md:28 56915c2feeb9402fb1210cdf27788c8a +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../topics/best-practices.md:37 4315b219d21742ac88f39415da6807d8 +msgid "" +"For more examples of providing metadata within CWL descriptions, see " +"[the Metadata and Authorship section of this User Guide](../topics" +"/metadata-and-authorship.md)." +msgstr "" + +#: ../../topics/best-practices.md:40 122f553a412d43bd9e55caaafb90b88f +msgid "" +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." +msgstr "" + +#: ../../topics/best-practices.md:44 b5fe5270c8534ad194dbf41bdec90e33 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." +msgstr "" + +#: ../../topics/best-practices.md:47 889a5c8d24464546a2a1156ef3791b28 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../topics/best-practices.md:50 7203be6d92a040c2b39f07f0618b7c37 +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../topics/best-practices.md:55 8ea3eee32d8044c5ad0a4caeab435b8b +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../topics/best-practices.md:58 3c033a88a5cd4bf19683add86436a8de +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." +msgstr "" + +#: ../../topics/best-practices.md:66 7731a6bd39a7444e82b96d2a5e8eb44b +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "" + +#: ../../topics/best-practices.md:69 fe8845e0d96f459bbcd69e176e7ff6b1 +msgid "" +"Each `CommandLineTool` description should focus on a single operation " +"only, even if the (sub)command is capable of more. Don't overcomplicate " +"your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../topics/best-practices.md:73 1ffe2266eef94941840c485ca77417b6 +msgid "" +"Custom types should be defined with one external YAML per type definition" +" for re-use." +msgstr "" + +#: ../../topics/best-practices.md:76 e5af104f7c2848c8ac0f97d13a9153a2 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../topics/best-practices.md:78 88c7bfbebad14cf9b39bd3e9488c7dfb +msgid "" +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." +msgstr "" + +#: ../../topics/best-practices.md:82 4f874eee6d884b6c8f2117f61788a4e5 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." +msgstr "" + +#: ../../topics/best-practices.md:85 6c481e56c4ff48fc9854a3c15375f5f7 +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../topics/best-practices.md:90 2e66f35622964ad6bc54faedbfec0eeb +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." +msgstr "" + +#: ../../topics/best-practices.md:93 c5551f6025e445f296d3de936029fab4 +msgid "" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../topics/best-practices.md:97 eff85713fb344bfb968bda07094485af +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/command-line-tool.po b/locales/en/LC_MESSAGES/topics/command-line-tool.po new file mode 100644 index 00000000..212158b9 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/command-line-tool.po @@ -0,0 +1,71 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/command-line-tool.md:1 48774f562479443fa878218b84edd4f0 +msgid "Command Line Tool" +msgstr "" + +#: ../../topics/command-line-tool.md:3 8cb2bbcf217f4a35acd6fe7aac1b9493 +msgid "" +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." +msgstr "" + +#: ../../topics/command-line-tool.md:8 9d7a6d6def0046c180c951e9ad94afeb +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../topics/command-line-tool.md:19 a6e02298d1fa432d9d6b54b420818901 +msgid "CWL command-line tool." +msgstr "" + +#: ../../topics/command-line-tool.md:50 a6638b2f0c184e95abc23d6207e81802 +msgid "`echo.cwl`" +msgstr "" + +#: ../../topics/command-line-tool.md:57 da7864a3fcf842459475b5b27a693ded +msgid "" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../topics/command-line-tool.md:68 0a222e61001a4a08bc2e82ca52105a09 +msgid "Network Access" +msgstr "" + +#: ../../topics/command-line-tool.md:69 988c4b4184d0405e9bc26bb7bcb05c8b +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. If a command-line tool is written manually in CWL v1.1+, there is" +" a need to specify when network access is required." +msgstr "" + +#: ../../topics/command-line-tool.md:83 2918cea6f64846c498fdf03b92533d94 +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " +"Network Access automatically." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po b/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po new file mode 100644 index 00000000..39b54f98 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po @@ -0,0 +1,104 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/creating-files-at-runtime.md:1 2bbf4c0a32054cfebe3b6b1b02ea3558 +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:3 c5010461c4fe4e8fb7c4f7da2653febe +msgid "" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:7 27879c9542e444dca1a80c1784891bf7 +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:9 61cf19e01c03473aa239bc42394bfcff +msgid "`createfile.cwl`" +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:15 +#: 8d1fb6bc4eed466391ad62fe5be90a13 +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:20 +#: 40e30b78078a4184b4c5bd69c0766cef +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:27 +#: c624145be5a04d65acaaa4bfa086c473 +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:29 +#: 202ff16474a04e29b0e363cb5241b53e +msgid "`echo-job.yml`" +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:35 +#: ea631a00fdd9484486e1ca60a90b6d8a +msgid "" +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:40 +#: 1dea9f63048f40528c904ec2fb4bef69 +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:51 +#: cff49a2cf48c43f0aeaa6241e1bcaabe +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:54 +#: c81ca28ee4d44d82b6cf3bdbf8460642 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/custom-types.po b/locales/en/LC_MESSAGES/topics/custom-types.po new file mode 100644 index 00000000..66cf4c6c --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/custom-types.po @@ -0,0 +1,99 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/custom-types.md:1 ab79908260aa4842b2322e6e4d615f72 +msgid "Custom Types" +msgstr "" + +#: ../../topics/custom-types.md:3 75b9b1f15a744e24b2f7333b6638bcc4 +msgid "" +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." +msgstr "" + +#: ../../topics/custom-types.md:9 7f4a9afccdad41b9892d8424e9fb539d +msgid "" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../topics/custom-types.md:12 8f03906168eb4bf0a6bf7ae0f6e0ecb1 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../topics/custom-types.md:18 0b8de32a79a14b2a841851ceab22b6b3 +msgid "`custom-types.yml`" +msgstr "" + +#: ../../topics/custom-types.md:24 8ba644c7152247959988abfcd2b4c2be +msgid "" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" +msgstr "" + +#: ../../topics/custom-types.md:30 975bdfc68b1841fa89a055b7f03fb0ec +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../topics/custom-types.md:46 d4efacf670184435a5729e0ba5e16a36 +msgid "" +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." +msgstr "" + +#: ../../topics/custom-types.md:53 ea6ca32a9e6e4f38be19487348cd45f7 +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../topics/custom-types.md:55 5bfed5519bc04c35aa6ad8626201f98f +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../topics/custom-types.md:61 066aef77545f4dc8b11f09caa710be9e +msgid "" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" +msgstr "" + +#: ../../topics/custom-types.md:76 7e35076a9b0347ff967c5271a3ccf881 +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number " +"of cores required for the tool to run successfully, as well as details of" +" the version of the software that the description was written for and " +"other useful metadata. These features are discussed further in other " +"chapters of this user guide." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/environment-variables.po b/locales/en/LC_MESSAGES/topics/environment-variables.po new file mode 100644 index 00000000..6ecd617f --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/environment-variables.po @@ -0,0 +1,45 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/environment-variables.md:1 498dbc0db9224aabbc9fd1bef778f8ef +msgid "Environment Variables" +msgstr "" + +#: ../../topics/environment-variables.md:3 9ce0f06bed3649339f666147b45c69e4 +msgid "" +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../topics/environment-variables.md:7 ef471bebcfc94b008c94a2e8056d7af0 +msgid "`env.cwl`" +msgstr "" + +#: ../../topics/environment-variables.md:13 df5ab6417f87475d8d94f2af498cee39 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../topics/environment-variables.md:18 642f1379ebdd4dd381e8f56343547b42 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/expression-tool.po b/locales/en/LC_MESSAGES/topics/expression-tool.po new file mode 100644 index 00000000..8d8ad3dc --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/expression-tool.po @@ -0,0 +1,53 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/expression-tool.md:1 2ed0674b02ee4cd7ac4e169086d02513 +msgid "Expression Tool" +msgstr "" + +#: ../../topics/expression-tool.md:3 95b1b27ad2a84cd9bd1207ff75536502 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." +msgstr "" + +#: ../../topics/expression-tool.md:8 80caa25305a74efdaed8ada05faaa018 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../topics/expression-tool.md:17 a664a455f4714071ba0158a4f83a127c +msgid "CWL expression tool." +msgstr "" + +#: ../../topics/expression-tool.md:48 bdfa455a230e4be79031e0777efc7233 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../topics/expression-tool.md:67 0df562c4585e43d1ae4ac8113b50ed71 +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains" +" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/expressions.po b/locales/en/LC_MESSAGES/topics/expressions.po new file mode 100644 index 00000000..f09d91d8 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/expressions.po @@ -0,0 +1,383 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/expressions.md:1 15bf6af8d07d476ea6996a0be17fdca0 +msgid "Expressions" +msgstr "" + +#: ../../topics/expressions.md:3 248bcdddada043abaaf9d53819dd3d01 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by " +"the CWL runner." +msgstr "" + +#: ../../topics/expressions.md:9 986c932e94e3496b8ab3ef5c9b1927c5 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." +msgstr "" + +#: ../../topics/expressions.md:16 a82f11177ce54f7f92b6e5b037a1b6d0 +msgid "`expression.cwl`" +msgstr "" + +#: ../../topics/expressions.md:22 e1c2a91028bc47238421457f323556db +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" +msgstr "" + +#: ../../topics/expressions.md:25 bddb2b6b6507418785bc194340313a39 +msgid "`empty.yml`" +msgstr "" + +#: ../../topics/expressions.md:31 6932ad2e25eb4e3c835bf37557efbf03 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." +msgstr "" + +#: ../../topics/expressions.md:35 51962babe16e4b8493cafe401f046510 +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../topics/expressions.md:37 f302523bb23049afa0dc534641abba94 +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../topics/expressions.md:47 5e672f895eb94028bb7fbc4ba7646c46 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" +msgstr "" + +#: ../../topics/expressions.md:54 913d17f1bb474dec91b467db5f45ffab +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." +msgstr "" + +#: ../../topics/expressions.md:62 8f26131c8cc94db88fc88100f0404bff +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../topics/expressions.md:64 ad6af4e35d014ce7bd122b00f99f13dd +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../topics/expressions.md:66 4b2eaee288a4421a91b304a186578361 +msgid "" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../topics/expressions.md:67 032d4eeaeda14354a8b059e4391f3448 +msgid "`arguments`" +msgstr "" + +#: ../../topics/expressions.md:68 ../../topics/expressions.md:76 +#: ../../topics/expressions.md:89 aebe22df1bf6432aa39e402802ce8fcd +#: dcc0d4a9abcb4e35ae4ee341893d757f fca0e4b343c940989ebbf8ce7cf87605 +msgid "`valueFrom`" +msgstr "" + +#: ../../topics/expressions.md:69 0b185807c14741bca2b1ce4252bded44 +msgid "`stdin`" +msgstr "" + +#: ../../topics/expressions.md:70 716a8fad0a5d46bb9d17d35c0866db31 +msgid "`stdout`" +msgstr "" + +#: ../../topics/expressions.md:71 e9d014cdaf794dacb4eee304c1364d1b +msgid "`stderr`" +msgstr "" + +#: ../../topics/expressions.md:72 81333fdf0ac84d4495ec32cd4b58f12e +msgid "" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../topics/expressions.md:73 ../../topics/expressions.md:78 +#: ../../topics/expressions.md:85 ../../topics/expressions.md:93 +#: bf75a275d26345bf86076cea5c44f5d8 c704d979a192458a9315971e6702478a +#: d29995b11d3f4157915f48c52f4eba90 ff462897cd0149c493e50ee87f9d1c0e +msgid "`format`" +msgstr "" + +#: ../../topics/expressions.md:74 ../../topics/expressions.md:79 +#: ../../topics/expressions.md:86 ../../topics/expressions.md:94 +#: 18e86fc5bf684862a30f373766d067eb 195022a4f28f419ea24095350e89c7dd +#: 403516ed7955408fa7a12d34fd1fbe82 dd2932a497104db096a8ecb1986381b6 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../topics/expressions.md:75 49d00678c3d8425db3852e408049e249 +msgid "" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../topics/expressions.md:77 8523d80e16a24adebc3fdad88141e646 +msgid "" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../topics/expressions.md:80 51af437d2c314f18895ae13e58dbd56e +msgid "" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../topics/expressions.md:81 9d9b304dceaa4cb38e01503ff57d726b +msgid "`glob`" +msgstr "" + +#: ../../topics/expressions.md:82 65bceca1c4f7447fa5f3e0c448a02af6 +msgid "`outputEval`" +msgstr "" + +#: ../../topics/expressions.md:83 5bc18fb8fa034c4281b715ab44a5cb75 +msgid "From `Workflow`" +msgstr "" + +#: ../../topics/expressions.md:84 fcfc00ff02d04e61bdc6d5432d04c7da +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../topics/expressions.md:87 e51177ae5daa42429266893d9467cd15 +msgid "From `steps`" +msgstr "" + +#: ../../topics/expressions.md:88 4e6a5b41b2f249b896d7a1e79b2aebbb +msgid "" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../topics/expressions.md:90 9233f867e33d41199e31ed9115442d7e +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../topics/expressions.md:91 60fc0bdd44614b61961aa204edae77b9 +msgid "`expression`" +msgstr "" + +#: ../../topics/expressions.md:92 2cf4288d3d594085af2a07026bc71371 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../topics/expressions.md:95 1455be996e7147c99d60cc9f198b78cb +msgid "" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../topics/expressions.md:96 0ac9b337923c4a2793fe198d6bf759f1 +msgid "`coresMin`" +msgstr "" + +#: ../../topics/expressions.md:97 993661b89e4945d0ad4f8a13931eeffb +msgid "`coresMax`" +msgstr "" + +#: ../../topics/expressions.md:98 22d35c6039754b6b96fed696f9a06a71 +msgid "`ramMin`" +msgstr "" + +#: ../../topics/expressions.md:99 53cce3babeac44c98bbfe68d122e5796 +msgid "`ramMax`" +msgstr "" + +#: ../../topics/expressions.md:100 ed43db0eedef4716800239b9c6c5c9f0 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../topics/expressions.md:101 e4e8d9975aa74847a49060459ace3edc +msgid "`tmpdirMax`" +msgstr "" + +#: ../../topics/expressions.md:102 13713c1adb7f4759b1792bbf3e720c29 +msgid "`outdirMin`" +msgstr "" + +#: ../../topics/expressions.md:103 d8c878c467f34807b98c156ad8705445 +msgid "`outdirMax`" +msgstr "" + +#: ../../topics/expressions.md:104 fb119535e57d4a55b6e9a86deaecc100 +msgid "" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../topics/expressions.md:105 dbe84d62840049e7b9ed3498d15847f6 +msgid "`listing`" +msgstr "" + +#: ../../topics/expressions.md:106 6db83a55040447c7903dd5d2d0bb00f8 +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../topics/expressions.md:107 8ff197dd79524f25912ef459fb7b20d1 +msgid "`entry`" +msgstr "" + +#: ../../topics/expressions.md:108 fcea352f4e4246bf8fba2f53665427df +msgid "`entryname`" +msgstr "" + +#: ../../topics/expressions.md:109 120885c8f41e4ad58458699a66b38fc6 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../topics/expressions.md:110 17cea5e071b0430d901810a76ff224d4 +msgid "" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../topics/expressions.md:111 5e6e3c6614d043e596be33cb9aba75c5 +msgid "`envValue`" +msgstr "" + +#: ../../topics/expressions.md:116 54b20c309ca543df81b8221c6d8f9eaa +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../topics/expressions.md:118 54df5f1a63554bf7989dccf12aa205a1 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" +" attribute that allows users to load external JavaScript files, or to " +"provide inline JavaScript code." +msgstr "" + +#: ../../topics/expressions.md:122 8e6566d5b3fd424fa95e77df42ae18ed +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." +msgstr "" + +#: ../../topics/expressions.md:128 50f2d063d4864db1b051a41769b3d928 +msgid "" +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." +msgstr "" + +#: ../../topics/expressions.md:135 e2c6c8b5d1b345368e0699a5a2a079cc +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" +msgstr "" + +#: ../../topics/expressions.md:139 1ce74804ca97479fb6bdacbdba2bbc5c +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../topics/expressions.md:146 fbe150d3864e4987ae145a8b7de60151 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" +msgstr "" + +#: ../../topics/expressions.md:149 7552ea9b4f714fbe8aea6db94fd8894f +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../topics/expressions.md:155 2f3154ec78274b43accde1409c59ec56 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../topics/expressions.md:158 ee2508f7faf74dd3a2928aebd3dc4314 +msgid "`custom-functions.js`" +msgstr "" + +#: ../../topics/expressions.md:164 9ba72aae0ff546e282aaa2518a5cd237 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../topics/expressions.md:171 e1b9ad0192e44844ab641c883e859510 +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../topics/expressions.md:175 3b40577e79f9432b9bad3fbaf5fc4b78 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../topics/expressions.md:181 6298a4cf813142e09b35c55fd7077cbc +msgid "" +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." +msgstr "" + +#: ../../topics/expressions.md:186 881975804cc246cdb81af6ad04734a19 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../topics/expressions.md:193 9369098b680540e2b6ea67f861e193ed +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../topics/expressions.md:200 ec09ac813f3142e9b333428a44bb1244 +msgid "" +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/file-formats.po b/locales/en/LC_MESSAGES/topics/file-formats.po new file mode 100644 index 00000000..73be3838 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/file-formats.po @@ -0,0 +1,93 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/file-formats.md:1 24ece5b3bfe646268d48b0339ba10e7b +msgid "File Formats" +msgstr "" + +#: ../../topics/file-formats.md:3 a7520d9841f044f8a33d1acf1f6234bf +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." +msgstr "" + +#: ../../topics/file-formats.md:8 544fcf8047db45c3aad991cfdf732309 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../topics/file-formats.md:14 12d2dc549a684fff9cb46320700143fa +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." +msgstr "" + +#: ../../topics/file-formats.md:17 c362c433ba544d1eaa19781db09aafbd +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../topics/file-formats.md:20 c1007004cc7a4c408a713c38208574c0 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../topics/file-formats.md:26 47ec32f1249f48149068417e431a20f5 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../topics/file-formats.md:32 f99998f5da604c9b827367670cd30879 +msgid "Sample Parameter Files" +msgstr "" + +#: ../../topics/file-formats.md:34 050ec30459884b1581d715038fe2b05a +msgid "" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." +msgstr "" + +#: ../../topics/file-formats.md:39 dd49f6afbc754b9083888cf822cc369e +msgid "`sample.yml`" +msgstr "" + +#: ../../topics/file-formats.md:45 7e1974e26afc40568d4e483d20c4b86f +msgid "" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../topics/file-formats.md:52 46649847e8d440b9b4f6726be286e067 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/index.po b/locales/en/LC_MESSAGES/topics/index.po new file mode 100644 index 00000000..b90b5d6b --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/index.po @@ -0,0 +1,24 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/index.md:1 55452f6967174ff5a1d8cf776874a90b +msgid "Topics" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/inputs.po b/locales/en/LC_MESSAGES/topics/inputs.po new file mode 100644 index 00000000..03f1b021 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/inputs.po @@ -0,0 +1,313 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/inputs.md:1 03f3a68492ca43bea79742a839864b86 +msgid "Inputs" +msgstr "" + +#: ../../topics/inputs.md:3 9772b8bb0b694b9e9eef5e65b4ffe333 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../topics/inputs.md:5 68cd0cab423c4d10a69989e6a3833e7a +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../topics/inputs.md:9 2a76b22fc015489b81d6c396f4f8ae30 +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*," +" and *null*; complex types are *array* and *record*; in addition there " +"are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../topics/inputs.md:13 ba487511ecd84b37af0796d5159e50e3 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." +msgstr "" + +#: ../../topics/inputs.md:16 59dd55e707cd49f385f5763aa54bc461 +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../topics/inputs.md:18 0d05676c671a420b87f3808010ccc207 +msgid "`inp.cwl`" +msgstr "" + +#: ../../topics/inputs.md:24 06e169026a20469cb6b04a216045cc87 +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../topics/inputs.md:26 05dd5f7e9edf4c379e66d8b6cfc1f86f +msgid "`inp-job.yml`" +msgstr "" + +#: ../../topics/inputs.md:33 f02466c6a7bf4795892d14963a8ad22e +msgid "" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../topics/inputs.md:40 5e5a2fe06ad04b2d8969d6cbfed213ec +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." +msgstr "" + +#: ../../topics/inputs.md:44 fafabc3b11f14bb68c16e3f497e26e40 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "" + +#: ../../topics/inputs.md:47 7e3d42ea93dd417195ab6b5559638326 +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." +msgstr "" + +#: ../../topics/inputs.md:53 0bbabcf2be26490dbe920f52f8cbe9b0 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" +msgstr "" + +#: ../../topics/inputs.md:64 c340c8aa7b80488ba6d16329e1ca2149 +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" +msgstr "" + +#: ../../topics/inputs.md:70 5c2e148fdb324017a685f5adefadd74d +msgid "" +"The field `inputBinding` is optional and indicates whether and how the " +"input parameter should appear on the tool's command line. If " +"`inputBinding` is missing, the parameter does not appear on the command " +"line. Let's look at each example in detail." +msgstr "" + +#: ../../topics/inputs.md:83 97d14a1cf8fc4b3687281aa93eb1ceb6 +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." +msgstr "" + +#: ../../topics/inputs.md:95 6c2008aed010466c8e4465c72a4b6d79 +msgid "" +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." +msgstr "" + +#: ../../topics/inputs.md:109 95f2a1493e50455ea6e546f70726fab1 +msgid "" +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../topics/inputs.md:124 3a48173a38904861b9994edddbc2f082 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." +msgstr "" + +#: ../../topics/inputs.md:131 54186920b4a14fbfa059779411b20192 +msgid "" +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../topics/inputs.md:134 920e8b7d7eee4239b327b0386a872492 +msgid "" +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." +msgstr "" + +#: ../../topics/inputs.md:142 690f556fa0854517a4e3e43747178461 +msgid "" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." +msgstr "" + +#: ../../topics/inputs.md:146 65ae530b9da84e7e98bcf5a5cf516c30 +msgid "Array Inputs" +msgstr "" + +#: ../../topics/inputs.md:148 21f30b0db29c4aa4989c39997b1a720c +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." +msgstr "" + +#: ../../topics/inputs.md:154 cefc841cd57c4b19b2be69aa80106c8b +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../topics/inputs.md:160 bae9c79fa8bb42f6922ee937a5c5ff7a +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../topics/inputs.md:166 b756a25aad9e4fcfb68cbe2123cac3c5 +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../topics/inputs.md:178 0a930f2019b748858ddc5ca5acbde210 +msgid "" +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." +msgstr "" + +#: ../../topics/inputs.md:185 57551982494e4152b2c2c11f04bae126 +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." +msgstr "" + +#: ../../topics/inputs.md:191 30d6b347401d4304b4dcc1ef2268ded2 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../topics/inputs.md:193 cf8b6d0ed47a4e57a39add29f91f0ec0 +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../topics/inputs.md:198 5aa374f61a2a41e383da4b960e3603d5 +msgid "`record.cwl`" +msgstr "" + +#: ../../topics/inputs.md:204 6557427907d0465695aa88f2f27d5bf1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../topics/inputs.md:215 3f39bfdadeb14b0d8dfb67fe5aad7790 +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." +msgstr "" + +#: ../../topics/inputs.md:217 30829196c2f54dbb9b1c35e462fe4e85 +msgid "`record-job2.yml`" +msgstr "" + +#: ../../topics/inputs.md:233 049396bf53d241cd9d03b9ff81468e0c +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." +msgstr "" + +#: ../../topics/inputs.md:236 a9036f0e32ff418482573d23ed074256 +msgid "`record-job3.yml`" +msgstr "" + +#: ../../topics/inputs.md:252 bc0b43accbf9452ca4b7c2d7d69c2984 +msgid "" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." +msgstr "" + +#: ../../topics/inputs.md:255 6cfc57be54f8458ebc9d784bc9ac2555 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../topics/inputs.md:257 0279c53e41c94ccc9f2de65d057dd903 +msgid "" +"If you use exclusive input parameters combined with expressions, you need" +" to be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." +msgstr "" + +#: ../../topics/inputs.md:262 b94737f481d343bfbb6ecf0fd81c9d6f +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." +msgstr "" + +#: ../../topics/inputs.md:265 b5335802dcd148e9bb8f72d75f1ff6cd +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../topics/inputs.md:271 08b50c80fd024f86ba9c6239895385d0 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as “fasta” (one of the values of the enum), " +"your command should execute successfully:" +msgstr "" + +#: ../../topics/inputs.md:280 77c08d3144b04e58a6733cbd01346102 +msgid "" +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to a `null` value, which does not match the expected type " +"for the output field (a `string`), resulting in failure when running your" +" workflow." +msgstr "" + +#: ../../topics/inputs.md:289 91280fddf3624696b90632ca8466ca59 +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript" +" expression when using exclusive parameters, or any parameter that allows" +" `null`. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value if none was " +"provided in the command line or job input file." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po b/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po new file mode 100644 index 00000000..fb846967 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po @@ -0,0 +1,70 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/metadata-and-authorship.md:1 e5511fed73914ceeaf73b9ca7020e8d2 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../topics/metadata-and-authorship.md:3 1a4f0cbf7a694f949646c7bfc1d6f5dc +msgid "" +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/) as described in the [Schema Salad specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../topics/metadata-and-authorship.md:13 f1dcef50a880467f82b93f383030501b +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." +msgstr "" + +#: ../../topics/metadata-and-authorship.md:16 1af01d43dfd9408ab58a960b62bf44f0 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../topics/metadata-and-authorship.md:22 ecd7d3e4f19146ef807219add82fff00 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../topics/metadata-and-authorship.md:28 a8b454c10d484726b194de1f8c0775da +msgid "Extended Example" +msgstr "" + +#: ../../topics/metadata-and-authorship.md:30 0e5960b6d60b4a73837d1ea4b36a896d +msgid "" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." +msgstr "" + +#: ../../topics/metadata-and-authorship.md:35 89713dbe4568459488494cf7f23ee622 +msgid "`metadata_example3.cwl`" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/operations.po b/locales/en/LC_MESSAGES/topics/operations.po new file mode 100644 index 00000000..dd111423 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/operations.po @@ -0,0 +1,73 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/operations.md:1 968848522a1c419e94cdb03a48f7bab8 +msgid "Operations" +msgstr "" + +#: ../../topics/operations.md:3 825f5584a57148e4ba1df435653351a1 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." +msgstr "" + +#: ../../topics/operations.md:7 1c8a712c12b54c26ac8d2d24270390cf +msgid "" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../topics/operations.md:10 e0e24f86682447ad88bb59f73f4c272f +msgid "`operations.cwl`" +msgstr "" + +#: ../../topics/operations.md:16 a1448ed2695b4b849c0e2879c38640d8 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like" +" a command line tool or an expression. You can also plot it with the CWL " +"Viewer or `cwltool`:" +msgstr "" + +#: ../../topics/operations.md:24 0ed9d93f0ead46fea1f3d5f28d22419b +msgid "" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx Graphviz directive (this" +" user guide is built with Sphinx):" +msgstr "" + +#: ../../topics/operations.md:55 4a03e03b140a45b3bfc26d7b0f677cb4 +msgid "" +"If you try running it with `cwltool`, the command will fail since " +"`cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../topics/operations.md:58 7794ec6d263c425bb423135f4025d2f1 +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../topics/operations.md:66 8c8423c44aec4a619ea9bbce986b3b96 +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/outputs.po b/locales/en/LC_MESSAGES/topics/outputs.po new file mode 100644 index 00000000..84287200 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/outputs.po @@ -0,0 +1,147 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/outputs.md:1 8b140307638c4baa9261df35f7372240 +msgid "Outputs" +msgstr "" + +#: ../../topics/outputs.md:3 59a76cb3f5b04cf391310d816bdd4759 +msgid "Returning Output Files" +msgstr "" + +#: ../../topics/outputs.md:5 f1e1c91b796e4c4bbb5c8e234852225d +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." +msgstr "" + +#: ../../topics/outputs.md:10 aa7076aea7e54d489af848f9523794fe +msgid "" +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or come from examining the content of those files." +msgstr "" + +#: ../../topics/outputs.md:16 7ee8d5efbc2d43c297960a3d851628f9 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." +msgstr "" + +#: ../../topics/outputs.md:19 ba6fcc05fcdd46f6b1f354295bf124de +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../topics/outputs.md:21 7534fb6a5894438f9da2167e08f4e218 +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../topics/outputs.md:26 3c50004d2d7d4695944015e40bf1f22f +msgid "`tar.cwl`" +msgstr "" + +#: ../../topics/outputs.md:32 cddecc6f8aa640d2b245eef27f5bb87e +msgid "`tar-job.yml`" +msgstr "" + +#: ../../topics/outputs.md:38 3d7918df94094da9b8ecc7ec1c5a1b3b +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../topics/outputs.md:45 7bf5e274a89048838c9fdf28633a5cec +msgid "" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../topics/outputs.md:51 fce348fc9cce4fdaa699b0d0f6f3b542 +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." +msgstr "" + +#: ../../topics/outputs.md:62 aa92f3f4f14e4025b874ffec26bff141 +msgid "" +"The `glob` field consists of the name of a file in the output directory. " +"If you don't know name of the file in advance, you can use a wildcard " +"pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../topics/outputs.md:65 1a5ab9a9e91640d48a0cb2c13e691cbc +msgid "Capturing Standard Output" +msgstr "" + +#: ../../topics/outputs.md:67 9896a750508f4a57b128f4e30e718814 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." +msgstr "" + +#: ../../topics/outputs.md:71 9345911f55b945eab39897e85e648ea4 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../topics/outputs.md:77 cea8fa310b0c471e8f6f6317b9ffcec6 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../topics/outputs.md:82 ../../topics/outputs.md:105 +#: 5e059fc800fa4f9f93e8a5b07e68de36 d62a95decb134c87a4280ce5526e03bd +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../topics/outputs.md:89 9d6affcf4fbd4ca2a3f8dbd8d50a5c27 +msgid "Array Outputs" +msgstr "" + +#: ../../topics/outputs.md:91 8c5ad552c70e49b09bdda33cda587fec +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." +msgstr "" + +#: ../../topics/outputs.md:93 0558868e3e554b5890eb69b275a6b14b +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../topics/outputs.md:99 4fae0201b0f64c03a134f0bd9aeae9ba +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../topics/outputs.md:112 9f9c8a4a10d444879c7984a95e40fdb4 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/parameter-references.po b/locales/en/LC_MESSAGES/topics/parameter-references.po new file mode 100644 index 00000000..89399c97 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/parameter-references.po @@ -0,0 +1,279 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/parameter-references.md:1 9f53de1545d2441eaca40a478ab3b2b5 +msgid "Parameter References" +msgstr "" + +#: ../../topics/parameter-references.md:3 86efaeb616844254ac6651e3b312d648 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../topics/parameter-references.md:13 e19913c8e6bb449aa55959dd82acda2d +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../topics/parameter-references.md:19 7e40643c4a474987aea13be5af260677 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../topics/parameter-references.md:25 46112899f2dd46ba828dc57245680909 +msgid "" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" +msgstr "" + +#: ../../topics/parameter-references.md:36 896da20f29e2465fae5555d1f51cb681 +msgid "" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../topics/parameter-references.md:47 2e0849d53b6b4491a5d779390ea1319e +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../topics/parameter-references.md:51 3dab2befe3e840738419f1dedaac04d5 +msgid "" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." +msgstr "" + +#: ../../topics/parameter-references.md:54 f92b2507989f4836bf33c78326bf8bc3 +msgid "" +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." +msgstr "" + +#: ../../topics/parameter-references.md:59 2a7ca85801a841f2acc94431a2accef8 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../topics/parameter-references.md:61 737a086da43644b3979fd3ebb16b2696 +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../topics/parameter-references.md:63 fcf3c4392e48496a8776ba9a49a6e867 +msgid "" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../topics/parameter-references.md:64 1b2a1714c66d4b2398c7fd614b3099c4 +msgid "`arguments`" +msgstr "" + +#: ../../topics/parameter-references.md:65 +#: ../../topics/parameter-references.md:73 +#: ../../topics/parameter-references.md:86 4458fac137854a9499a9afd221c344ac +#: 96f0d31f8d3549689bdfd4908698eed2 b234d82653a44b4ab1f9532e71e5e962 +msgid "`valueFrom`" +msgstr "" + +#: ../../topics/parameter-references.md:66 e6857e57ba424ec1bd86789a27458c8c +msgid "`stdin`" +msgstr "" + +#: ../../topics/parameter-references.md:67 8544dee0d05a492ca7f7727d277001ba +msgid "`stdout`" +msgstr "" + +#: ../../topics/parameter-references.md:68 a73a304246064187a5ef01aa04c528c8 +msgid "`stderr`" +msgstr "" + +#: ../../topics/parameter-references.md:69 8a86bb148ba9488185ac8f7a621aeba9 +msgid "" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../topics/parameter-references.md:70 +#: ../../topics/parameter-references.md:75 +#: ../../topics/parameter-references.md:82 +#: ../../topics/parameter-references.md:90 26f25bcad002476287ac6597033b3a68 +#: 2911d4b287444e159b2a1cfb9880a977 3657033c01b847febc8d6cdae2cf62b6 +#: 65f8db3faadb4fb59f8f26e7084b7a02 +msgid "`format`" +msgstr "" + +#: ../../topics/parameter-references.md:71 +#: ../../topics/parameter-references.md:76 +#: ../../topics/parameter-references.md:83 +#: ../../topics/parameter-references.md:91 3e57f5d7e1934e19a0f5de1bf11516ef +#: 40e34ff2cf47440a87f6548d3fa0ee65 64382062a5d5464fbf679cc774d0b886 +#: 99c94c256ce444a5a7a2ed4f52498c54 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../topics/parameter-references.md:72 9a7a2dc3b4854f998fe36bd55d062abe +msgid "" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../topics/parameter-references.md:74 9f9ebe1562de4739bdf432fa9f51df65 +msgid "" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../topics/parameter-references.md:77 d0ed73eea69a488da98f09b5da9e956a +msgid "" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../topics/parameter-references.md:78 153b0efcb519496b89acf861c4cc0af6 +msgid "`glob`" +msgstr "" + +#: ../../topics/parameter-references.md:79 e3ff712139e640b19b06a9270570ac3d +msgid "`outputEval`" +msgstr "" + +#: ../../topics/parameter-references.md:80 4ab6c83d91eb438a972136acae6c128c +msgid "From `Workflow`" +msgstr "" + +#: ../../topics/parameter-references.md:81 d34255008ec94e0cbbf48381fd81a642 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../topics/parameter-references.md:84 be964cd5acd74de6bf636baa4299eb81 +msgid "From `steps`" +msgstr "" + +#: ../../topics/parameter-references.md:85 038484e05e724c868a2d1d53cfced2c6 +msgid "" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../topics/parameter-references.md:87 1ee43a5c98f6440e95d688afdb6e4822 +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../topics/parameter-references.md:88 bf82bae8614f4d3f8e57c20a086ce013 +msgid "`expression`" +msgstr "" + +#: ../../topics/parameter-references.md:89 f708c3a4d3fd404c95285558b8cc6d91 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../topics/parameter-references.md:92 fa914a651d5444ebbcff86b1b6226212 +msgid "" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../topics/parameter-references.md:93 683a5eb1aa8e41adb89b1e7aec649a36 +msgid "`coresMin`" +msgstr "" + +#: ../../topics/parameter-references.md:94 151709a04a0a455481b9458c535a2e54 +msgid "`coresMax`" +msgstr "" + +#: ../../topics/parameter-references.md:95 93ec484b73bd457b9a34b681e62dba55 +msgid "`ramMin`" +msgstr "" + +#: ../../topics/parameter-references.md:96 3e17671a4aca4443b24bca32b1898bbf +msgid "`ramMax`" +msgstr "" + +#: ../../topics/parameter-references.md:97 b9d4ba2a422542609db7c994b9c89971 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../topics/parameter-references.md:98 fdab43c7a8bb420d84154aa70e24d05a +msgid "`tmpdirMax`" +msgstr "" + +#: ../../topics/parameter-references.md:99 fe3f4e63d6014e34a01243d6e1d54b1a +msgid "`outdirMin`" +msgstr "" + +#: ../../topics/parameter-references.md:100 6db5ab1a64ec40e9a6bc16060657b284 +msgid "`outdirMax`" +msgstr "" + +#: ../../topics/parameter-references.md:101 79f66c8ecf60493697c03d90e111f5aa +msgid "" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../topics/parameter-references.md:102 c42fe7e8d1dd4e35a255a5fe1f0dbdd0 +msgid "`listing`" +msgstr "" + +#: ../../topics/parameter-references.md:103 2d14a16d2a354839bcfdbcdd473c59e3 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../topics/parameter-references.md:104 5545855b55f34682b2a4e78dfa401952 +msgid "`entry`" +msgstr "" + +#: ../../topics/parameter-references.md:105 b267ab6613524236b50e698be4381087 +msgid "`entryname`" +msgstr "" + +#: ../../topics/parameter-references.md:106 6eb7f722fe294d2c81bb97e5bb193c0b +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../topics/parameter-references.md:107 43feefec5bc54adf9340f754e3bbe6fd +msgid "" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../topics/parameter-references.md:108 154d6c865631433d89589bd0748c9850 +msgid "`envValue`" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/requirements-and-hints.po b/locales/en/LC_MESSAGES/topics/requirements-and-hints.po new file mode 100644 index 00000000..380aa5be --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/requirements-and-hints.po @@ -0,0 +1,24 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/requirements-and-hints.md:5 1a39722a112b48beb8cf24e0f5e6ad88 +msgid "Requirements and Hints" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po b/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po new file mode 100644 index 00000000..c5cd86e9 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po @@ -0,0 +1,68 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/specifying-software-requirements.md:1 +#: 206f3f103faf4ac19eccdce6e038ed49 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../topics/specifying-software-requirements.md:3 +#: 4a6f03a974fc4a9e86e260d9bd48b908 +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may " +"also help to avoid confusion about which version of a tool the " +"description was written for." +msgstr "" + +#: ../../topics/specifying-software-requirements.md:13 +#: 8bd36ba850bc4f04bd886ae39e361dbb +msgid "" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." +msgstr "" + +#: ../../topics/specifying-software-requirements.md:25 +#: 8a5b0083c986452e82183cdc78d2da87 +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../topics/specifying-software-requirements.md:29 +#: 52df6af7c58b4f099c194b28b0a34de6 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a `SoftwareRequirement`, " +"search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/staging-input-files.po b/locales/en/LC_MESSAGES/topics/staging-input-files.po new file mode 100644 index 00000000..36848e63 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/staging-input-files.po @@ -0,0 +1,48 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/staging-input-files.md:1 da94c2c9fedf40f789a8afe9ff97abe7 +msgid "Staging Input Files" +msgstr "" + +#: ../../topics/staging-input-files.md:3 57675258a9ef4d948e3ebf0edd7779af +msgid "" +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use `InitialWorkDirRequirement` to stage input files into" +" the output directory. In this example, we use a JavaScript expression to" +" extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../topics/staging-input-files.md:9 0cf7fa6cd86c41bf92cd35616a4399e2 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../topics/staging-input-files.md:15 79ff820bc8d34c3ea37d396d98b56688 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../topics/staging-input-files.md:20 5f9403a7426941cb806bb76578d53987 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/troubleshooting.po b/locales/en/LC_MESSAGES/topics/troubleshooting.po new file mode 100644 index 00000000..7658928c --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/troubleshooting.po @@ -0,0 +1,101 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/troubleshooting.md:1 29507aa59aff4e249fcd12240b9fed91 +msgid "Troubleshooting" +msgstr "" + +#: ../../topics/troubleshooting.md:3 fac133f1d79f49599d516794dd45517e +msgid "" +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." +msgstr "" + +#: ../../topics/troubleshooting.md:6 68f47e9e268248af8a07b4b35080a918 +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../topics/troubleshooting.md:8 4ce1b123ee4745a3aa149e0f98ebe310 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." +msgstr "" + +#: ../../topics/troubleshooting.md:14 afa8d683568747839d41d2e9051d06ec +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." +msgstr "" + +#: ../../topics/troubleshooting.md:20 699bac84262647c7bc091c7cea92a4ba +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../topics/troubleshooting.md:27 c4ce2451329d468a8a5a489eca901262 +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" +msgstr "" + +#: ../../topics/troubleshooting.md:35 31f0242e1c5a4c3bb621ce4414e34add +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" +msgstr "" + +#: ../../topics/troubleshooting.md:44 7294bf3bcfd447bf9b894ffef0b2873a +msgid "" +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." +msgstr "" + +#: ../../topics/troubleshooting.md:48 a18b5467b1c643d987e494d5a9ced7c7 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." +msgstr "" + +#: ../../topics/troubleshooting.md:59 7925dcec83bc48cd88eaf2e6860304fd +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/using-containers.po b/locales/en/LC_MESSAGES/topics/using-containers.po new file mode 100644 index 00000000..6779614b --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/using-containers.po @@ -0,0 +1,106 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/using-containers.md:1 33c3ff349c68416e8968af39e5e588e0 +msgid "Using Containers" +msgstr "" + +#: ../../topics/using-containers.md:3 5c50f28d3926477e965a32d31e5329ee +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../topics/using-containers.md:5 5cb16dd51c1d41aeb34c4aa1fb2e0940 +msgid "" +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." +msgstr "" + +#: ../../topics/using-containers.md:15 e0e83e827b734355aa97b19dc4c7e0d5 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the " +"container." +msgstr "" + +#: ../../topics/using-containers.md:18 38f82d201fa2455f94afacae2c1c76b2 +msgid "" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../topics/using-containers.md:21 00459eae5fef4f5f907ceb53eee857dd +msgid "`docker.cwl`" +msgstr "" + +#: ../../topics/using-containers.md:27 7e59171b12eb46e98ffa08a05ccebf16 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../topics/using-containers.md:33 d90442f3550f4e9b84905bb76ecb6fc1 +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that " +"is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../topics/using-containers.md:44 feb03506a2614ea3a0fc97f3154425c2 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." +msgstr "" + +#: ../../topics/using-containers.md:52 fa521c85542c410ba187c69fe5b3aebd +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../topics/using-containers.md:55 f3012553a17a42fca78b210ecec92003 +msgid "`hello.js`" +msgstr "" + +#: ../../topics/using-containers.md:69 fd0ad3c4cd904765ae5b043b44078a1c +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." +msgstr "" + +#: ../../topics/using-containers.md:72 60fa9a28e9bf4a4fa54289516e22f4cd +msgid "" +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/workflows.po b/locales/en/LC_MESSAGES/topics/workflows.po new file mode 100644 index 00000000..9c8321d5 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/workflows.po @@ -0,0 +1,504 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/workflows.md:1 d6acbcdd75704f7b966a49edb8af28d9 +msgid "Workflows" +msgstr "" + +#: ../../topics/workflows.md:3 4d3032eb6fcc4cf8a2a67958877d7850 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../topics/workflows.md:13 89e89efbb04b47909df04a046169442c +msgid "CWL workflow." +msgstr "" + +#: ../../topics/workflows.md:41 a6e739c210e54652aa8833825f58e36f +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier " +"examples." +msgstr "" + +#: ../../topics/workflows.md:51 5b187be9b5314039a7e16d35fe4672e3 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../topics/workflows.md:81 59c9035c8eb94a4984c2fdf66c1cb787 +msgid "" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../topics/workflows.md:91 0e790b8a77874eeca2efcdf8254226e1 +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../topics/workflows.md:150 176b128d31d549ec947e2112bda59e10 +msgid "" +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../topics/workflows.md:160 058879c518a24859933efd7c62d2b3e4 +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." +msgstr "" + +#: ../../topics/workflows.md:165 9e596d54fc074e3dbb622429244304dc +msgid "Writing Workflows" +msgstr "" + +#: ../../topics/workflows.md:167 14760ea2dd594df4a11af3c2b267e2ee +msgid "" +"This workflow extracts a java source file from a tar file and then " +"compiles it." +msgstr "" + +#: ../../topics/workflows.md:170 73d971cacade4ed4893f03978d930b3b +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../topics/workflows.md:179 ../../topics/workflows.md:180 +#: 54719da53e4043758f29194fda1b0448 652551d8f4cf49fbb785e56b9bccf2ea +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../topics/workflows.md:180 84d558ae6abc432695ccb49d050d92c7 +msgid "" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../topics/workflows.md:183 9ced46957b8b4f20b2315979aecb30b9 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" +msgstr "" + +#: ../../topics/workflows.md:185 bda955c302b2489fa76f54a08f6a4119 +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../topics/workflows.md:191 e57cce93798d4cb3a2e7a50f88549049 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." +msgstr "" + +#: ../../topics/workflows.md:198 0270321fc2554e318de95a5684e9b6ea +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../topics/workflows.md:205 e7035e4184a14b1bb2a33b9a22e06df3 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../topics/workflows.md:212 b242d87aa48241c094c78051fd1b4e6d +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a " +"workflow." +msgstr "" + +#: ../../topics/workflows.md:221 fef2e2bdae81488bb23e6a63b8fec415 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." +msgstr "" + +#: ../../topics/workflows.md:233 7e9c2fbfcebf45f0a8c906d32ad4ddb7 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." +msgstr "" + +#: ../../topics/workflows.md:248 f5dd8d4b1e324d7f81b12657f847c040 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." +msgstr "" + +#: ../../topics/workflows.md:256 76d103db569b4ec6ab33fbd3d8c11e79 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." +msgstr "" + +#: ../../topics/workflows.md:261 36ae3b2a1dab47b18b3896d208393e73 +msgid "" +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." +msgstr "" + +#: ../../topics/workflows.md:267 e0e1cf7c5e86443eaf7717b5c683ed89 +msgid "" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." +msgstr "" + +#: ../../topics/workflows.md:278 91eceaf92e5441ce8b70e57e59fcda75 +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../topics/workflows.md:285 6112278376cb4e84ba05ebe6db7b039f +msgid "Nested Workflows" +msgstr "" + +#: ../../topics/workflows.md:287 19b5cd110ef149819d91c5bb86f56def +msgid "" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../topics/workflows.md:297 5d4aca9586434f40917c3532ae97bb22 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" +msgstr "" + +#: ../../topics/workflows.md:300 a32ab81c1a4a4150a0cf6fc792104a2a +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../topics/workflows.md:309 a28860105216475ab93a1fcd2b740b52 +msgid "" +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../topics/workflows.md:314 b3a4a7cfd77340029137a2cc9462b65c +msgid "" +" \"Visualization" +msgstr "" + +#: ../../topics/workflows.md:322 88aff05f9f3a45b297dd3eda9f52bc91 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." +msgstr "" + +#: ../../topics/workflows.md:336 d5bc4016a294455baef3fe1e32c5c636 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." +msgstr "" + +#: ../../topics/workflows.md:341 5d59589eef4d44d69d2ef65821aaae45 +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." +msgstr "" + +#: ../../topics/workflows.md:347 d39c9aba4eda4252964711369c0ca9d6 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../topics/workflows.md:366 dd9b058b571347deb207200501a54651 +msgid "" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../topics/workflows.md:383 c2d3d7b3f62344b3841dadd0c2dd4981 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../topics/workflows.md:389 847d59018c6940f0b7248bc82abf4818 +msgid "" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." +msgstr "" + +#: ../../topics/workflows.md:394 f041304d817446d39cd9dd41b00e2e78 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." +msgstr "" + +#: ../../topics/workflows.md:398 a232c586c24045d7ad0813aabe2c62b7 +msgid "Scattering Steps" +msgstr "" + +#: ../../topics/workflows.md:400 f1d87f16200142318d6ec00d19ae9dcb +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." +msgstr "" + +#: ../../topics/workflows.md:411 884b61d0625a4561a963b381fcff7344 +msgid "" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" +msgstr "" + +#: ../../topics/workflows.md:415 35097a2dfc3c421bab46e81a53c34087 +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../topics/workflows.md:421 44c8319f97b242f197f1311fcb2719b5 +msgid "" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../topics/workflows.md:429 839e0cd993b44899a4049b44eb8aacfa +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." +msgstr "" + +#: ../../topics/workflows.md:441 333b64b5ab4a4078b9189c8bbb5924b9 +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." +msgstr "" + +#: ../../topics/workflows.md:445 73aa0f6708264bc39b0c6398827f1e6e +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../topics/workflows.md:450 5f6a3bf1dc314cb8beb9b336fc2c8f6f +msgid "Using the following input file:" +msgstr "" + +#: ../../topics/workflows.md:452 d5808863a44b4a6695e36ac1ae4a22f2 +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../topics/workflows.md:458 2c642b5be9c94763aee4bdf73d8bc2a1 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../topics/workflows.md:466 dcf2a0d97e4a4afa842a971b304e23b4 +msgid "" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" +msgstr "" + +#: ../../topics/workflows.md:469 2aea56527429469c8af125414e4f4f00 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" +msgstr "" + +#: ../../topics/workflows.md:472 a4279d75f660475d82c4bc8f869c17cc +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../topics/workflows.md:480 33ac7f4c0b1040b89811c0445b1f6824 +msgid "" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" +msgstr "" + +#: ../../topics/workflows.md:483 17b1da21293d40f7b246abb4f3a6fcd7 +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../topics/workflows.md:489 5aff13d9cf7841b29e2285ce2fdc90ad +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" +msgstr "" + +#: ../../topics/workflows.md:491 53afeb0f6b4f405782b0eb2e74d3acfe +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../topics/workflows.md:497 fbab18460296443daddb7bc1bcafe4fc +msgid "" +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." +msgstr "" + +#: ../../topics/workflows.md:509 52b2dee5459b4bbdab9f09576ec96f65 +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../topics/workflows.md:513 24185616ce374615a6966a70df77693b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../topics/workflows.md:519 7302c1e575bf4457a04243e9e0ef6f59 +msgid "" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." +msgstr "" + +#: ../../topics/workflows.md:522 6ac74585b69d4197a26c8230f53f75cb +msgid "Conditional Workflows" +msgstr "" + +#: ../../topics/workflows.md:524 f189ba0d5e7547d1a6540abde5c4da78 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../topics/workflows.md:527 257301405fda4c6aa98195f4344b496d +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../topics/workflows.md:566 189ea6307a25445ca573ff93cd8c4f1d +msgid "" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../topics/workflows.md:573 b0701c43575d4dc79c4abe2c932928c3 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." +msgstr "" + +#: ../../topics/workflows.md:587 7de691f8e339422e8b027297e3d16fa6 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../topics/workflows.md:607 246e5e7c82aa48c9a7f5f2c3b7b4d707 +msgid "" +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../topics/workflows.md:627 b28362ad11bb44c9b7247f411e58caa4 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/yaml-guide.po b/locales/en/LC_MESSAGES/topics/yaml-guide.po new file mode 100644 index 00000000..4b225c2e --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/yaml-guide.po @@ -0,0 +1,193 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/yaml-guide.md:1 153f05199ec24a5da81da49288e2679a +msgid "YAML Guide" +msgstr "" + +#: ../../topics/yaml-guide.md:6 95951c4a95d943c89be9252a898018d8 +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../topics/yaml-guide.md:13 60a16d7722724500b0a31194b6958cea +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../topics/yaml-guide.md:16 61f0a8fcfa2044ada7761d35e6ee6bbb +msgid "Contents" +msgstr "" + +#: ../../topics/yaml-guide.md:18 3c5dd09c0fbc4079abff7f8ee9c1bd03 +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../topics/yaml-guide.md:19 c7fa245866d0430fb8fcef9392869999 +msgid "[Comments](#comments)" +msgstr "" + +#: ../../topics/yaml-guide.md:20 dde5f9ad058445d1b0131ddf1fd80b74 +msgid "[Maps](#maps)" +msgstr "" + +#: ../../topics/yaml-guide.md:21 fdb88e5dafea4cb0876cea846eccca7d +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../topics/yaml-guide.md:22 f2ae9d617f274c7eb84a2d87c10a4cc5 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../topics/yaml-guide.md:24 47bffc9bb7b64047a25903eb42bde019 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../topics/yaml-guide.md:26 283f64df8dcf4abc8f00ee515d0cc9bb +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" +msgstr "" + +#: ../../topics/yaml-guide.md:42 51a3cd8bd6d2403daadc57d0091e99dc +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." +msgstr "" + +#: ../../topics/yaml-guide.md:51 7d58fe0504534589adfadf74e82de41a +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../topics/yaml-guide.md:61 35e8c97a24344c7d9933f1910d6bd995 +msgid "Comments" +msgstr "" + +#: ../../topics/yaml-guide.md:63 5ba35d4bbb4644949c37993a77a50bf6 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" +msgstr "" + +#: ../../topics/yaml-guide.md:76 e63546bf4b144bfba77767ec7248d63d +msgid "" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" +msgstr "" + +#: ../../topics/yaml-guide.md:79 25ac6edc52bd484cac8eb4fe4d5b6e1c +msgid "Maps" +msgstr "" + +#: ../../topics/yaml-guide.md:81 20e1be6499d9470fa74dde6da33f2120 +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../topics/yaml-guide.md:104 a99731edefb049299d313941156c41a6 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." +msgstr "" + +#: ../../topics/yaml-guide.md:127 51d8ad7d937540ee88b46fc790319b4a +msgid "Arrays" +msgstr "" + +#: ../../topics/yaml-guide.md:129 bfeee0ef93e44a0ea50e3970e027b2f1 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" +msgstr "" + +#: ../../topics/yaml-guide.md:146 297035119d42476e8dbebd1ed2241ac3 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../topics/yaml-guide.md:167 563dd83823d745b6aebeb956fca51aa3 +msgid "JSON Style" +msgstr "" + +#: ../../topics/yaml-guide.md:169 7edbeea182fe4043be66f02bc5952114 +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" +msgstr "" + +#: ../../topics/yaml-guide.md:177 37ddb7add5ea4fde94c97ab2bd2c85e7 +msgid "and:" +msgstr "" + +#: ../../topics/yaml-guide.md:184 ed9f6a7d062c43f099b5181e2c930303 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../topics/yaml-guide.md:194 9cb613e445b5429196ced3d66fe95e45 +msgid "Reference" +msgstr "" + +#: ../../topics/yaml-guide.md:196 030fd9aede23463d981faf746e2b070f +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/tutorials.po b/locales/en/LC_MESSAGES/tutorials.po new file mode 100644 index 00000000..5222f765 --- /dev/null +++ b/locales/en/LC_MESSAGES/tutorials.po @@ -0,0 +1,58 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../tutorials.md:1 99ae22e436b042009833051fac79e2c9 +msgid "Tutorials" +msgstr "" + +#: ../../tutorials.md:5 2ffee614f02343cb94399b8199803149 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to " +"the list." +msgstr "" + +#: ../../tutorials.md:7 1831288df8f14081b13cf52d587c678a +msgid "Beginner Tutorials" +msgstr "" + +#: ../../tutorials.md:9 bc1fd03f560340d68bdcf39455d25c8d +msgid "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" +msgstr "" + +#: ../../tutorials.md:11 47d068326ee34835a7a00ce7e24ef711 +msgid "Advanced Tutorials" +msgstr "" + +#: ../../tutorials.md:13 bcee717d8bf740c49c79200b0c660f3e +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../tutorials.md:15 5e55349fd3d749de964e8fcfca5959f3 +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../tutorials.md:17 77245b1c0ebe437f89dc07b45c5fa95e +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" + diff --git a/setup.cfg b/setup.cfg index f4315385..7ccac7d0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -40,6 +40,8 @@ install_requires = sphinx==5.* sphinx-reredirects==0.1.* sphinxcontrib-runcmd==0.2.* + python-Levenshtein + sphinx-intl [options.packages.find] include = cwl* diff --git a/src/conf.py b/src/conf.py index bcba3134..c5000204 100644 --- a/src/conf.py +++ b/src/conf.py @@ -234,3 +234,7 @@ "doc_path": "src", "default_mode": "light" } + +gettext_uuid = True +gettext_compact = False +locale_dirs = ['locales/'] From 712e507c51f778466e22f0fcf2f5a8f80a5fd536 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 24 Jan 2023 17:20:50 +0100 Subject: [PATCH 29/49] include template for new languages --- locales/LICENSE.pot | 102 +++++ locales/_includes/what-is-cwl.pot | 22 ++ locales/episodes.pot | 27 ++ locales/faq.pot | 292 ++++++++++++++ locales/index.pot | 57 +++ locales/introduction/basic-concepts.pot | 217 ++++++++++ locales/introduction/index.pot | 27 ++ locales/introduction/prerequisites.pot | 257 ++++++++++++ locales/introduction/quick-start.pot | 167 ++++++++ locales/setup.pot | 27 ++ locales/sphinx.pot | 27 ++ .../additional-arguments-and-parameters.pot | 62 +++ locales/topics/best-practices.pot | 137 +++++++ locales/topics/command-line-tool.pot | 62 +++ locales/topics/creating-files-at-runtime.pot | 77 ++++ locales/topics/custom-types.pot | 77 ++++ locales/topics/environment-variables.pot | 42 ++ locales/topics/expression-tool.pot | 47 +++ locales/topics/expressions.pot | 373 +++++++++++++++++ locales/topics/file-formats.pot | 77 ++++ locales/topics/index.pot | 22 ++ locales/topics/inputs.pot | 247 ++++++++++++ locales/topics/metadata-and-authorship.pot | 57 +++ locales/topics/operations.pot | 62 +++ locales/topics/outputs.pot | 134 +++++++ locales/topics/parameter-references.pot | 278 +++++++++++++ locales/topics/requirements-and-hints.pot | 22 ++ .../specifying-software-requirements.pot | 42 ++ locales/topics/staging-input-files.pot | 42 ++ locales/topics/troubleshooting.pot | 72 ++++ locales/topics/using-containers.pot | 82 ++++ locales/topics/workflows.pot | 374 ++++++++++++++++++ locales/topics/yaml-guide.pot | 157 ++++++++ locales/tutorials.pot | 57 +++ 34 files changed, 3824 insertions(+) create mode 100644 locales/LICENSE.pot create mode 100644 locales/_includes/what-is-cwl.pot create mode 100644 locales/episodes.pot create mode 100644 locales/faq.pot create mode 100644 locales/index.pot create mode 100644 locales/introduction/basic-concepts.pot create mode 100644 locales/introduction/index.pot create mode 100644 locales/introduction/prerequisites.pot create mode 100644 locales/introduction/quick-start.pot create mode 100644 locales/setup.pot create mode 100644 locales/sphinx.pot create mode 100644 locales/topics/additional-arguments-and-parameters.pot create mode 100644 locales/topics/best-practices.pot create mode 100644 locales/topics/command-line-tool.pot create mode 100644 locales/topics/creating-files-at-runtime.pot create mode 100644 locales/topics/custom-types.pot create mode 100644 locales/topics/environment-variables.pot create mode 100644 locales/topics/expression-tool.pot create mode 100644 locales/topics/expressions.pot create mode 100644 locales/topics/file-formats.pot create mode 100644 locales/topics/index.pot create mode 100644 locales/topics/inputs.pot create mode 100644 locales/topics/metadata-and-authorship.pot create mode 100644 locales/topics/operations.pot create mode 100644 locales/topics/outputs.pot create mode 100644 locales/topics/parameter-references.pot create mode 100644 locales/topics/requirements-and-hints.pot create mode 100644 locales/topics/specifying-software-requirements.pot create mode 100644 locales/topics/staging-input-files.pot create mode 100644 locales/topics/troubleshooting.pot create mode 100644 locales/topics/using-containers.pot create mode 100644 locales/topics/workflows.pot create mode 100644 locales/topics/yaml-guide.pot create mode 100644 locales/tutorials.pot diff --git a/locales/LICENSE.pot b/locales/LICENSE.pot new file mode 100644 index 00000000..0460a73e --- /dev/null +++ b/locales/LICENSE.pot @@ -0,0 +1,102 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../LICENSE.md:2 +#: 3d749a78eb3e47c991d603c2cabd1b91 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 +#: 4689ade8475a4c8a9d5e325f072c1392 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: ef8ec0f072d947fbba997c4b2191abc2 +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 696f3824ca814c9eb314abae51be8202 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 72ebe92edf58434e9d7a4fc6bddf8880 +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 9b403f96d4194ffaab3f309d7d12f360 +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: 10b1befd0f834d79880c8aeb70b595d4 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 9017d0b760bb4370926d511b97a604c6 +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." +msgstr "" + +#: ../../LICENSE.md:22 +#: 1faadcaead6748dfb34886e5819af9b9 +msgid "Under the following terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 7a49ed3a728349c9b486f3d0b1dbf577 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 57da6294edce46eab00e7d15e6f6d4fa +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 8fc8a30cd63c4a0a9d8ba1b913687029 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: fe59e74a4d024831a6d5cbcfd3e4ee38 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: 3ea41d5a14ad46729cabb387a33814b0 +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 23751e2552ff450c83e3dd255da56dac +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 13fb5eb48a8a434e95dbbb717ccaef8a +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../LICENSE.md:57 +#: e262fbd0e7de4f148f31afe39d1cb9e9 +msgid "Trademark" +msgstr "" diff --git a/locales/_includes/what-is-cwl.pot b/locales/_includes/what-is-cwl.pot new file mode 100644 index 00000000..22d33219 --- /dev/null +++ b/locales/_includes/what-is-cwl.pot @@ -0,0 +1,22 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_includes/what-is-cwl.md:1 +#: 44a9467c5d3b4a128ceade82a521b6da +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" diff --git a/locales/episodes.pot b/locales/episodes.pot new file mode 100644 index 00000000..8a04d6ae --- /dev/null +++ b/locales/episodes.pot @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/episodes.md:5 +#: 0cbb5e7334a647c3bcae7333ec3ced90 +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: fabb221482cb4ac0a98bbe10943ed025 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" diff --git a/locales/faq.pot b/locales/faq.pot new file mode 100644 index 00000000..7a9282b8 --- /dev/null +++ b/locales/faq.pot @@ -0,0 +1,292 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/faq.md:1 +#: 5daa5afac36f46dd8329e5629056384c +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 40c8efda3caf4c6089bda3027c522f37 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: ee854bcb685941cab45ae7f33b0efe48 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: a4cdd5ab6fe341a3ad3e3055556d96c3 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: d1f359d47f124dfab23a75b196cd5884 +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: d83ced40605e411c92c4ae38761d7ffa +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: bc8997df2e6746cebc2068534f30ee82 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 20b6ae57e1cf4410877a60fb3ef87264 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 73c66b809e9a4218b624338ccb88a05e +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 9be72b7d5d604526b125b63148e99320 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: fd96d178901545008a43fa99e3aa6cf3 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: db58a582e66244468f4d31e9213933d1 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 3e70f0da5cd7460b90c1690366f40820 +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: db28dc27c82b4b29a7a9a768550bba9b +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 4474b16fb3fd4cdc85da931159804967 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: 23c9b2e21cec4ee8ade087e6630f62c2 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c01309dcd65c4f1080c396e6a9efb75d +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 0a36801172fd4e24a04b3ba85cf74e29 +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: 433e788ba01141e98ea5a9e73ef71e6f +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: b6de2761ce454992904775a06b7ba326 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: e36c2d53e8ba40f4a602b489a6688e24 +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: a9310166cb514e4e8824bba7fcfcb277 +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: f6144f77152e4284963951abaa30adb2 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 790709dfc2854e4a89fcc4769f84b0f4 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: 438789c8def549d1b4b8a187d5acc48e +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: 23ede7dfd5c84492baee1d5bbb9a91d9 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 37c0474e48164160b23c4094d583d2d3 +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 3b2be0a4a87041b7a5bda20c6df2ffc8 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: 886300d2dcff4861aae503d34b0bee44 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: fe393ecdff25428da6cbcd30171c7811 +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: ebfd4991d917413b858da8b437a55805 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: 2919ff4f51254e69aea40146e2d911f1 +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 61ed4e87457c41eea31f51740557597e +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 1e6624104b024eb092682cd0dd0f6a3c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: b741b8333e104feaa6d1f41fd4476304 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 334673ae870a4dada817857f3a49326e +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: 362f85270df04712b2e2f21c7019e3cb +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: ad6997f24c7c42fe965b5d7bfd1e633e +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99dce9d60b6a4f99bc39899b7c8c10ef +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 6b68fe24cbf64624b49ea56fce2eecad +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: d23326837eb74e7faf1f54e25f8309c4 +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 2e2eabe92670412e95474b25ad9cda4c +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: 81f9308adbee4a3c9e585b8e0f0c4844 +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: a5d3ed6cac28415288e7fc7fbfc6e8a6 +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: 72f9692803304daf9f846e2b90139660 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: a7eb20c817704811b3bcf2f94ec2e51d +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 20fa869849ef4b358a11db46111017de +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: 35032fcd9f23403ca006d62a7d6e7be7 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: f6d6a4e3691446378c8fb01a2d19f8ad +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: 44608fed1048458e999e13b014327e7e +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 96ede8a8f1f34786aabd4004bf2e7acc +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 84634a368e704e8d828678785c784595 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 545c4db9c24f42ee946081254d9ca7a8 +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 1c1e6d583d5646a8a5c9316dcd743d9f +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: cf7d336d444e4f59aa83585b7abb1fe5 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" diff --git a/locales/index.pot b/locales/index.pot new file mode 100644 index 00000000..1d9fcd30 --- /dev/null +++ b/locales/index.pot @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/index.md:1 +#: a58ca61ccefc401588f91699bc98bd32 +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: 6dcf12053f104cb3a8d23ce8d4f90363 +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 1cc90206170d46119c5756f31a9e8799 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: b54801d84a944dadb4e4637551e3f7b9 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 860afd2eda4847e0a0d8834de3af4aa8 +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: d6046316c84b40ffb5478c90b2604911 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: c3c89ac756a74d9688e179b8718c9bf0 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: 0eb795062b484537b090c4d5c361f7f4 +msgid "Table of Contents" +msgstr "" diff --git a/locales/introduction/basic-concepts.pot b/locales/introduction/basic-concepts.pot new file mode 100644 index 00000000..ceeed500 --- /dev/null +++ b/locales/introduction/basic-concepts.pot @@ -0,0 +1,217 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/basic-concepts.md:1 +#: 570f94ae2d4d4e19a9cf3a9bbceba835 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: 67f2ebceccce441caa8279166f8f901d +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: b7c949f867b8475f8969622abc045729 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:2 +#: 744c9501df5d47dc93962d217838f312 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: 0a0131d9b3be4af484b43fb3d12f804e +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 6c2f26b24ece4319bc9ecbd147f928e0 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: 0305e3bc2de04b15a64a1b1c1188da2a +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: 21d7e31a2abf4d36ba5acef1faa76b97 +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 1c7e942576304977954be9ddcc9b2927 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: 920cf7f770054d87807273e8901630b4 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: a4c286729d884042aa9f6703ae958896 +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: ea9dc3c2e83246508ee111cbeb5e5379 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: c40f991cf70a4eefbf5b04e4089f809d +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: b3a1d362a96b426992cc37c11e13e09f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 201d5104011e4178adf564f969e45951 +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: d2027b38193f4252908c9f1fa8a1999e +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: df6be4b832ac4bbe9ef1eb5fc8cfc1ec +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 521eb59a379444afa0478b4536923f28 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: b600a21001d24203855b9d972365de5d +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 60b8285020a34af9b8a22688953899e6 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: aac2f76a1da1470cab9ff221c35134a3 +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 1adb2eda9c8a4e2493872e33a13bb77a +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 08847ed6cc8d4b76b23fe54117ecd929 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: d5fa5caa377e4cac9cb9736d54ee312b +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: f1c84c485ad9400aa80dd46eb5c75241 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 500a1a4565f24639ba5e248c382b2c45 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 1b407a21568b4c4da8a90d3eb33611b6 +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: d715b520274949bf9f9e3e7235f6d3f6 +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: 5c18ffe7e7254167a02be50ebab5e285 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: b9cdc830853f45bab2876305373f35b8 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 6d839e88664f41f0b5d01d38053ede18 +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 3e4b846a939a43929c4a45af1a7eafe8 +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: b19094f1044648718b9fdea72eda8994 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: 33191f1525334cc398892bb867135b42 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 6fe0b86d8a3b4bb0ac1f075fbac8988c +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: b206be2c6a5043429a1213b2989a0f53 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: f45e3dc2b0a74948a0977c47aab8db4a +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: afaa1ed8a0b949959992d4f4d7e00356 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: 51073c8b56864cca84600f12048a6036 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: 1215f39220b441a79f56cfe7cd61aa92 +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" diff --git a/locales/introduction/index.pot b/locales/introduction/index.pot new file mode 100644 index 00000000..f4ae1f30 --- /dev/null +++ b/locales/introduction/index.pot @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/index.md:1 +#: 6c33d560fcc64807a04e7a1536b1032a +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: ad616e9a47d14c5bb4532e5266d61ff5 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" diff --git a/locales/introduction/prerequisites.pot b/locales/introduction/prerequisites.pot new file mode 100644 index 00000000..519e8ca7 --- /dev/null +++ b/locales/introduction/prerequisites.pot @@ -0,0 +1,257 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/prerequisites.md:1 +#: 789e7b95b23d4bdb8398d691587613ee +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 53432372af8c447cbeb5f05892daee72 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: 36f42adbc26f42a891d996f8b9730589 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: 090df41a03204aac91aa7f663c6a5209 +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: 57ad125f7c2e4f01982acbabb1ff3d80 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: edfd6bf214d042feb6662b1c2d2fa48e +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: a44cd70295f5442fb6651d85794528ba +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: df31f7835d544160be90401bd20993a3 +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: f5e9ef0126f74353bc4c30a6e92bd92a +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: d11b1c901d004a10a7b8cda2e727bae9 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 37e363cb5987436d86e5725a63984e5c +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 1a19bd057d3c48679e2ae844c6b8291a +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 2a18beeff42d4cf8a4315e4a171cdede +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 17f353c8e861492d91e51b78b5da3351 +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: 5f178532a9004163b795c1433248eb77 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: d2ff1f8e720f4bd49912ccd7040f2ccc +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 77e4e1e5b4764d59a990b43ed93a7459 +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 22b4c40f082d4bacac051617b617cbae +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: 7f97cf170a854ce685bae8f30a16572b +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: 11fdbc38c5ed45a4976e16844729a3cd +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: c513823812a5423da694e85a20f86506 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 7be568d02d7e4593a1c0ef719d0f83ac +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 36ee569c74ac4602a51818a92c95f031 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: 06defabc17634ceea15e1f4523164a23 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: ac847d3d1587499ea6e1b3796e16282c +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: a4d5291859bb415b981a7dd6dff3c313 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: d80356bf607b4f7d9572b925c69163f1 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 54ddcf5f932c40c4bbec2f88114e6e20 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: f159836854c14187929cf24f716ccee0 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: 728b24fff1f14726b27168dbf46e4e7b +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 5590cd84de1c4f9382ab37644a5adac7 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: 5a066c4dcd034cfd8902ae01128134c5 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 846f1eaf4f81477c84b885f7c17ab030 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: a972f3ea3b5f41f6b78f682a42616197 +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3165d673bd7341518d2b259932917b53 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: d23de68e21e1429886b3814af9cc3104 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: 9538d8b0944f4e72bceec9ebf1fb5832 +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2e710620d21f44a0a036431453ed5e20 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 25c6c7a87e1847f9aec1c32cbc83cf4c +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: a90b90e926324cd687a29436e82eef38 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 91a2b9d7d7b642c2904bd55d29690254 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: e0cdb48ef04846cd9a39008260b18777 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: ac55bc8b751d440086043c4af6776d10 +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: be04aba59f3c40f1aa90316090792441 +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 2d4790bd46124cd8be789927c25fbbbd +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:196 +#: af2e128598294dee9330002a2f7bfc63 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: f4ffd0d89ef1406f9e957a05a4172c57 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 00fa0dd045054fcbbe3322e10e591430 +msgid "The Python `venv` module: " +msgstr "" diff --git a/locales/introduction/quick-start.pot b/locales/introduction/quick-start.pot new file mode 100644 index 00000000..62c7c9fc --- /dev/null +++ b/locales/introduction/quick-start.pot @@ -0,0 +1,167 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/quick-start.md:1 +#: 1f7df6c4ef354b4284ffca2f01ba7a40 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: 98a2ea8175314bf5b6fbdd2464402c82 +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 924b8fd198fc487f87a8de4948261bee +msgid "“Hello World”" +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:2 +#: 1d89d9d6798a4e38adc28680ceec1a29 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: ca24ba5ebb324a90b34fb1b28468fbcf +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 7a3bbeb141914c0daee451f2bca9a081 +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: cdd3578d507d41539c38a601701e8854 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 767cf30acc9d4f81b8d34bfc90a8891c +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 8acd83b581f2499fb640153186711660 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: 46d1f843730a4c848a327de9a03c04e2 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 939e54e81c304d21a4eb33f99407ee50 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: 4db304a983cb46fe917563a1884659cd +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: 72d657288bf248b6a53080e6295302e3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: a03263ff919e4777afdca4fc20efc673 +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: 2f6d2f41de974a469babd97d1106608c +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: cef66179a76a432c9b0c1a49b0f6bf69 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 133d0f054f784d7ab5f2fd5f028d80eb +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 454aec8aa868430da0449434df741b21 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 5f7a1d2d705145a58fb37d6b7fe66add +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: 18c580026a2346c8b1e020fa9b2f3f8a +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: 0051eb403e43451390f5775976d11818 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: dbbb23a79b1143a7aa7c91a1277851ce +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:94 +#: f0ad9eabc2c04cde941bf78f0bfcb641 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 0e14c76da55e4501b6fb8ed246a344a7 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 6e813c00aa564fc1a407cc7aae77475a +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 6029a1f35b10455389c63c680a468d3c +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: c1312d1ce89e4a48b31597c5a8b2e603 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 18cdf73c71574ce9a74c189aeaae971b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: 5488abc1abcd4aa68e7e8a702834c619 +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: 4cf8dc5e58244810866649259ac13f9f +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" diff --git a/locales/setup.pot b/locales/setup.pot new file mode 100644 index 00000000..10900ecf --- /dev/null +++ b/locales/setup.pot @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/setup.md:5 +#: 29bb5c68be6042e5aa4a370e9c4024b3 +msgid "This page has moved" +msgstr "" + +#: ../../src/setup.md:9 +#: 8bcf31398c34491da1a1590422a72cbe +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" diff --git a/locales/sphinx.pot b/locales/sphinx.pot new file mode 100644 index 00000000..0c4554c5 --- /dev/null +++ b/locales/sphinx.pot @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:27+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: b896fd5e11fe4674a7f46ad489476692 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: acede4e78f7e4aefa0ad9425928cbb42 +msgid "Section Navigation" +msgstr "" diff --git a/locales/topics/additional-arguments-and-parameters.pot b/locales/topics/additional-arguments-and-parameters.pot new file mode 100644 index 00000000..c447e7c6 --- /dev/null +++ b/locales/topics/additional-arguments-and-parameters.pot @@ -0,0 +1,62 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 4ad19837b80f40af88edf443c4d4e743 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: a51e98f4fab24b42b225e24b69471869 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: 78e7111611734004b650bdde36fe8079 +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: 0c5cc374383a4f058a6c8d7a3d83c7d4 +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: 67cfc6cc46764b07a6738691bc1cb1f6 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 744b2343db934429b7a04b4ab4f84d15 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: abea839860f447f1b767c3a028ce1ca9 +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 5a44c7cd8feb4593802cdf56254b79d7 +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d5f29eae1af646d5be22c816c5d1a4fd +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" diff --git a/locales/topics/best-practices.pot b/locales/topics/best-practices.pot new file mode 100644 index 00000000..d4460047 --- /dev/null +++ b/locales/topics/best-practices.pot @@ -0,0 +1,137 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/best-practices.md:1 +#: e93667d13f1c481c9ffec6bb3062c073 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 685dedff3cf54c4b95bc56b30a5d7fce +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 2e4c3af1016e4269b6eb3eb7c37b609b +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: ee2f52f0a96449a7b6e49b2c824288d1 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 426fc5489a1a44d2b037f1456b6556c2 +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: ecf6e24373f944a0a3e9453c31e03e8e +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 0ad7fe10c6584f01991d87544f1d5649 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: b589adbe3f324ecc9670c2355be1e308 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: 50184e2a39fb4a2086afbb236efa603f +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: f000d979ab914d94bbfe988792cf1629 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: a11d2c6e1408411d89cf7d434448a414 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 3e379d3bd38b40d38a2a448e907918b1 +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: b8eb7c78ffcc4093aea11fa21cef762e +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: ef540052516840638bb7e5bf4dadb945 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 378f73d8fd864d0bb3ac5d027224ef08 +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: fb1fee0d5583488ea2091dbf9b36eded +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 210127c58cd44557b60d603d8d68725d +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: 6b657c5d109646f5bf7a38cef1b903e3 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: 14951e1b672248f095c31c4c96bf5183 +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: ff9dbfab87a24cfab3734882216d40af +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 444b5580319b4ee69a1439c7ccf703df +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: 9ba7fd2784b2430fb6964b9a16d2d553 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: 0e88ebb9e45c41db83482ccf848ca1ca +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 3b2fe5ca68944df5baf04c7b5705e207 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" diff --git a/locales/topics/command-line-tool.pot b/locales/topics/command-line-tool.pot new file mode 100644 index 00000000..422115ac --- /dev/null +++ b/locales/topics/command-line-tool.pot @@ -0,0 +1,62 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/command-line-tool.md:1 +#: 595e9cc7e0a448f695e27b1cd0427d9e +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: ac9188b4b9dc45589f2173a73dc9d3dc +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: a6dd1084b9b248e08ec2659999f82ac6 +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: 9119bb87ef4b48e7946f5412d197ce0a +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 312c6373a25b498db63c67abed6c6289 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: 84b6964c9cbb4d67af2794624de86337 +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: c276e21332454452bc814d33f007a670 +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: 1321360b42da4f65975569e2b7314bf0 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: 70739268c7674a99834cf6c166231149 +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" diff --git a/locales/topics/creating-files-at-runtime.pot b/locales/topics/creating-files-at-runtime.pot new file mode 100644 index 00000000..c427c32e --- /dev/null +++ b/locales/topics/creating-files-at-runtime.pot @@ -0,0 +1,77 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: d4e5cee7a82447a696e1e9516ccc2e38 +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 6121650880d4447e9b5a6b66e0f3367c +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: e81edd66cbb2461e905a7adf6bff23fa +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: cb4602ae814b4b47abe61ab3bd88b046 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: f6f5c6dc8ff74db3b1c5aa2403ee12d4 +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 87abe95ca4054b48a8fb76d7916db1d4 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: de2366c1d2d1459ba23fe1410f2b86f4 +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: 28906471c2fb41358706f624e3c8bd8f +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 449fdfe14172498fb80e2f57ca0c05f9 +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 9a9ce102e4ed4dc68eeb161746ab4689 +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 447b2199a76646be8afacb72203e9719 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: aaae789101c742b292ebdcec727b1762 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" diff --git a/locales/topics/custom-types.pot b/locales/topics/custom-types.pot new file mode 100644 index 00000000..f338bd21 --- /dev/null +++ b/locales/topics/custom-types.pot @@ -0,0 +1,77 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/custom-types.md:1 +#: e1169af9b1ed419b80cd7b2ee432c37d +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: e297aa8753564accac64cbad1be99d0b +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: aa76f57cb1eb4a81ba6560ca7b7d47fa +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: 7644b22f9154413cb88f46e9a2a1a9fb +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 1d259a15f1884950953d8536b74d437a +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: db1612c92c3c4d63869aa3d589960ab9 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: 4c7038e3a8d6484e9eecb348e825605a +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: 960610e43cd247dfa5921477558f6a2c +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: cd7d7cb81be74acd81bd3af2ecbeba8c +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: b0b4eb8206f54104a7fe02492cd3c0c5 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: 2d0fc88b5d524b4e814f47a147b7e555 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 8e99e8e00d3340e6bf7025622bdfbf47 +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" diff --git a/locales/topics/environment-variables.pot b/locales/topics/environment-variables.pot new file mode 100644 index 00000000..294a71e7 --- /dev/null +++ b/locales/topics/environment-variables.pot @@ -0,0 +1,42 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/environment-variables.md:1 +#: 201d52b060fb44e3b988d1cf08b32569 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 5438cfdc5df24a2098fc3014731bceb2 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: 295b041049874673b1c4f93e3c8932c8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/environment-variables.md:13 +#: e2076a2e3c4e43228e69f9b4ee535e3a +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/environment-variables.md:18 +#: 74c67839550148b98f8a681f53baae9e +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" diff --git a/locales/topics/expression-tool.pot b/locales/topics/expression-tool.pot new file mode 100644 index 00000000..329b21fd --- /dev/null +++ b/locales/topics/expression-tool.pot @@ -0,0 +1,47 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/expression-tool.md:1 +#: a1a763367700488eaeeeeb6c1d4aaf3f +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 1baaf7f3bda34cabb4081708f8eb676f +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: cf8f9f21b8bc4cba9e947b631e0452d4 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: 01ad0d7c0c9d4051906424dceb702361 +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: af1958ad56b64631a111aaaa41413a09 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: f50a9dc71c7f4beab2525ce6e6fca385 +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" diff --git a/locales/topics/expressions.pot b/locales/topics/expressions.pot new file mode 100644 index 00000000..012628cd --- /dev/null +++ b/locales/topics/expressions.pot @@ -0,0 +1,373 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/expressions.md:1 +#: 6b0faa9c10ad4da783e2155070095a8d +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 9e44e4e737b545a2b10b97e923027bd9 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: ad6d3dddfda445a5bfce2665cb195605 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: f487ea31d38142839ce5667701b894cd +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: 47d7f42a657a4547af1be1e13662effc +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: c331468453dd4e60a76bc753417b72ce +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 6b9b7057eb154a95847ec56652de07d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: 6facbcd083f04a60941589da7e21621f +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: a08110192e264a109ee6a568351135e4 +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 1a260934cee04059b4765d154f6388e1 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: ebee54b00af643aba0d53e774b0ac188 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: 02ad120e9a72482780f062ae3cadcce7 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: 8bb623ae7a9646ff992d7a79856aac8a +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: 4437b8ae6fb04a1fa06f494ead97b1c7 +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: 145b4d4cbfaa4c5d914455b0b5b6ef1b +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: b187028dafc040e8ab04d2a69c547874 +#: ecb148c1da01445a8149b500b5ea50f5 +#: 87f7f23e14e54b87b6f1b4f8c148bf8b +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: 9132968dd34f4a9c99ebabcae48a4a3f +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: 34b31b4554b442ab9d9bac1e95cc3029 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: 33e3e471fafb4f609694af59556dedcb +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 941720c894bd45a895e3a8e682b7e884 +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: e2c648a9a5794879b74cf02e489f0c5a +#: 15692bd5c6204aa9b72259e6dae69bec +#: 1a506a3ea7614043a67dd4d93015b19c +#: 166fd96ec8b64db88e1837feaf65df1c +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: 8c65f558109142048b8831f800264bb4 +#: a4e5f9d5354d483392c157f736cd8c20 +#: 9ec2e908459a468b837b572a426bcd8d +#: 2d82125ff94c441ea29b3da5ff5dbb08 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 6eecf3fa29d9465882a2b6be02504ac0 +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: 92267f3d8f4e4b3fa129e3bec3b16413 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: b9b5551681d046e7a0071eee29987b04 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: b148af79351e4ba49604e24861388496 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: 4c48b367e5494d559484c5395af3a5a4 +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: 5541a07628174dd6a843afa2c37f4973 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: bf6e4a2101654e15bc27ac3db0c6bb6d +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: a295cb00ea034ce7820897606999ae4c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 5fd2e9df08404efa9d24d8bfccf91a18 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: 51f8b42f4e7d4c8484133a18f83be491 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: 73fef9b1b2074077a2525f72b2efaf62 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: cf19b246bc20476899a83e68113dd3d1 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: dfe56b4ea35a440d91f579efcc2c039b +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: 918bc6b265a549f28f027da29368cac4 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: a9182179ebce4c99b4eafe59ba122799 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: 984ceb05b6b24e4986a28436bdca88e7 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: 9a3f6db0d7f64468bbf2f6f861eab96a +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: b7557357360d454dba7ab3c3471b5a23 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: 839ac0ddca374746972ead6d22427edc +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: 89bfd53638504c7aa437c2140afb6035 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: f0af6b4cfc23480aae61f42422ad3afb +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 67ccc10e77d644078b170a28a8ebed3d +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: fcb8b8003fc84ab890ce241e63d43b5d +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 584682d4db424108b89ea8e315838de3 +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: 77439e7f4f214db781edc777a8a03b78 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: 4ba274f6d9c44ad7a05891725299a759 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: 1b751542a9f34fe19ae5f91174e01cb7 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: aca9ad053f5441caa5cd51170e35532d +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: 37c96fdc52c443faa1d1e462ff034425 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 4bcf5cd130b148f7b3f601902ad0b7b4 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: d6f0074d025742a6b3fe7f91f1dff335 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: c664d4710c404ed0af90dc22c8f273b1 +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: bd8dfef3aa934750bdd790e1de6bced6 +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: 1ae20d38a1574d828ca7cb8e955906da +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: bcda020047784e4191d4de456afc7449 +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: a9ccc2da748644dfb28b590eae974f63 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: aede8f2c722c49f18cd2a86c051bb1d4 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7d1bd9bfba9c496a90fc45f575505e22 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: 8b906fa3b98c48c68de46f80667d4d2f +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: daa9689f15c746a38dcd22a3f169a4c6 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: d0d8193fbb304f0281db0c6c1147545b +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: e5e1179082c14621bafbd14d887db62a +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 193379258f254ac5a25fcfb61b1c3540 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: ec0d1c972b9942f8a55b7b68fc9cfe07 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 63ff0565300a493f8c84935139c23552 +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: f8bb29ee047e407ea226599bccd86196 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" diff --git a/locales/topics/file-formats.pot b/locales/topics/file-formats.pot new file mode 100644 index 00000000..86733f1a --- /dev/null +++ b/locales/topics/file-formats.pot @@ -0,0 +1,77 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/file-formats.md:1 +#: f2a1cf1e81e54737af8d81bcef76d88a +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: f81bab33b2ad46d3a852e15d88858879 +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: c1dd91bf59804358be63bcde0614bd31 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 785ed7d362824bb99887694670aac50e +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: c3f54f4d6df44e628c59c1e70124667f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 6c3942038fd3446db254260530291732 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: db9222078ef04bd29ac45af0cf8a4ebd +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 3b17d233095a40cfae0540e678088860 +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a7900a2fa76c46e6854d09a7b31df272 +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: ac34d1ad2274499f9ea1413b5648f7dd +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 04198e0858a6415a8e3235c29d15c5f1 +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/file-formats.md:52 +#: 265ff7e37ebd4e9fa85b26a6deb1cd74 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" diff --git a/locales/topics/index.pot b/locales/topics/index.pot new file mode 100644 index 00000000..9f895c55 --- /dev/null +++ b/locales/topics/index.pot @@ -0,0 +1,22 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/index.md:1 +#: 8ecce715c6084f74acf91e896775f6b3 +msgid "Topics" +msgstr "" diff --git a/locales/topics/inputs.pot b/locales/topics/inputs.pot new file mode 100644 index 00000000..6ec07f47 --- /dev/null +++ b/locales/topics/inputs.pot @@ -0,0 +1,247 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/inputs.md:1 +#: 9a97be0420e54706a7c73bc1eb856b96 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d4b396558d594c84b82369a138358fd6 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: a3966840a8844e1999e21bcecc96a6f7 +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: ebeb58f7ebd541f581415a43d790811c +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 95cf3ab046b44241ba399c56d4b0c6eb +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: 6e6066facc2141739cac77bf9792572a +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: e257868f6c6646e6a0d1feef62de079d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: 2f2885adf6214b9a8f770097bb02b1e5 +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: 01ec3e60c2f24f9c912d44d3d5dac4c5 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 8c803c9f11414a9f9b92643923a79c65 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: df2b1f41e3e149309ae8b19aaf6034ca +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: df5bd15a6b084bce879270be669f2923 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: e73d20dd91574bcbb7b24932d9ff04e4 +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 56461c62effc487c9e73d1e82ddd3390 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: df42caf04d5f48baa8e5734d6100cdf4 +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: f8db1efc2092415387e4e16dc24775dd +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: 859f5479b2cd4e919e3ba19a3f084b01 +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: d04258dca228411ab16f82585ee53985 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: 760c0af7e36d48d1b1681928ad195eaa +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: 4e5d3fb805f04593b34d5ae88dd6fa83 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: 7b97d452561c4c158a835fd308feafb8 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: c63782e8b8524857a1683578534f8382 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: fe66dc3c9aa743e0a2060a8280e6a59d +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 04993bbb8c7b488d8b1b2517f4333f8d +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: e33e6fd2e8a8472e88c9333c7b44fc2c +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: adc2cd5bd81b459b996ff65de5d25436 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 67da943c4d6d49cab1931606fb6938d9 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: 0be87de7fd5e41da895dfc9369da7b5a +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 535a8e26cc3b4e3db43680f030d57879 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 61c26186c1734233bb7d9e5cd3056506 +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 66ec7048099f4720989c8de5be49ea2a +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: efa9d841028c4135a513f3226b37bdfc +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: b3543061283e4bf286ed9fb7127238df +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: afeff005e15d49edbd8222e95b4d6388 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 0eb5e94bf86a4c84bb112d612c290bce +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 3d1f591442f54f9fa8effb98f4cc4f7f +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1a8735c689ff4e13bd207eed62d0bc1b +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: f802a2e638764c95bef8889b958f6872 +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 54ffe9e897ff4682aa9d17e9239a5b40 +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: 892a899a9365419c8cdc95e9f05f9e3d +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2cca4db8543145c0a59da034c82db1fd +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: 1f42c1eba9f44397942d6bf2dd37855f +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 1c0caf1fd3a4411f83dfc4866edeecfe +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: d0a92fe266614a5db77f32b0fc40ee83 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: e3a608fbb7e14213831c564128421cc2 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: a24cd12cc01b4e23b0ed878a27fcaa46 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" diff --git a/locales/topics/metadata-and-authorship.pot b/locales/topics/metadata-and-authorship.pot new file mode 100644 index 00000000..2d77396e --- /dev/null +++ b/locales/topics/metadata-and-authorship.pot @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: c79f6e6491bb4b6b9f1b2677b79c0ce1 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: 73dd0c3f814b4b77a9fe0ad09be7e00a +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 9dbb204051604ffc8b40ff902f1d6c7e +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: a4bd38b9be374a9da651b4c8a876f57f +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:22 +#: 6d6d2685e0a74c8ab242594fff8885ff +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d8261a4cdde0456db33aa7e6bea9774d +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 11af70cc279a4cb29135aa440d560999 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 5a3a6d2577544ff1a996b7b7d15693e0 +msgid "`metadata_example3.cwl`" +msgstr "" diff --git a/locales/topics/operations.pot b/locales/topics/operations.pot new file mode 100644 index 00000000..ea3332ce --- /dev/null +++ b/locales/topics/operations.pot @@ -0,0 +1,62 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/operations.md:1 +#: 8766c4065dfa467f9001aa50564f4812 +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: b37c530cac0a4d18b50271b5b5ec4d1b +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 54e76a0465cf40bf8b76896643cc521b +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 9e16b384ac494d07951ad589a0413d2c +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: cfd13e0311104c95b7de0510f0fb54ab +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 468b0b4219a84df49286a95115c5d3fe +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 362bd499ed6b40b8bbf3237a9a08895e +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 24454b17abae4cd9a8a17cfc5bd79e39 +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: f33e158f449e4594b4f0f1c4660e2be2 +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" diff --git a/locales/topics/outputs.pot b/locales/topics/outputs.pot new file mode 100644 index 00000000..eaaa0c37 --- /dev/null +++ b/locales/topics/outputs.pot @@ -0,0 +1,134 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/outputs.md:1 +#: 30d1617ac85d41a0956ef5f7eb30c112 +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 13aaa50a038f460f829a5554ea950a8b +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: e26db82dbb934d4aac5a7918c39245f4 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: 747f0575223f42cd90157c2ec684ab4e +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: c251eb8f22c54cdbb8683e98d4e527a7 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: e0fc3bde9de84b2ea5e2b9d7d1491ed1 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: cbc068a7d2bc4c1682577ef6b854309a +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f2923e674d574ea1a52dab96a12e38a7 +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ebe4a9bec6cd42c089e790108b0ddbff +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: 89c371e54934472e9c09681be5f1ecc3 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 508663424d2f4eb494ca8611cca4073a +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 1ee12d2ed35a414d818127ebaaac2364 +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 0e0fa84bee1042d88386826c22466619 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 9a37679c41eb4287b43d254a8fd823e2 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: 7041b9a7b7034bf881bccccc2b691a44 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 53075db7e4ca436594d4fd3f3e00917d +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:77 +#: 0860836ece81420dba1b2a080e825f6c +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 40d221f9b5b642648b918aa0e6902f1c +#: 7ad8f592f52b4aeeaa703a85e79f6356 +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 6f6a26ee1ade4b4f9ed3a82ed44030f8 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 61a149a84abf40e7ace2248dc0119838 +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: 1322f83871ee49b3a87aa71a0ec5a79f +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: 6f92d0458a924c88aaba9e7336eef87c +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: ce294dbd94ee4624915c398389eaf1f6 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" diff --git a/locales/topics/parameter-references.pot b/locales/topics/parameter-references.pot new file mode 100644 index 00000000..b17a5e7a --- /dev/null +++ b/locales/topics/parameter-references.pot @@ -0,0 +1,278 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/parameter-references.md:1 +#: 0d925f42133646899f4bb3367057e07d +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: 473a89b059e14f649354a76bf882142e +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 4c57e8c446a0441c810493d34311ace7 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 014e74e995bf49eca1c3b09ca011619f +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 0d475fd8c50c4dc986643c14b82d0576 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: ff886a60af2b49499ef0a0d31386998e +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: d1e080ff809946919ed35e2b1055b6e5 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 52e0d66811bc433b8c21b91e5ac6945d +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: 6252fd49bc814c1c97c2a825a6b1b49f +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: 97abdf2838c444f684629c0578a8ed31 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 3fd741db4c014ea6a53b6bc2fad63e21 +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 986da8d3c56b4227a9481c9e2b0ea0a7 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:64 +#: 1beb8e88637545b8ad365441de547b59 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: 8349b7acc74346e0ac0d18dddafe2205 +#: 9b2e0b712ec146e1a636ed8d1f408c56 +#: eac9f2c8f0c0424ca5e70425fa60f677 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/parameter-references.md:66 +#: cb1036ef7aa449dc8728bf72cf7281e9 +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/parameter-references.md:67 +#: 713a83cfde5e4d4181ec8477f20ac2c4 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/parameter-references.md:68 +#: 8d666991bcc94c83b1259746ced7e43f +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 7ce52aad9f624afeb40e9829ab150651 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: 4207d80deafd4b12a944b4b61e7494bf +#: 0b9493de338a4717bdf643991c72d92c +#: 489bac6cabeb4aeaaf90112969f0bafb +#: 34de0217785146c4ac0130e52319581e +msgid "`format`" +msgstr "" + +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 026108b0d1c344df883689be95db8fad +#: 0b32cdfd79ee469e83a629285223cc0b +#: fbe04046dc744f72b3a88da56f15b483 +#: 9065d837c83d4dd78cd3d664f882300a +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 7f5bdccc51a14535891b13d8e787251b +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: daff49176fca4fd8b12369f4f92eb22d +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: d0208c0307b04cf384c7a9334046bb9b +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:78 +#: b384a85509344ad5bbc3873684a19b9a +msgid "`glob`" +msgstr "" + +#: ../../src/topics/parameter-references.md:79 +#: 83d6911ab8994e55a87871c8a238f4fa +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/parameter-references.md:80 +#: b0298c96113742f6981316ad0e33b018 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: 636f6c50ac274d88a7ca32f7bafbaca4 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:84 +#: d72570d062e54cfb89c82a1ce1a286b8 +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: 5b8e3e7c420c4490ac4a5905189cd166 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:87 +#: 22c6afe7aab84038a74f8478f8d97d64 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:88 +#: 88877e67206e48b3b10e30ddead266fd +msgid "`expression`" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: e763d3be7c3347718bb851b0e601d466 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: d7837cc8e8064348b2698f80e4bf47b5 +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:93 +#: d87be82c3bcb4e1fb33946573d62037c +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/parameter-references.md:94 +#: 2362c7e8e16240e288fbaa49521951a6 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/parameter-references.md:95 +#: f9d381b7bf2c4caeb6a5a3bace39b6a3 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/parameter-references.md:96 +#: f957b015fbb64e448083a5a9b4ff4b0b +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/parameter-references.md:97 +#: be4bb996b5954fb8a90c57e5e6456ec2 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/parameter-references.md:98 +#: 00eb0fff1cc64e41bcbcf63ebb58ee11 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/parameter-references.md:99 +#: 073bb4a51bcf4447bde792e41e876bbd +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/parameter-references.md:100 +#: ed9e837c60a14da0879a309194213033 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 160c7ce007564ee2825517bc29750c65 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:102 +#: 24755cdacd024d949fc6015b43983e22 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 4ad1d82ee80844c581197cb14eab518a +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:104 +#: 6542359022cd4a1ebfb08e8c104620b4 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/parameter-references.md:105 +#: fa4a51155be34b10aa8c1eaecd2cdbbf +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/parameter-references.md:106 +#: c51af125685146dea16c2dcd7f290aef +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: e31fc3370fd948c79e945ab30dacf99e +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/parameter-references.md:108 +#: 7982f559dcff4178b222cdba267d1283 +msgid "`envValue`" +msgstr "" diff --git a/locales/topics/requirements-and-hints.pot b/locales/topics/requirements-and-hints.pot new file mode 100644 index 00000000..a566fb29 --- /dev/null +++ b/locales/topics/requirements-and-hints.pot @@ -0,0 +1,22 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/requirements-and-hints.md:5 +#: 15273fbf009b4036a2574d157740db98 +msgid "Requirements and Hints" +msgstr "" diff --git a/locales/topics/specifying-software-requirements.pot b/locales/topics/specifying-software-requirements.pot new file mode 100644 index 00000000..d65ed83d --- /dev/null +++ b/locales/topics/specifying-software-requirements.pot @@ -0,0 +1,42 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b34314bdb71244f2a263427f22172b5a +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: c8609548e7904e65a5c395bfc07ad808 +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: e4c1c25793884b5aaead1fb15c2e6bbc +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 91586b8767734e0ab01903f2562a7cf2 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: dd7c487024b44a67a26765e59b5bf64b +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" diff --git a/locales/topics/staging-input-files.pot b/locales/topics/staging-input-files.pot new file mode 100644 index 00000000..f9d75eff --- /dev/null +++ b/locales/topics/staging-input-files.pot @@ -0,0 +1,42 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/staging-input-files.md:1 +#: 3064f17a9bae442aaef41b9434cb71fd +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 09bb659a5cbe40948b59208f0fb77ddb +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: a1bcfead8f7f4270945e5512dfa9aea6 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/staging-input-files.md:15 +#: cc0cd8765dac4baab9072a90e82e4f8e +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/staging-input-files.md:20 +#: 77ac403083ff41e0a94b4376d57c4310 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" diff --git a/locales/topics/troubleshooting.pot b/locales/topics/troubleshooting.pot new file mode 100644 index 00000000..cfd4aa74 --- /dev/null +++ b/locales/topics/troubleshooting.pot @@ -0,0 +1,72 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/troubleshooting.md:1 +#: 628f6b4dad6d4b2e87d3c34d99b3bc9a +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: c2f444d8af5b47b389a53f047f42f7fc +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: b4d58509c2874a3a9a4aca8b0eb54b8e +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: cf0d233ea286443d9b4cd7b8e9b03090 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: e742b4b7517a4461ab38cd572fd02412 +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 8d0d5c4374ff4659b0a34f86a106915e +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: 2c4194ab026e41cb807e7cb15bc37e34 +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 0d287a4115ea4e34b239790ceee5d9be +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: b72ee99d9aee4c88bf4ae1a493b40415 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 6541e0afd1784cdd890cae031fc6b13e +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 3881a8c9e89c42c3a4a9fb99dffd6de8 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" diff --git a/locales/topics/using-containers.pot b/locales/topics/using-containers.pot new file mode 100644 index 00000000..03e278eb --- /dev/null +++ b/locales/topics/using-containers.pot @@ -0,0 +1,82 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/using-containers.md:1 +#: 3a1cb28acbf64b36b328af24b8ad3896 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: b0788dc4a9694fcface9c2d1122053ee +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: fdb03600e95f43248a8841308892f95f +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7e27ca6ce9974ef8a68e4955c377a7cc +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: 7162dac152a344b78a196ab9b304ff96 +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7ecf64fbdd774b298455e9cdf5be38df +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 7ec954f8c1cd4ba3946ed2b3bd675083 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: b80d058d42c2414299eca96c4edd908b +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: c6ddaf94bc9f49e2b507a3eedaf597ee +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: d0770aeb8b0546ed943d60a3ae3b9f9a +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: d8c679b90ba14cf29280c1f1d271358d +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: c10409c624084be79a3378ae056d50c8 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 28514dd1b76648eb9bcec48290d7b66e +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" diff --git a/locales/topics/workflows.pot b/locales/topics/workflows.pot new file mode 100644 index 00000000..9847836f --- /dev/null +++ b/locales/topics/workflows.pot @@ -0,0 +1,374 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/workflows.md:1 +#: f87317cca4ba43af87f6a19b8fff6751 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: 00756723cfea4c79ab17ae39e400fd4c +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: ee41e057c6be476e9c56ac3c1f4aefad +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 4e06945e9d794db58ebf5953a7bfc169 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: 3bb6bd3fa9a241b18f725f765f6d8f89 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: bd0042b64ca14e5fa4abe0b696ed8cc0 +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: f640b8cc119544ddb698828751335eef +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: ef0a22597b7b43a09b9d930eb733b181 +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 08e47d409fad4688b3fa893aac699505 +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 979f0abe51a7435991c062b239ab77ce +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9e7ebb3fd64e4d9b89d10aab7ff6ef5a +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: a8bb6a54010c4563af5dd0e287e19ea9 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 3ca49084a67e48e196a29fce16266ebe +#: 2e5e721e9dcf477aacc5fd7970c8965f +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: cd69af46dab64758a7eeb25b8dd5ada4 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 1370172b5e4d41dfa0f00268853c4a0c +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: df872d487e3d4e35b68bebcb27948577 +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 5039994944944010990efb63a1423bd2 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:198 +#: ce1bf8dbbe3c448b8d413993b986bee1 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: a72841d1fc594789adca91a6cec6b4c8 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: ab3448be251d454fbaf3e2e40e2a6179 +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: b24bc7e75b5e45a6b40f99122f7a46c6 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: 9eab201c6c314cf682f7623de820f007 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: 7aee0e6910f841eaad08091daaa43819 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: ad9e578cb5154c06b323ed8934f70359 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 6edc6273c5e84842a74b8921875481e9 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: 1d4faf0025bc4fc7bf53b87e4b3477e9 +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: 2185db6e6c9c470abc4e9a4dc95a921d +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: 91c1093736ea45e59fafba7d071bfda4 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 17955d02a70d484f8b2654feffc3f853 +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 4e9524ce607243b9a6bd749bc436d796 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 6d24477bbd3245a9be26954768605af8 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: 5525e4fa9a1e4245b5cd3a5465952fa8 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: b9dc7d7eab974749953065c7b7a92077 +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 268089a26de840e8a01026a3d4ad93c8 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: 1523ed6264e84a0ea3a2c00857a71bb2 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 125add3880f84620bc124f21096e1d1a +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 423dd287ac0c4cc4a39b17dcc380fe45 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: d0fb2fada3c74bc2bb81928891b284a3 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 27e720818d69436d8c85931749918ad7 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: efe03781d801470db0950ca5c33e10b7 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: f21f8ee263e043a1b57dc8148a502b85 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: 5c91e32bd51045ec8442b28875e914a9 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: dbef641be8bb4a18ae974357ecb32f78 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: e86d663e2c39446b8c20c5eaf94a8802 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 19ae2b52a9ab4b6ea4d8d8e57f40c170 +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: b711df1f3b1b4456b015701700c3c818 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: 60fb4221648d40968e1a0965a3b6693c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: c249bd4f52b348faa46918dee778a75d +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: ba039b00b2ea4de693b3358a036fd993 +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: a50560beb0f84c59b52a03b755e4e028 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: b1bde49eb1d6496a8d54094076e9c0f2 +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: 18d238a1bba943778f951b22e777af50 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 1fef76f43e2048718f82b67f66f48197 +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 6c2c8927cadf49858e0e1b3033c22168 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 7482860af6ec4b519585837fee90289a +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: b9a64729a3c34bb2aaf4d9f780b29022 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: f3ad56146ff3429db2018fcdcef05724 +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: 4050c846b1144a5985b37c76bb24670d +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: fc2512823ca24060992b321fcf0d56db +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: 2eae7d61ffcd485aac22fc1fbbe7093a +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: 39971661faa74b58bf2f64c18a27fa76 +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: b36f484b8f904da58838aac09e7c14ff +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: 0db1e2093f8645df8f13fe394e8bf018 +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: 38a16292b8bb4ec48ae169292db7a2f2 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 2c07c2968b53407686a8dd3f869b4fc4 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 61f0704412654df781833ffb6d5f33e3 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: d6634b5ec49e4113a90faec6b8de482d +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 9e6488eb6e60434eaf3148208a31a8aa +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: 3fe08f086e374050a89a39fcb3db0b78 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: ec35b97546eb42c28cc9bbdbf2ac2067 +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 22cf017e76d74584991ded94417c19d8 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" diff --git a/locales/topics/yaml-guide.pot b/locales/topics/yaml-guide.pot new file mode 100644 index 00000000..eb8a5519 --- /dev/null +++ b/locales/topics/yaml-guide.pot @@ -0,0 +1,157 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/yaml-guide.md:1 +#: c28a6abcd8334321b7d1c84192b42caa +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 3e16eeaccec8491dacfde122153d5bd0 +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: 363eb3871f5d4c1288138dbd5f89be62 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: 31d7b17c34e0405b94f95e273bb22ac5 +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 60197a7f2b7c40c48ede3d59626a09d8 +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: 7b76a198bd154da99e38146a74ecec6c +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: 024a6818d1b9492bb6e1f1c11d932953 +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: d0c550b003fa48c8b1b16888c7e9bc5f +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 7c2f8ceba9a141f097767ae8c3688aee +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 5cfa92e1509e41cf9dec646d3a5dad86 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: f76bccaee68c4eec96822d00013395a9 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 5591f710f08a4e8c8d974224cdf018b5 +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: e383736713e243d487b883e669fb7065 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: c50eafc65e8b4b8a81318694098a42e5 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 3d8de32c3f3448e5beb19d395099e27d +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 20edeb5c184f4df2ade328131365d751 +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: 7f436640365249568802a846d4ad896b +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 7514de6b828f44b1b1d8683d8324a1da +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 01288d81ae2e466d94bbee33751b3bd6 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: 3e6ba9083cdd4ed586110f76cd071896 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 2c23b44142ba4969bd30c33c97142aed +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: 5956220b3839466aa491e84d2d0a5757 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 0ff275ae871b49449ec789b1bdc814c6 +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: f5215b7de4994cc5890886ac2914be23 +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 48dec799be364824a5dcbf5329f1f0ce +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: b4d3a3a2823147c9aa7a37ad2fe5ce06 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: 6998b8bd38a944f19c9ca758b14babe8 +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: bcc40a813d344c0abd960add8685e132 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" diff --git a/locales/tutorials.pot b/locales/tutorials.pot new file mode 100644 index 00000000..7864fea7 --- /dev/null +++ b/locales/tutorials.pot @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/tutorials.md:1 +#: d32522e2993f4b48a789f46537fa5ebf +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 63a51dccb29045fd8f78d5e396c6e050 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: cb5f8748a5544be2835467ab07eb7a1c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 685d0cb2faa04703bcef408ecc2b92f4 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 20f45705145d45fc8420c4119b06a49f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 2bccd19d542d4458a1ba8616236f1840 +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: c491c73e4c00476980438ffc79c6e4d3 +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: b8485449206542e097584eca7363c8ce +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" From 0eacbc67346d67fd2ab95f202993f2fd409e0d71 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 24 Jan 2023 18:36:02 +0100 Subject: [PATCH 30/49] don't translate English into English --- locales/en/LC_MESSAGES/LICENSE.po | 120 ----- .../en/LC_MESSAGES/_includes/what-is-cwl.po | 28 - locales/en/LC_MESSAGES/episodes.po | 31 -- locales/en/LC_MESSAGES/faq.po | 307 ----------- locales/en/LC_MESSAGES/index.po | 68 --- .../introduction/basic-concepts.po | 270 ---------- locales/en/LC_MESSAGES/introduction/index.po | 31 -- .../LC_MESSAGES/introduction/prerequisites.po | 298 ----------- .../LC_MESSAGES/introduction/quick-start.po | 191 ------- locales/en/LC_MESSAGES/setup.po | 31 -- locales/en/LC_MESSAGES/sphinx.po | 28 - .../additional-arguments-and-parameters.po | 84 --- .../en/LC_MESSAGES/topics/best-practices.po | 191 ------- .../LC_MESSAGES/topics/command-line-tool.po | 71 --- .../topics/creating-files-at-runtime.po | 104 ---- locales/en/LC_MESSAGES/topics/custom-types.po | 99 ---- .../topics/environment-variables.po | 45 -- .../en/LC_MESSAGES/topics/expression-tool.po | 53 -- locales/en/LC_MESSAGES/topics/expressions.po | 383 ------------- locales/en/LC_MESSAGES/topics/file-formats.po | 93 ---- locales/en/LC_MESSAGES/topics/index.po | 24 - locales/en/LC_MESSAGES/topics/inputs.po | 313 ----------- .../topics/metadata-and-authorship.po | 70 --- locales/en/LC_MESSAGES/topics/operations.po | 73 --- locales/en/LC_MESSAGES/topics/outputs.po | 147 ----- .../topics/parameter-references.po | 279 ---------- .../topics/requirements-and-hints.po | 24 - .../specifying-software-requirements.po | 68 --- .../LC_MESSAGES/topics/staging-input-files.po | 48 -- .../en/LC_MESSAGES/topics/troubleshooting.po | 101 ---- .../en/LC_MESSAGES/topics/using-containers.po | 106 ---- locales/en/LC_MESSAGES/topics/workflows.po | 504 ------------------ locales/en/LC_MESSAGES/topics/yaml-guide.po | 193 ------- locales/en/LC_MESSAGES/tutorials.po | 58 -- 34 files changed, 4534 deletions(-) delete mode 100644 locales/en/LC_MESSAGES/LICENSE.po delete mode 100644 locales/en/LC_MESSAGES/_includes/what-is-cwl.po delete mode 100644 locales/en/LC_MESSAGES/episodes.po delete mode 100644 locales/en/LC_MESSAGES/faq.po delete mode 100644 locales/en/LC_MESSAGES/index.po delete mode 100644 locales/en/LC_MESSAGES/introduction/basic-concepts.po delete mode 100644 locales/en/LC_MESSAGES/introduction/index.po delete mode 100644 locales/en/LC_MESSAGES/introduction/prerequisites.po delete mode 100644 locales/en/LC_MESSAGES/introduction/quick-start.po delete mode 100644 locales/en/LC_MESSAGES/setup.po delete mode 100644 locales/en/LC_MESSAGES/sphinx.po delete mode 100644 locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po delete mode 100644 locales/en/LC_MESSAGES/topics/best-practices.po delete mode 100644 locales/en/LC_MESSAGES/topics/command-line-tool.po delete mode 100644 locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po delete mode 100644 locales/en/LC_MESSAGES/topics/custom-types.po delete mode 100644 locales/en/LC_MESSAGES/topics/environment-variables.po delete mode 100644 locales/en/LC_MESSAGES/topics/expression-tool.po delete mode 100644 locales/en/LC_MESSAGES/topics/expressions.po delete mode 100644 locales/en/LC_MESSAGES/topics/file-formats.po delete mode 100644 locales/en/LC_MESSAGES/topics/index.po delete mode 100644 locales/en/LC_MESSAGES/topics/inputs.po delete mode 100644 locales/en/LC_MESSAGES/topics/metadata-and-authorship.po delete mode 100644 locales/en/LC_MESSAGES/topics/operations.po delete mode 100644 locales/en/LC_MESSAGES/topics/outputs.po delete mode 100644 locales/en/LC_MESSAGES/topics/parameter-references.po delete mode 100644 locales/en/LC_MESSAGES/topics/requirements-and-hints.po delete mode 100644 locales/en/LC_MESSAGES/topics/specifying-software-requirements.po delete mode 100644 locales/en/LC_MESSAGES/topics/staging-input-files.po delete mode 100644 locales/en/LC_MESSAGES/topics/troubleshooting.po delete mode 100644 locales/en/LC_MESSAGES/topics/using-containers.po delete mode 100644 locales/en/LC_MESSAGES/topics/workflows.po delete mode 100644 locales/en/LC_MESSAGES/topics/yaml-guide.po delete mode 100644 locales/en/LC_MESSAGES/tutorials.po diff --git a/locales/en/LC_MESSAGES/LICENSE.po b/locales/en/LC_MESSAGES/LICENSE.po deleted file mode 100644 index 29b53dd1..00000000 --- a/locales/en/LC_MESSAGES/LICENSE.po +++ /dev/null @@ -1,120 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../../LICENSE.md:2 f0c9a54a904e42249441ee22e39d6f3a -msgid "Licenses" -msgstr "" - -#: ../../../LICENSE.md:4 6c99230ebe4d48689e09e2da1484abc9 -msgid "Instructional Material" -msgstr "" - -#: ../../../LICENSE.md:6 327a6405608b4df488fc6aee756f94b7 -msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." -msgstr "" - -#: ../../../LICENSE.md:12 91d85fe9673942658f5d17e286ac6b69 -msgid "You are free:" -msgstr "" - -#: ../../../LICENSE.md:14 c010a0b9145e4532896b114d4e0c7768 -msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "" - -#: ../../../LICENSE.md:15 8e7d2d9301a8452994e4b33edb3c7ea0 -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" - -#: ../../../LICENSE.md:17 0fdc0b2074bc4cfd8cd020d51a3d4f3b -msgid "for any purpose, even commercially." -msgstr "" - -#: ../../../LICENSE.md:19 220eba84dd874fb59ac0d4f7a95695fc -msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms." -msgstr "" - -#: ../../../LICENSE.md:22 c21178abaf374ca5ae83fb9b94761e7e -msgid "Under the following terms:" -msgstr "" - -#: ../../../LICENSE.md:24 90e30b28cfdb4c8fb6bf2e2687ac47c3 -msgid "" -"**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." -msgstr "" - -#: ../../../LICENSE.md:32 c40a837670f84762bffc0cc8d697d45d -msgid "" -"**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" -msgstr "" - -#: ../../../LICENSE.md:36 233edb183ff44c7293756df599b2a130 -msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." -msgstr "" - -#: ../../../LICENSE.md:39 027339c3a92747e8948b11671ace4145 -msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." -msgstr "" - -#: ../../../LICENSE.md:44 89dcc55f3d5d445b97912648ee5dba03 -msgid "Software" -msgstr "" - -#: ../../../LICENSE.md:46 070952c76313480d92f0b78321a6a1e2 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" - -#: ../../../LICENSE.md:51 3279f7573aa44853af83dbf9dd9748a9 -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." -msgstr "" - -#: ../../../LICENSE.md:57 979969ab3c3f4080b6c7e879efe9f351 -msgid "Trademark" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/_includes/what-is-cwl.po b/locales/en/LC_MESSAGES/_includes/what-is-cwl.po deleted file mode 100644 index bc854eb9..00000000 --- a/locales/en/LC_MESSAGES/_includes/what-is-cwl.po +++ /dev/null @@ -1,28 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../_includes/what-is-cwl.md:1 ffc6d3382e944f22a8b13062eb1badc4 -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/episodes.po b/locales/en/LC_MESSAGES/episodes.po deleted file mode 100644 index ed5b10aa..00000000 --- a/locales/en/LC_MESSAGES/episodes.po +++ /dev/null @@ -1,31 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../episodes.md:5 0c99dd9365d14d26b9b3bb5e88f33570 -msgid "This page has moved" -msgstr "" - -#: ../../episodes.md:9 2718a75eccf84a1fa22356367d3b772e -msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. Please use the new [Table of Contents](index.md#table-of-" -"contents) to browse the User Guide." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/faq.po b/locales/en/LC_MESSAGES/faq.po deleted file mode 100644 index c74aeb6e..00000000 --- a/locales/en/LC_MESSAGES/faq.po +++ /dev/null @@ -1,307 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../faq.md:1 1479ffe379ea483290f2c16ddc8d6358 -msgid "FAQ" -msgstr "" - -#: ../../faq.md:11 b6cd88863b754a7d8467948ea72063ac -msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" - -#: ../../faq.md:41 29876633f61f4befa1ba764a8e14909a -msgid "Rename an Input File" -msgstr "" - -#: ../../faq.md:43 c523a45d4fff4ac5b451b8c9e947a0c1 -msgid "" -"This example demonstrates how to change the name of an input file as part" -" of a tool description. This could be useful when you are taking files " -"produced from another step in a workflow, and don't want to work with the" -" default names that these files were given when they were created." -msgstr "" - -#: ../../faq.md:59 6761f620fae44513ba675bb845dad5af -msgid "Rename an Output File" -msgstr "" - -#: ../../faq.md:61 83312f5876ea492c9a881b8d1d8ec232 -msgid "" -"This example demonstrates how to change the name of an output file from " -"the default name given to it by a tool:" -msgstr "" - -#: ../../faq.md:82 da3f295db7584f2ab5532fb915c8ada7 -msgid "Referencing a Local Script" -msgstr "" - -#: ../../faq.md:84 e4aec7bca9bf4ef0a3d709fd0771d886 -msgid "There are two ways to reference a local script:" -msgstr "" - -#: ../../faq.md:86 f6fcb55812944ad98053fee5243125fb -msgid "" -"The first method involves adding the folder containing your scripts to " -"the `PATH` environment variable. This allows you to run the shell script " -"directly without using `sh` or `bash` commands." -msgstr "" - -#: ../../faq.md:89 7a83b32f4124408ab1f0dc3303d5d640 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" - -#: ../../faq.md:95 c59ec88c1d1545699fd0c00f6173dccc -msgid "" -"After that, make the script executable with the command `chmod +x " -"scriptname.sh`" -msgstr "" - -#: ../../faq.md:97 dbd4fb58d2e34ccbb9544f2106ee56e5 -msgid "" -"Finally, modify your `PATH` to add the directory where your script is " -"located. (It is good practice to use `$HOME/bin` for storing your own " -"scripts)." -msgstr "" - -#: ../../faq.md:104 9fb24ecdc09b438bb46e8107880e77a0 -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" - -#: ../../faq.md:113 b8624be7349d472b9b86409bd5b786cd -msgid "" -"When you wish to share your work later, you can place your script in a " -"software container in the Docker format." -msgstr "" - -#: ../../faq.md:115 fdcc23c875974ee58a4e5ae702eaac67 -msgid "" -"The second method involves including an input of `type: File` in the " -"script itself:" -msgstr "" - -#: ../../faq.md:135 da2ee2848dbc4dff8663c1fbf00c863f -msgid "In CWL, everything must be directly stated." -msgstr "" - -#: ../../faq.md:138 782152c8aab84a12bb04375096f492b6 -msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" - -#: ../../faq.md:140 da2600292146447aa527f24c69cfb776 -msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their " -"input binding makes use of `self`. Below is an example workaround for " -"this, pending a more sophisticated fix." -msgstr "" - -#: ../../faq.md:165 dc07a65c25854ef6b21cb4a43bee4d31 -msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" - -#: ../../faq.md:167 76bfb57ea05647748b60e36712a8b100 -msgid "" -"Below is an example showing how to specify different strings to be added " -"to a command line, based on the value given to a Boolean parameter." -msgstr "" - -#: ../../faq.md:188 be450f9113f3451691eea5f0d30c3c74 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" - -#: ../../faq.md:190 a328ad7be4e44194b8a1fb5a436d1265 -msgid "" -"Using " -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../faq.md:194 d86e24a5d27b418ba29e5439b34a5c13 -msgid "merge_nested" -msgstr "" - -#: ../../faq.md:196 f9b6d21ce7f3405da57fa7443e623b8a -msgid "" -"The input must be an array consisting of exactly one entry for each input" -" link. If \"merge_nested\" is specified with a single link, the value " -"from the link must be wrapped in a single-item list." -msgstr "" - -#: ../../faq.md:199 1ac676ef33bb45c4b7fc371e7bd84f07 -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" - -#: ../../faq.md:201 75cef09a92cc44c397a18f81840743b2 -msgid "" -"Or in other words: if the destination is of type `File[]` (an array of " -"`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " -"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" -" destination step." -msgstr "" - -#: ../../faq.md:229 5bd33a98001148e7b8e83b9bb83b62ee -msgid "Optional Inputs 💯" -msgstr "" - -#: ../../faq.md:231 70651f1b65fd4e20b0f1719c3b8ea3f8 -msgid "" -"To make an input parameter optional, add a question mark to the type " -"declaration." -msgstr "" - -#: ../../faq.md:247 cb3f5cae1479448c9669e2751fd34460 -msgid "" -msgstr "" - -#: ../../faq.md:248 74eafea819d6405b8f573da4ec712445 -msgid "Enum Inputs ⚜️" -msgstr "" - -#: ../../faq.md:250 4955ef4f959143b096125f95ec32c1e2 -msgid "" -"For command line flags that require a specific input as the argument an " -"enum type can be declared in CWL. **Specifying null here is known as long" -" form style. It does the same thing as the question mark on the other " -"inputs.**" -msgstr "" - -#: ../../faq.md:267 bdf0e5bf3c754f639fbb4ad24076bc4a -msgid "" -msgstr "" - -#: ../../faq.md:268 64c7ae1eaf6b4b0cb4a5fc23feb6349e -msgid "Record Inputs 📀" -msgstr "" - -#: ../../faq.md:270 ad83e44a7f914cfbb46aa191a17d4c85 -msgid "" -"For commandline flags that are either **mutually exclusive** or " -"**dependent** a special record type can be defined. You can also specify " -"null here to create optional inputs." -msgstr "" - -#: ../../faq.md:322 68e228ecf0be4753832a31ceb933fc19 -msgid "Setting Mutually Exclusive Parameters" -msgstr "" - -#: ../../faq.md:324 e2f19825601845b59d5cbeeeb0024622 -msgid "" -"To properly set fields in a record input type, you need to pass a " -"dictionary to the input to properly set the parameters. This is done by " -"using inline JavaScript and returning the dictionary with the key of the " -"field you want to set. The source field is set to indicate the input from" -" the workflow to be used as the value." -msgstr "" - -#: ../../faq.md:342 0824a9e1f5684da481163cd16fed94b9 -msgid "Setting Booleans" -msgstr "" - -#: ../../faq.md:344 192e416a398845838d55bdb71190bb70 -msgid "These can be set by using the default field" -msgstr "" - -#: ../../faq.md:349 eb6a00b2ff3a4ec384a0308f00dd8c4c -msgid "Concatenating Strings in Inputs" -msgstr "" - -#: ../../faq.md:351 9a7df9d0f389421298e6d456822e52a4 -msgid "The valueFrom field must be used instead of default." -msgstr "" - -#: ../../faq.md:359 9cab760a07114447a817f63ff61ff346 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" - -#: ../../faq.md:361 9ccf1286db084b67a37b2217a9764584 -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" - -#: ../../faq.md:363 33ea1db2582f4fe78436fb1a8f431b15 -msgid "" -"For example, the filename `a space is here.txt` includes 3 space " -"characters." -msgstr "" - -#: ../../faq.md:371 0f8a3fc6e622464fae1366a053baa78c -msgid "" -"If you can not avoid these dangerous characters, then pass `--relax-path-" -"checks` to `cwltool`." -msgstr "" - -#: ../../faq.md:373 6a3ba881461642aa8d7654dad772ccd3 -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" - -#: ../../faq.md:375 253cbea8229743b8a064d4d2fac24f12 -msgid "If `cwltool --validate` returns valid" -msgstr "" - -#: ../../faq.md:384 63190f04254b4459880b1ee84886bbab -msgid "But executing it causes an error like:" -msgstr "" - -#: ../../faq.md:396 61d3a0026a274eafa31b02220bc4bd0e -msgid "The file is here" -msgstr "" - -#: ../../faq.md:410 2a99b8770636429693ff44563f0ac148 -msgid "Problem caused by `-` (hyphen character)." -msgstr "" - -#: ../../faq.md:423 a0d1eff495924aeaaad2ed92010e92f4 -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" - -#: ../../faq.md:436 a901e5d22e644dcc848d347bcf87d59b -msgid "" -"If it is not possible to change the input identifier, then you can use an" -" alternative CWL Parameter Reference syntax:" -msgstr "" - -#: ../../faq.md:442 5baccb1d1e604c849cce7b27223b1f9f -msgid "Use CWL and cwltool with Singularity" -msgstr "" - -#: ../../faq.md:445 b8421426848c470db2324fde8ae8f05d -msgid "" -"The CWL standards are built around (optional) Docker format containers. " -"The reference runner and several other CWL implementations support " -"running those Docker format containers using the Singularity engine. " -"Directly specifying a Singularity format container is not part of the CWL" -" standards." -msgstr "" - -#: ../../faq.md:450 1a3fecc9eb7a4dcdaf577983c505ba13 -msgid "Debug JavaScript Expressions" -msgstr "" - -#: ../../faq.md:452 b17460fcb17e40da879383df593f2a93 -msgid "" -"You can use the --js-console option of cwltool," -" or you can try creating a JavaScript or TypeScript project for your " -"code, and load it using expressionLib, e.g.: " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/index.po b/locales/en/LC_MESSAGES/index.po deleted file mode 100644 index 2437acd8..00000000 --- a/locales/en/LC_MESSAGES/index.po +++ /dev/null @@ -1,68 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../index.md:1 618bf3fb1f364be791cc5f2bf77667d5 -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../index.md:3 67f4f01edc5b4261a70e4efc3d792f64 -msgid "" -"This guide will introduce you to writing workflows using the [Common " -"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " -"guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../index.md:7 284c0f5ead3142649c3c6d4f04da4851 -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../index.md:9 75a3c6a67c2e4593a098c839483ae47f -msgid "" -"If you find that something is missing from this guide, or if you would " -"like to provide other feedback, file an Issue on the [project repository " -"for this guide][repo]. You can also suggest changes directly in a Pull " -"Request by clicking the \"Edit this page\" button at the right sidebar of" -" each page." -msgstr "" - -#: ../../index.md:16 6061795c74ce415eb3e4f1ca3ed91de6 -msgid "Navigating the User Guide" -msgstr "" - -#: ../../index.md:18 c74efbca9bcd4fda9c4e94d774caa91c -msgid "" -"If you are a beginner user get started with the " -"[Introduction](/introduction/index.md) section. For advanced users the " -"subsections of the [Topics](/topics/index.md) have detailed information " -"about the most common topics for CWL." -msgstr "" - -#: ../../index.md:23 f2bc70925dea4573ab177c5d2f2b5dcb -msgid "" -"The Table of Contents is displayed at the top menu and also on the left " -"sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each " -"page, and the Search form is on the left sidebar." -msgstr "" - -#: ../../index.md:28 3e4e62c52c5547c6a4e77131ab1dee39 -msgid "Table of Contents" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/introduction/basic-concepts.po b/locales/en/LC_MESSAGES/introduction/basic-concepts.po deleted file mode 100644 index 3fe5662f..00000000 --- a/locales/en/LC_MESSAGES/introduction/basic-concepts.po +++ /dev/null @@ -1,270 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../introduction/basic-concepts.md:1 5f43861a84a2494b8e1bc973ac85b3d0 -msgid "Basic Concepts" -msgstr "" - -#: ../../introduction/basic-concepts.md:3 90cc7b0ef1404f72ae0f5b17f6f2a966 -msgid "" -"This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are " -"expected to be familiar with workflow managers, YAML, and comfortable " -"with following instructions for the command-line. The other sections of " -"the user guide cover the same concepts, but in more detail. If you are " -"already familiar with CWL or you are looking for more advanced content, " -"you may want to skip this section." -msgstr "" - -#: ../../introduction/basic-concepts.md:10 1685ddf11a014fe28df75dedb7c39e07 -msgid "The CWL Specification" -msgstr "" - -#: ../../_includes/what-is-cwl.md:2 9cb90a376bfe4058922b1c91ea4ce184 -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../introduction/basic-concepts.md:21 cc05f8193ee6403daca03d2d19ccfcd7 -msgid "" -"The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered " -"in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../introduction/basic-concepts.md:25 f5a0ba9dfc1f49ab937e8122fe4761e0 -msgid "" -"The specification version can have up to three numbers separated by `.`s " -"(dots). The first number is the major release, used for backward-" -"incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes " -"that are backward-compatible. The last number is used for bug fixes, like" -" typos and other corrections to the specification." -msgstr "" - -#: ../../introduction/basic-concepts.md:33 8100683970154870993d19d7a5a6bd22 -msgid "" -"The model used for the specification version is called Semantic " -"Versioning. See the end of this section to [learn more](#learn-more) " -"about it." -msgstr "" - -#: ../../introduction/basic-concepts.md:37 cc5c29f65655465db44dd4eed8f11c7b -msgid "Implementations" -msgstr "" - -#: ../../introduction/basic-concepts.md:39 c07822e70e774ea2bb3da2cfd69aa360 -msgid "" -"An implementation of the CWL specification is any software written " -"following what is defined in a version of the specification document. " -"However, implementations may not implement every aspect of the " -"specification. CWL implementations are licensed under both Open Source " -"and commercial licenses." -msgstr "" - -#: ../../introduction/basic-concepts.md:44 6735911046aa466aa2a371ffff22a9fe -msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud" -" and high performance computing environments where tasks are scheduled in" -" parallel across many nodes." -msgstr "" - -#: ../../introduction/basic-concepts.md:51 795e23a746c749deacb68a18d9a3333b -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../introduction/basic-concepts.md:105 e7c0b2155a024860b8d3fd7c9ef75f38 -msgid "Processes and Requirements" -msgstr "" - -#: ../../introduction/basic-concepts.md:107 cf57f60e189e40c09e946f56a1fdf0b8 -msgid "" -"A process is a computing unit that takes inputs and produces outputs. The" -" behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification" -" {{ cwl_version }}:" -msgstr "" - -#: ../../introduction/basic-concepts.md:112 6201ed50ccf944c2aaf7795d411e236d -msgid "A command-line tool." -msgstr "" - -#: ../../introduction/basic-concepts.md:113 a6f9f66dec354e09bd1778d2bf71a7ef -msgid "An expression tool." -msgstr "" - -#: ../../introduction/basic-concepts.md:114 43927a824e584c3c8914119bcdfdffbc -msgid "An operation." -msgstr "" - -#: ../../introduction/basic-concepts.md:115 98f30716f9154c51bcf95a9a26613c6e -msgid "A workflow." -msgstr "" - -#: ../../introduction/basic-concepts.md:118 07807b77a0a444568348e8c20e540296 -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../introduction/basic-concepts.md:119 f7dd65df72be46e88ad933e85d2cfe32 -msgid "" -"A command-line tool is a wrapper for a command-line utility like `echo`, " -"`ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../introduction/basic-concepts.md:122 7c12205b897c4d6ea918fc8b371ba329 -msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be " -"used to simplify workflows and command-line tools, moving common parts of" -" a workflow execution into reusable JavaScript code that takes inputs and" -" produces outputs like a command-line tool." -msgstr "" - -#: ../../introduction/basic-concepts.md:127 965bd0c3dedc43d188c9c7b5db33b1f5 -msgid "" -"Operation is an abstract process that also takes inputs, produces " -"outputs, and can be used in a workflow. But it is a special operation not" -" so commonly used. It is discussed in the [Operations " -"section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../introduction/basic-concepts.md:131 7299dcb09d2b4967a9d46d3b433d439e -msgid "" -"The workflow is a process that contains steps. Steps can be other " -"workflows (nested workflows), command-line tools, or expression tools. " -"The inputs of a workflow can be passed to any of its steps, while the " -"outputs produced by its steps can be used in the final output of the " -"workflow." -msgstr "" - -#: ../../introduction/basic-concepts.md:137 ea9d197aab4c41788a4a0e3d48c1c168 -msgid "" -"The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through " -"*requirements*. There are many requirements defined in the CWL " -"specification, for instance:" -msgstr "" - -#: ../../introduction/basic-concepts.md:141 592f212970f84365a86a69cfb8c26369 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../introduction/basic-concepts.md:142 57e5ad64e68545a788b43e4e921bb23f -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../introduction/basic-concepts.md:143 397171706bf349feb2c9bee5a993ea1e -msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input " -"directory." -msgstr "" - -#: ../../introduction/basic-concepts.md:145 fa9d473ae58b4053981a45a888470655 -msgid "" -"Some CWL runners may provide requirements that are not in the " -"specification. For example, GPU requirements are supported in `cwltool` " -"through the `cwltool:CUDARequirement` requirement, but it is not part of " -"the {{ cwl_version }} specification and may not be supported by other CWL" -" runners." -msgstr "" - -#: ../../introduction/basic-concepts.md:151 b9cc1fd288764bd78eda4703a2700a02 -msgid "" -"Hints are similar to requirements, but while requirements list features " -"that are required, hints list optional features. Requirements are " -"explained in detail in the [Requirements](../topics/requirements-and-" -"hints.md) section." -msgstr "" - -#: ../../introduction/basic-concepts.md:155 cf12d86b4e7c48c892d6be8233ea2bc9 -msgid "FAIR Workflows" -msgstr "" - -#: ../../introduction/basic-concepts.md:157 a83ecf7c5eaa4af3a676060d12ec7e7e -msgid "" -"The FAIR principles have laid a foundation for sharing and publishing " -"digital assets, and in particular, data. The FAIR principles emphasize " -"machine accessibility and that all digital assets should be Findable, " -"Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created." -" It is thus important that workflows support the creation of FAIR data " -"and adhere to the FAIR principles. — [FAIR Computational " -"Workflows](https://workflows.community/groups/fair/), Workflows Community" -" Initiative." -msgstr "" - -#: ../../introduction/basic-concepts.md:167 7451c042271941d6b283bf6d54b76acb -msgid "" -"CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\"," -" CWL tasks are isolated, and you must be explicit about your inputs and " -"outputs." -msgstr "" - -#: ../../introduction/basic-concepts.md:171 d356140962c244d78b4a2c888bf03963 -msgid "" -"The benefit of explicitness and isolation are flexibility, portability, " -"and scalability; tools and workflows described with CWL can transparently" -" leverage technologies such as Docker and be used with CWL " -"implementations from different vendors." -msgstr "" - -#: ../../introduction/basic-concepts.md:176 8fee6b5cd95144e1bced764b112a9d3f -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../introduction/basic-concepts.md:178 38ce1ceb880b4421b9ea2ee52e1153da -msgid "Learn More" -msgstr "" - -#: ../../introduction/basic-concepts.md:180 9a631f69c9504527bcd02a8f40f21c3f -msgid "Semantic Versioning - " -msgstr "" - -#: ../../introduction/basic-concepts.md:181 6141f823850e411691c2ef7047c9ecab -msgid "" -"The CWL Specification page in the CWL website: " -"" -msgstr "" - -#: ../../introduction/basic-concepts.md:182 6a07a8b45dc54851b5b78597891be763 -msgid "" -"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../introduction/basic-concepts.md:183 f246c41bb0f946c590736c40713af684 -msgid "" -"The list of Implementations in the CWL website: " -"" -msgstr "" - -#: ../../introduction/basic-concepts.md:184 d9d8d29e5c0e427299f696073dfbfc1b -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../introduction/basic-concepts.md:185 581a427aed9e483489b6123ee1879d80 -msgid "" -"CWL Operations are covered in the [Operations](../topics/operations.md) " -"section of this user guide." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/introduction/index.po b/locales/en/LC_MESSAGES/introduction/index.po deleted file mode 100644 index 3b6add35..00000000 --- a/locales/en/LC_MESSAGES/introduction/index.po +++ /dev/null @@ -1,31 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../introduction/index.md:1 b93db93ee9a24f03805cc032d22ca212 -msgid "Introduction" -msgstr "" - -#: ../../introduction/index.md:3 f77b8595af564c688c37097c43e04c86 -msgid "" -"This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that" -" are useful to know before reading the rest of the user guide." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/introduction/prerequisites.po b/locales/en/LC_MESSAGES/introduction/prerequisites.po deleted file mode 100644 index f8f47a94..00000000 --- a/locales/en/LC_MESSAGES/introduction/prerequisites.po +++ /dev/null @@ -1,298 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../introduction/prerequisites.md:1 7bbfeec267824100866390bfcfa6cec9 -msgid "Prerequisites" -msgstr "" - -#: ../../introduction/prerequisites.md:6 aa8e8b6a8dfa499f99598f30dca4074f -msgid "" -"The software and configurations listed in this section are prerequisites " -"for following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements " -"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" -"compatible runner or workflow system, but the results and interface may " -"look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../introduction/prerequisites.md:12 cf4757d4aef2456397017d2ff13499ba -msgid "CWL Implementations" -msgstr "" - -#: ../../introduction/prerequisites.md:14 502c3afa077249b98a51051b23698a6d -msgid "" -"There are many implementations of the CWL standards. Some are complete " -"CWL runners, while others could be plug-ins or extensions to workflow " -"engines. We have a better explanation in the [Implementations](basic-" -"concepts.md#implementations) section." -msgstr "" - -#: ../../introduction/prerequisites.md:19 9a788e46f9d64d30aeff30a86182884c -msgid "Operating System" -msgstr "" - -#: ../../introduction/prerequisites.md:21 cc76660874a944369f69207bb1e0e856 -msgid "" -"We recommend using an up-to-date operating system. You can choose any of " -"the following options for your operating system:" -msgstr "" - -#: ../../introduction/prerequisites.md:24 77c62d947e894088afc8520451c79ac1 -msgid "Linux" -msgstr "" - -#: ../../introduction/prerequisites.md:25 32cd53abe1744596b3b33835cd8d1eb1 -msgid "macOS" -msgstr "" - -#: ../../introduction/prerequisites.md:26 1a7b4392aec64e3e9c053288362f342a -msgid "Windows" -msgstr "" - -#: ../../introduction/prerequisites.md:29 dcea6593d35c40bc9c0d39d4a788fbc1 -msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem" -" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " -"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" -"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " -"details on installing WSL2. Your operating system also needs internet " -"access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../introduction/prerequisites.md:35 45bde9e20d0d45eb93427f5b6a3634dd -msgid "CWL Runner" -msgstr "" - -#: ../../introduction/prerequisites.md:41 998f8c45ed8f4075a577d4e6af1eda5b -msgid "" -"The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL " -"community. It is also the CWL reference runner, which means it must " -"support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../introduction/prerequisites.md:46 813a16e6431744b1aad3bc11a2402e44 -msgid "" -"`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create " -"and activate a Python virtual environment using the `venv` module, and " -"install `cwltool` in that environment:" -msgstr "" - -#: ../../introduction/prerequisites.md:51 297d141896a84499a91f312a0016547f -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../introduction/prerequisites.md:62 ad7893d4a87d441c8aedbf168d3ca9ad -msgid "" -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` " -"and `conda`." -msgstr "" - -#: ../../introduction/prerequisites.md:65 5dbc4e8a1c544a258d5b2d965db08be2 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../introduction/prerequisites.md:67 380bf05c4a754d008499fa6206e86e90 -msgid "`true.cwl`" -msgstr "" - -#: ../../introduction/prerequisites.md:73 6d772529b43746a9bbb7c3bd2fb033a2 -msgid "" -"The `cwltool` command has an option to validate CWL tool and workflow " -"descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the " -"CWL standards. However, these actions will be performed without running " -"the document. To validate CWL workflows (or even a standalone command " -"line tool description like the above) pass the `--validate` option to the" -" `cwltool` command:" -msgstr "" - -#: ../../introduction/prerequisites.md:79 d48c1d5aab4d4b78b610a6a8cecbac3f -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../introduction/prerequisites.md:84 50a41a581e2045fd9fcd7149162d1b43 -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../introduction/prerequisites.md:86 35183394d2db4b0797e6a5533cf91eed -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../introduction/prerequisites.md:91 b59575e71904478e8833c13b38d53c91 -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../introduction/prerequisites.md:93 c784985a2d3d4d5c9583fe8d76037a90 -msgid "" -"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be " -"invoked independently, and is not reliant on a particular CWL runner " -"program name. Users can invoke `cwl-runner` instead of invoking a CWL " -"runner like `cwltool` directly. The `cwl-runner` is installed by a system" -" administrator or user to point to the preferred CWL implementation. This" -" is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../introduction/prerequisites.md:101 1fa903efc96d46c79a00a49b9ed778ee -msgid "" -"The CWL community publishes a Python package with the name `cwlref-" -"runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../introduction/prerequisites.md:104 ebecb9c15b7549c1bf82cbc381721378 -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../introduction/prerequisites.md:111 4290343102b746a6987d45a33fb75e8f -msgid "" -"Now you can validate and run your workflow with the `cwl-runner` " -"executable, which will invoke `cwltool`. You should have the same results" -" and output as in the previous section." -msgstr "" - -#: ../../introduction/prerequisites.md:115 95dd822409aa414d848cf74a0882f12d -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../introduction/prerequisites.md:120 be41ce025e294eef8015ac9ffaecd31d -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../introduction/prerequisites.md:125 6ff60669f1ec486e9c80cd32f2f0b8da -msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For" -" that, the first thing you need to do is copy `true.cwl` workflow into a " -"new file: `true_shebang.cwl`, and include a special first line, a " -"*shebang*:" -msgstr "" - -#: ../../introduction/prerequisites.md:129 284249ed02604c479e8a7f9ae098a936 -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../introduction/prerequisites.md:135 2830ba8ada494febaa3cab175aae5c96 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../introduction/prerequisites.md:137 b4a5c084f47a4524b4bbc783481ddb80 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../introduction/prerequisites.md:144 09daa94a2e764c588ed9bdf05686195c -msgid "" -"And finally, you can execute it directly in the command-line. On " -"execution, the program specified in the shebang (`cwl-runner`) will be " -"used to execute the rest of the file." -msgstr "" - -#: ../../introduction/prerequisites.md:148 16b2246ddcde4bd4bab4c9b85a3245cd -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../introduction/prerequisites.md:154 8e5ac54df4264041a8766f683a530806 -msgid "" -"The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute " -"the script using the executable specified after the shebang. It is " -"considered a good practice to use `/usr/bin/env ` rather than" -" using a hard-coded location, since `/usr/bin/env ` looks for" -" the `` program in the system `PATH`," -msgstr "" - -#: ../../introduction/prerequisites.md:161 98043798d4f04488b47f65f6a3d0cbdf -msgid "Text Editor" -msgstr "" - -#: ../../introduction/prerequisites.md:163 dd5138ef1899479eb6a8419834dc94d4 -msgid "" -"You can use any text editor with CWL, but for syntax highlighting we " -"recommend an editor with YAML support. Popular editors are Visual Studio " -"Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../introduction/prerequisites.md:167 2c49302420ca4ef58824a611f6e21631 -msgid "" -"There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting" -" and better auto-complete:" -msgstr "" - -#: ../../introduction/prerequisites.md:171 121e8e64431f49159424ed4ffad079e0 -msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " -"" -msgstr "" - -#: ../../introduction/prerequisites.md:172 786d0c2fb6c44f5c8ddb42ad714b43cc -msgid "" -"cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../introduction/prerequisites.md:174 0a7322840cc64223985de5eaf3f6e5ef -msgid "" -"The CWL community also maintains a list of editors and viewers: " -"" -msgstr "" - -#: ../../introduction/prerequisites.md:177 adf7801f93e54841935427ad5fa76ee1 -msgid "Docker" -msgstr "" - -#: ../../introduction/prerequisites.md:181 2d5c42927e8347efa27e75882e59f27d -msgid "" -"`cwltool` uses Docker to run tools, workflows, and workflow steps that " -"specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: " -"." -msgstr "" - -#: ../../introduction/prerequisites.md:185 58f717b8eb5546459d0e97cf3f4eef0a -msgid "" -"You do not need to know how to write and build Docker containers. In the " -"rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models " -"with and without containers." -msgstr "" - -#: ../../introduction/prerequisites.md:191 2c0ad9dee73c4e278ef0ad7f731c4931 -msgid "" -"`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for " -"pulling images." -msgstr "" - -#: ../../introduction/prerequisites.md:196 a80ae1bdfdb04e1598f06d5115d624eb -msgid "Learn More" -msgstr "" - -#: ../../introduction/prerequisites.md:198 baf0ff9fd9314b5884cf6f2110d964b3 -msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the " -"next section, Basic Concepts." -msgstr "" - -#: ../../introduction/prerequisites.md:199 958ac076e60a420b8b8d790cd49f6da8 -msgid "The Python `venv` module: " -msgstr "" - diff --git a/locales/en/LC_MESSAGES/introduction/quick-start.po b/locales/en/LC_MESSAGES/introduction/quick-start.po deleted file mode 100644 index 077b542d..00000000 --- a/locales/en/LC_MESSAGES/introduction/quick-start.po +++ /dev/null @@ -1,191 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../introduction/quick-start.md:1 47ace6396c93455bb9b8cb8a70be0679 -msgid "Quick Start" -msgstr "" - -#: ../../introduction/quick-start.md:3 17131fb92d5a46d99b7665d0c2890a46 -msgid "" -"This section will show you a brief overview of what CWL is, and where you" -" can learn more about it. No previous knowledge of CWL is required, but " -"you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../introduction/quick-start.md:7 ad577f43c1ec4d79b9cbe4cd5125a31a -msgid "“Hello World”" -msgstr "" - -#: ../../_includes/what-is-cwl.md:2 4d26ec28a1fa419bb9a1f536e4168925 -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../introduction/quick-start.md:12 12247e5c020e4eabaddc0a62364c45e2 -msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " -"The example below shows a simple CWL “Hello World” workflow annotated " -"with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../introduction/quick-start.md:16 60c57d9de0e449bbb1ec517663e9047f -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../introduction/quick-start.md:22 0a89aaf525d349349bb23ecf11f00a1e -msgid "" -"The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the" -" same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../introduction/quick-start.md:27 f33aad86b3194d92b87e51b8551de335 -msgid "" -"In CWL, there is a distinction between a command-line tool and a " -"workflow. But for the sake of simplicity, we are using the term " -"“workflow” here. You will learn more about this in the [basic concepts" -"](basic-concepts.md) section." -msgstr "" - -#: ../../introduction/quick-start.md:32 bba033bcce684da99d8561c644a288b9 -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../introduction/quick-start.md:34 74c2a60629734132baf21f950f51a2a8 -msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the " -"CWL *Reference Runner* for the specification, and it is compliant with " -"the latest version of the specification: {{ cwl_version }}. You can " -"install `cwltool` using `pip`:" -msgstr "" - -#: ../../introduction/quick-start.md:39 688e1f06579d44b8975c3db85d5969f6 -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../introduction/quick-start.md:47 77a52c31fce14347bbb47d80f59489e7 -msgid "" -"If installing the cwltool using the pip command doesn't work for you, the" -" [prerequisites](prerequisites.md) section contains other ways to install" -" `cwltool` and a more detailed list of software and libraries used for " -"following the rest of this user guide." -msgstr "" - -#: ../../introduction/quick-start.md:51 235356675f8b492b86a59fe345d67184 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../introduction/quick-start.md:53 4caaccb9352a46678835a5bfb413803b -msgid "" -"The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the " -"`hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../introduction/quick-start.md:57 ccbc60f4811e4a479530094958219224 -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../introduction/quick-start.md:62 3b3cd61bd0fe4dddbab7ce4fabc16421 -msgid "" -"Or you can override the default value of the input parameter `message`, " -"similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../introduction/quick-start.md:65 71f096c461ef47f8a920339e164bf314 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../introduction/quick-start.md:70 cbaa83776dc041dd963ce47a67b3b405 -msgid "" -"Another way of passing values to your workflow input parameters is via an" -" *Inputs Object*. This is a file containing the input fields with their " -"corresponding values. The Inputs Objects file can be written in JSON or " -"YAML. For example:" -msgstr "" - -#: ../../introduction/quick-start.md:74 04e272f684be44be911dc6e50ac1660b -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../introduction/quick-start.md:80 5d1ebc06dc2d44439135ee1e75cc714a -msgid "" -"You can use this Inputs Object file now to execute the “Hello World” " -"workflow:" -msgstr "" - -#: ../../introduction/quick-start.md:82 6ad6b44a644b482382cec3bfda23e4ac -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../introduction/quick-start.md:88 bf7a0bd183f64f6883ecee1dae23607a -msgid "" -"We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but " -"it is not a requirement. You can choose any name for your workflows and " -"Inputs Object files." -msgstr "" - -#: ../../introduction/quick-start.md:94 002680b62d5d4d8fbf8d730e38ef154a -msgid "Learn More" -msgstr "" - -#: ../../introduction/quick-start.md:96 716e6ec03d974ee9ac59a055fcdabe41 -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../introduction/quick-start.md:97 a098326c57f34af5972578ebb580d6a2 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../introduction/quick-start.md:98 cba27320bbe844fc8bfbad0ba2aa9c01 -msgid "" -"The [`common-workflow-language` organization](https://github.com/common-" -"workflow-language) at GitHub." -msgstr "" - -#: ../../introduction/quick-start.md:99 e377948d6db94e1aa5c3b28c44a9707c -msgid "" -"[Common Workflow Language at " -"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../introduction/quick-start.md:100 b554f9e0572e4b02a5cc1cb817c70539 -msgid "" -"[YAML.org](http://yaml.org/) and [YAML at " -"Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../introduction/quick-start.md:101 a2ce57a5a0a24bb0bb858e076df51e6c -msgid "" -"The {{'[CWL Specification " -"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " -"cwl_version_text) }}." -msgstr "" - -#: ../../introduction/quick-start.md:102 edb34dacc1674731a7b5fa510c81d38b -msgid "" -"[Workflow management system at " -"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/setup.po b/locales/en/LC_MESSAGES/setup.po deleted file mode 100644 index 15bfffe9..00000000 --- a/locales/en/LC_MESSAGES/setup.po +++ /dev/null @@ -1,31 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../setup.md:5 27e5c491bbd4441d96d85f6d8f66181e -msgid "This page has moved" -msgstr "" - -#: ../../setup.md:9 4b442c302c2d4c84a462c1fa1781b35d -msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. The information on this page has been migrated to the " -"[FAQ](/faq.md) section of the new user guide." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/sphinx.po b/locales/en/LC_MESSAGES/sphinx.po deleted file mode 100644 index d097c6cb..00000000 --- a/locales/en/LC_MESSAGES/sphinx.po +++ /dev/null @@ -1,28 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../_templates/sidebar-nav-bs.html:1 94578a793f824c289114eb8091fcbb83 -msgid "Main navigation" -msgstr "" - -#: ../../_templates/sidebar-nav-bs.html:3 0004714627914a26a46506c14c85806d -msgid "Section Navigation" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po b/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po deleted file mode 100644 index 0adab36c..00000000 --- a/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po +++ /dev/null @@ -1,84 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/additional-arguments-and-parameters.md:1 -#: 245426859a1e4d2db7facb0504eb028c -msgid "Additional Arguments and Parameters" -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:3 -#: 6be40170e1d14af08a2b49daecae8df7 -msgid "" -"Sometimes tools require additional command line options that don't " -"correspond exactly to input parameters." -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:6 -#: a3f17f29d2ab4ad2993696400f7be61b -msgid "" -"In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files " -"in the same directory as the source file. However, CWL input files (and " -"the directories in which they appear) may be read-only, so we need to " -"instruct \"javac\" to write the class file to the designated output " -"directory instead." -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:13 -#: 77443a85f1a14fef94fc4d6d4add43ca -msgid "`arguments.cwl`" -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:19 -#: 42d3138cc25d4570ada1a25ac13fb8bc -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:24 -#: 1a7130850048412fa12f6fcec745e4ee -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:30 -#: f4fcf30ed13c42d3a93817dc29651686 -msgid "" -"And now invoke `cwltool` providing the tool description and the input " -"object on the command line:" -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:36 -#: c470ae16de004280a2bd2b0a99f391b3 -msgid "" -"Here we use the `arguments` field to add an additional argument to the " -"command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:43 -#: a31eeefe78ab4442bcfea3e1106cf8a9 -msgid "" -"This example references a runtime parameter. Runtime parameters provide " -"information about the hardware or software environment when the tool is " -"actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include " -"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " -"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " -"Environment][runtime] section of the CWL specification for details." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/best-practices.po b/locales/en/LC_MESSAGES/topics/best-practices.po deleted file mode 100644 index 30c7c72e..00000000 --- a/locales/en/LC_MESSAGES/topics/best-practices.po +++ /dev/null @@ -1,191 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/best-practices.md:1 400480770c074343aae662a25b257a31 -msgid "Best Practices" -msgstr "" - -#: ../../topics/best-practices.md:3 fe9e19076d74462cab67b4a3cb340724 -msgid "" -"The following are a set of recommended good practices to keep in mind " -"when writing a Common Workflow Language description for a tool or " -"workflow. These guidelines are presented for consideration on a scale of " -"usefulness: although more is better, not all are required." -msgstr "" - -#: ../../topics/best-practices.md:8 caab132559d84593ac23530e36ec6c21 -msgid "" -"No `type: string` parameters for names of input or reference " -"files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../topics/best-practices.md:11 e15eb191624846c4b1d3e3e96731a8ff -msgid "" -"A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that" -" the usual rules of software licensing apply to this document. For " -"example, if the workflow is shared publicly, licensing terms must be " -"clear so that a future user understands under what conditions they can " -"run the workflow, modify it and/or combine it with other workflows. For " -"this reason, please consider including a license field in the document. " -"The authors of this guide urge you to choose a pre-existing license " -"rather than trying to write your own (see the link below to learn more " -"about choosing a license), and our recommended practice is to choose a " -"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" -"license]." -msgstr "" - -#: ../../topics/best-practices.md:20 d5c2b325d05f4afca4008f4733d92100 -msgid "" -"If possible, the license should be specified with its corresponding [SPDX" -" identifier][spdx]. Construct the metadata field for the license by " -"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " -"`SPDX-ID` is taken from the list of identifiers linked above. See the " -"example snippet below for guidance. For non-standard licenses without an " -"SPDX identifier, provide a URL to the license." -msgstr "" - -#: ../../topics/best-practices.md:26 99b89f6ce812463093ee0da9255178bb -msgid "" -"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" -"Programmer][sci-license]\"" -msgstr "" - -#: ../../topics/best-practices.md:28 56915c2feeb9402fb1210cdf27788c8a -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../topics/best-practices.md:37 4315b219d21742ac88f39415da6807d8 -msgid "" -"For more examples of providing metadata within CWL descriptions, see " -"[the Metadata and Authorship section of this User Guide](../topics" -"/metadata-and-authorship.md)." -msgstr "" - -#: ../../topics/best-practices.md:40 122f553a412d43bd9e55caaafb90b88f -msgid "" -"Include [attribution information][license-example] for the author(s) of " -"the CWL tool or workflow description. Use unambiguous identifiers like " -"[ORCID][orcid]." -msgstr "" - -#: ../../topics/best-practices.md:44 b5fe5270c8534ad194dbf41bdec90e33 -msgid "" -"In tool descriptions, list dependencies using short name(s) under " -"`SoftwareRequirement`." -msgstr "" - -#: ../../topics/best-practices.md:47 889a5c8d24464546a2a1156ef3791b28 -msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in " -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../topics/best-practices.md:50 7203be6d92a040c2b39f07f0618b7c37 -msgid "" -"All `input` and `output` identifiers should reflect their conceptual " -"identity. Use informative names like `unaligned_sequences`, " -"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " -"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../topics/best-practices.md:55 8ea3eee32d8044c5ad0a4caeab435b8b -msgid "" -"In tool descriptions, include a list of version(s) of the tool that are " -"known to work with this description under `SoftwareRequirement`." -msgstr "" - -#: ../../topics/best-practices.md:58 3c033a88a5cd4bf19683add86436a8de -msgid "" -"`format` should be specified for all input and output `File`s. " -"Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " -"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" -"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " -"types). For non-bioinformatics tools, use or build an appropriate " -"ontology/controlled vocabulary in the same way. Please edit this page to " -"let us know about it." -msgstr "" - -#: ../../topics/best-practices.md:66 7731a6bd39a7444e82b96d2a5e8eb44b -msgid "" -"Mark all input and output `File`s that are read from or written to in a " -"streaming compatible way (only once, no random-access), as `streamable: " -"true`." -msgstr "" - -#: ../../topics/best-practices.md:69 fe8845e0d96f459bbcd69e176e7ff6b1 -msgid "" -"Each `CommandLineTool` description should focus on a single operation " -"only, even if the (sub)command is capable of more. Don't overcomplicate " -"your tool descriptions with options that you don't need or use." -msgstr "" - -#: ../../topics/best-practices.md:73 1ffe2266eef94941840c485ca77417b6 -msgid "" -"Custom types should be defined with one external YAML per type definition" -" for re-use." -msgstr "" - -#: ../../topics/best-practices.md:76 e5af104f7c2848c8ac0f97d13a9153a2 -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../topics/best-practices.md:78 88c7bfbebad14cf9b39bd3e9488c7dfb -msgid "" -"If useful, include a top-level `doc` as well. This should provide a " -"longer, more detailed description than was provided in the top-level " -"`label` (see above)." -msgstr "" - -#: ../../topics/best-practices.md:82 4f874eee6d884b6c8f2117f61788a4e5 -msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list" -" of valid values." -msgstr "" - -#: ../../topics/best-practices.md:85 6c481e56c4ff48fc9854a3c15375f5f7 -msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. " -"One common example: manipulating `File` names and paths? Consider whether" -" one of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc., could be used instead." -msgstr "" - -#: ../../topics/best-practices.md:90 2e66f35622964ad6bc54faedbfec0eeb -msgid "" -"Give the tool description to a colleague (preferably at a different " -"institution) to test and provide feedback." -msgstr "" - -#: ../../topics/best-practices.md:93 c5551f6025e445f296d3de936029fab4 -msgid "" -"Complex workflows with individual components which can be abstracted " -"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" -" their workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../topics/best-practices.md:97 eff85713fb344bfb968bda07094485af -msgid "" -"Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics" -" software\"][containers] (also useful to other disciplines)." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/command-line-tool.po b/locales/en/LC_MESSAGES/topics/command-line-tool.po deleted file mode 100644 index 212158b9..00000000 --- a/locales/en/LC_MESSAGES/topics/command-line-tool.po +++ /dev/null @@ -1,71 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/command-line-tool.md:1 48774f562479443fa878218b84edd4f0 -msgid "Command Line Tool" -msgstr "" - -#: ../../topics/command-line-tool.md:3 8cb2bbcf217f4a35acd6fe7aac1b9493 -msgid "" -"A command-line tool is a type of Process object that can be run by itself" -" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " -"`tar`, etc. The command-line tool is defined in the `baseCommand` " -"attribute of the command-line tool CWL document." -msgstr "" - -#: ../../topics/command-line-tool.md:8 9d7a6d6def0046c180c951e9ad94afeb -msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The " -"following example contains a minimal example of a CWL command-line tool " -"for the `echo` Linux command, using inputs and outputs." -msgstr "" - -#: ../../topics/command-line-tool.md:19 a6e02298d1fa432d9d6b54b420818901 -msgid "CWL command-line tool." -msgstr "" - -#: ../../topics/command-line-tool.md:50 a6638b2f0c184e95abc23d6207e81802 -msgid "`echo.cwl`" -msgstr "" - -#: ../../topics/command-line-tool.md:57 da7864a3fcf842459475b5b27a693ded -msgid "" -"The example above uses a simplified form to define inputs and outputs. " -"You will learn more about in the [Inputs](../topics/inputs.md) and in the" -" [Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../topics/command-line-tool.md:68 0a222e61001a4a08bc2e82ca52105a09 -msgid "Network Access" -msgstr "" - -#: ../../topics/command-line-tool.md:69 988c4b4184d0405e9bc26bb7bcb05c8b -msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network " -"access. If a command-line tool is written manually in CWL v1.1+, there is" -" a need to specify when network access is required." -msgstr "" - -#: ../../topics/command-line-tool.md:83 2918cea6f64846c498fdf03b92533d94 -msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " -"Network Access automatically." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po b/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po deleted file mode 100644 index 39b54f98..00000000 --- a/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po +++ /dev/null @@ -1,104 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/creating-files-at-runtime.md:1 2bbf4c0a32054cfebe3b6b1b02ea3558 -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:3 c5010461c4fe4e8fb7c4f7da2653febe -msgid "" -"Sometimes you need to create a file on the fly from input parameters, " -"such as tools that expect to read their input configuration from a file " -"rather than the command line parameters, or need a small wrapper shell " -"script." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:7 27879c9542e444dca1a80c1784891bf7 -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:9 61cf19e01c03473aa239bc42394bfcff -msgid "`createfile.cwl`" -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:15 -#: 8d1fb6bc4eed466391ad62fe5be90a13 -msgid "" -"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the " -"value at the input `message`." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:20 -#: 40e30b78078a4184b4c5bd69c0766cef -msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later" -" during command line tool invocation. That means that any genuine need " -"for the character `$` must be **escaped** with `\\`. For instance, " -"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " -"be evaluated by the shell script instead of the CWL engine." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:27 -#: c624145be5a04d65acaaa4bfa086c473 -msgid "" -"To test the above CWL tool, use this job to provide the input value " -"`message`:" -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:29 -#: 202ff16474a04e29b0e363cb5241b53e -msgid "`echo-job.yml`" -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:35 -#: ea631a00fdd9484486e1ca60a90b6d8a -msgid "" -"Before we run this, let us look at each step in a little more detail. The" -" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " -"command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:40 -#: 1dea9f63048f40528c904ec2fb4bef69 -msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " -"YAML array, we need a `-` on the first line of each element of the array," -" in this case we have just one element. `entryname:` can have any value, " -"but it must match what was specified in the `baseCommand`. The final part" -" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " -"means that you are using a multiline string (without it, we would need to" -" write the whole script on one line)." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:51 -#: cff49a2cf48c43f0aeaa6241e1bcaabe -msgid "" -"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " -"formatting." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:54 -#: c81ca28ee4d44d82b6cf3bdbf8460642 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/custom-types.po b/locales/en/LC_MESSAGES/topics/custom-types.po deleted file mode 100644 index 66cf4c6c..00000000 --- a/locales/en/LC_MESSAGES/topics/custom-types.po +++ /dev/null @@ -1,99 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/custom-types.md:1 ab79908260aa4842b2322e6e4d615f72 -msgid "Custom Types" -msgstr "" - -#: ../../topics/custom-types.md:3 75b9b1f15a744e24b2f7333b6638bcc4 -msgid "" -"Sometimes you may want to write your own custom types for use and reuse " -"in CWL descriptions. Use of such custom types can reduce redundancy " -"between multiple descriptions that all use the same type, and also allow " -"for additional customisation/configuration of a tool/analysis without the" -" need to fiddle with the CWL description directly." -msgstr "" - -#: ../../topics/custom-types.md:9 7f4a9afccdad41b9892d8424e9fb539d -msgid "" -"The example below is a CWL description of the [biom convert format][biom]" -" tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../topics/custom-types.md:12 8f03906168eb4bf0a6bf7ae0f6e0ecb1 -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../topics/custom-types.md:18 0b8de32a79a14b2a841851ceab22b6b3 -msgid "`custom-types.yml`" -msgstr "" - -#: ../../topics/custom-types.md:24 8ba644c7152247959988abfcd2b4c2be -msgid "" -"___Note:___ To follow the example below, you need to [download the " -"example input file](https://github.com/common-workflow-" -"language/user_guide/blob/main/src/_includes/cwl/custom-" -"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " -"`wget`:" -msgstr "" - -#: ../../topics/custom-types.md:30 975bdfc68b1841fa89a055b7f03fb0ec -msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to " -"be used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../topics/custom-types.md:46 d4efacf670184435a5729e0ba5e16a36 -msgid "" -"The reference to a custom type is a combination of the name of the file " -"in which the object is defined (`biom-convert-table.yaml`) and the name " -"of the object within that file (`table_type`) that defines the custom " -"type. In this case the `symbols` array from the imported `biom-convert-" -"table.yaml` file define the allowable table options. For example, in " -"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" -" to create an OTU table in hdf5 format." -msgstr "" - -#: ../../topics/custom-types.md:53 ea6ca32a9e6e4f38be19487348cd45f7 -msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../topics/custom-types.md:55 5bfed5519bc04c35aa6ad8626201f98f -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../topics/custom-types.md:61 066aef77545f4dc8b11f09caa710be9e -msgid "" -"In order for the custom type to be used in the CWL description, it must " -"be imported. Imports are described in " -"`requirements:SchemaDefRequirement`, as below in the example `custom-" -"types.cwl` description:" -msgstr "" - -#: ../../topics/custom-types.md:76 7e35076a9b0347ff967c5271a3ccf881 -msgid "" -"Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number " -"of cores required for the tool to run successfully, as well as details of" -" the version of the software that the description was written for and " -"other useful metadata. These features are discussed further in other " -"chapters of this user guide." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/environment-variables.po b/locales/en/LC_MESSAGES/topics/environment-variables.po deleted file mode 100644 index 6ecd617f..00000000 --- a/locales/en/LC_MESSAGES/topics/environment-variables.po +++ /dev/null @@ -1,45 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/environment-variables.md:1 498dbc0db9224aabbc9fd1bef778f8ef -msgid "Environment Variables" -msgstr "" - -#: ../../topics/environment-variables.md:3 9ce0f06bed3649339f666147b45c69e4 -msgid "" -"Tools run in a restricted environment and do not inherit most environment" -" variables from the parent process. You can set environment variables " -"for the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../topics/environment-variables.md:7 ef471bebcfc94b008c94a2e8056d7af0 -msgid "`env.cwl`" -msgstr "" - -#: ../../topics/environment-variables.md:13 df5ab6417f87475d8d94f2af498cee39 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../topics/environment-variables.md:18 642f1379ebdd4dd381e8f56343547b42 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/expression-tool.po b/locales/en/LC_MESSAGES/topics/expression-tool.po deleted file mode 100644 index 8d8ad3dc..00000000 --- a/locales/en/LC_MESSAGES/topics/expression-tool.po +++ /dev/null @@ -1,53 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/expression-tool.md:1 2ed0674b02ee4cd7ac4e169086d02513 -msgid "Expression Tool" -msgstr "" - -#: ../../topics/expression-tool.md:3 95b1b27ad2a84cd9bd1207ff75536502 -msgid "" -"An expression tool is a type of Process that can be run by itself or as a" -" Workflow step. It executes a pure JavaScript expression. It is meant to " -"be used as a way to isolate complex JavaScript expressions that need to " -"operate on input data and produce some result as output." -msgstr "" - -#: ../../topics/expression-tool.md:8 80caa25305a74efdaed8ada05faaa018 -msgid "" -"Similar to the command-line tool it requires `inputs` and `outputs`. But " -"instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" - -#: ../../topics/expression-tool.md:17 a664a455f4714071ba0158a4f83a127c -msgid "CWL expression tool." -msgstr "" - -#: ../../topics/expression-tool.md:48 bdfa455a230e4be79031e0777efc7233 -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../topics/expression-tool.md:67 0df562c4585e43d1ae4ac8113b50ed71 -msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains" -" a JavaScript call in `.toUpperCase()`. This means to tools using the " -"expression tool that JavaScript is a requirement." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/expressions.po b/locales/en/LC_MESSAGES/topics/expressions.po deleted file mode 100644 index f09d91d8..00000000 --- a/locales/en/LC_MESSAGES/topics/expressions.po +++ /dev/null @@ -1,383 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/expressions.md:1 15bf6af8d07d476ea6996a0be17fdca0 -msgid "Expressions" -msgstr "" - -#: ../../topics/expressions.md:3 248bcdddada043abaaf9d53819dd3d01 -msgid "" -"If you need to manipulate input parameters, include the requirement " -"`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by " -"the CWL runner." -msgstr "" - -#: ../../topics/expressions.md:9 986c932e94e3496b8ab3ef5c9b1927c5 -msgid "" -"JavaScript expressions should only be used when absolutely necessary. " -"When manipulating file names, extensions, paths etc, consider whether one" -" of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " -"practices](best-practices.md)." -msgstr "" - -#: ../../topics/expressions.md:16 a82f11177ce54f7f92b6e5b037a1b6d0 -msgid "`expression.cwl`" -msgstr "" - -#: ../../topics/expressions.md:22 e1c2a91028bc47238421457f323556db -msgid "" -"As this tool does not require any `inputs` we can run it with an (almost)" -" empty job file:" -msgstr "" - -#: ../../topics/expressions.md:25 bddb2b6b6507418785bc194340313a39 -msgid "`empty.yml`" -msgstr "" - -#: ../../topics/expressions.md:31 6932ad2e25eb4e3c835bf37557efbf03 -msgid "" -"`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object" -" is represented simply by a set of empty brackets." -msgstr "" - -#: ../../topics/expressions.md:35 51962babe16e4b8493cafe401f046510 -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../topics/expressions.md:37 f302523bb23049afa0dc534641abba94 -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../topics/expressions.md:47 5e672f895eb94028bb7fbc4ba7646c46 -msgid "" -"Note that requirements can be provided with the map syntax, as in the " -"example above:" -msgstr "" - -#: ../../topics/expressions.md:54 913d17f1bb474dec91b467db5f45ffab -msgid "" -"Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" -" describe the additional command line arguments." -msgstr "" - -#: ../../topics/expressions.md:62 8f26131c8cc94db88fc88100f0404bff -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../topics/expressions.md:64 ad6af4e35d014ce7bd122b00f99f13dd -msgid "" -"Just like [parameter references](parameter-references.md), you can use " -"JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../topics/expressions.md:66 4b2eaee288a4421a91b304a186578361 -msgid "" -"From " -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../topics/expressions.md:67 032d4eeaeda14354a8b059e4391f3448 -msgid "`arguments`" -msgstr "" - -#: ../../topics/expressions.md:68 ../../topics/expressions.md:76 -#: ../../topics/expressions.md:89 aebe22df1bf6432aa39e402802ce8fcd -#: dcc0d4a9abcb4e35ae4ee341893d757f fca0e4b343c940989ebbf8ce7cf87605 -msgid "`valueFrom`" -msgstr "" - -#: ../../topics/expressions.md:69 0b185807c14741bca2b1ce4252bded44 -msgid "`stdin`" -msgstr "" - -#: ../../topics/expressions.md:70 716a8fad0a5d46bb9d17d35c0866db31 -msgid "`stdout`" -msgstr "" - -#: ../../topics/expressions.md:71 e9d014cdaf794dacb4eee304c1364d1b -msgid "`stderr`" -msgstr "" - -#: ../../topics/expressions.md:72 81333fdf0ac84d4495ec32cd4b58f12e -msgid "" -"From " -"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../topics/expressions.md:73 ../../topics/expressions.md:78 -#: ../../topics/expressions.md:85 ../../topics/expressions.md:93 -#: bf75a275d26345bf86076cea5c44f5d8 c704d979a192458a9315971e6702478a -#: d29995b11d3f4157915f48c52f4eba90 ff462897cd0149c493e50ee87f9d1c0e -msgid "`format`" -msgstr "" - -#: ../../topics/expressions.md:74 ../../topics/expressions.md:79 -#: ../../topics/expressions.md:86 ../../topics/expressions.md:94 -#: 18e86fc5bf684862a30f373766d067eb 195022a4f28f419ea24095350e89c7dd -#: 403516ed7955408fa7a12d34fd1fbe82 dd2932a497104db096a8ecb1986381b6 -msgid "`secondaryFiles`" -msgstr "" - -#: ../../topics/expressions.md:75 49d00678c3d8425db3852e408049e249 -msgid "" -"From " -"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../topics/expressions.md:77 8523d80e16a24adebc3fdad88141e646 -msgid "" -"From " -"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../topics/expressions.md:80 51af437d2c314f18895ae13e58dbd56e -msgid "" -"From " -"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../topics/expressions.md:81 9d9b304dceaa4cb38e01503ff57d726b -msgid "`glob`" -msgstr "" - -#: ../../topics/expressions.md:82 65bceca1c4f7447fa5f3e0c448a02af6 -msgid "`outputEval`" -msgstr "" - -#: ../../topics/expressions.md:83 5bc18fb8fa034c4281b715ab44a5cb75 -msgid "From `Workflow`" -msgstr "" - -#: ../../topics/expressions.md:84 fcfc00ff02d04e61bdc6d5432d04c7da -msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../topics/expressions.md:87 e51177ae5daa42429266893d9467cd15 -msgid "From `steps`" -msgstr "" - -#: ../../topics/expressions.md:88 4e6a5b41b2f249b896d7a1e79b2aebbb -msgid "" -"From " -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../topics/expressions.md:90 9233f867e33d41199e31ed9115442d7e -msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../topics/expressions.md:91 60fc0bdd44614b61961aa204edae77b9 -msgid "`expression`" -msgstr "" - -#: ../../topics/expressions.md:92 2cf4288d3d594085af2a07026bc71371 -msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../topics/expressions.md:95 1455be996e7147c99d60cc9f198b78cb -msgid "" -"From " -"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../topics/expressions.md:96 0ac9b337923c4a2793fe198d6bf759f1 -msgid "`coresMin`" -msgstr "" - -#: ../../topics/expressions.md:97 993661b89e4945d0ad4f8a13931eeffb -msgid "`coresMax`" -msgstr "" - -#: ../../topics/expressions.md:98 22d35c6039754b6b96fed696f9a06a71 -msgid "`ramMin`" -msgstr "" - -#: ../../topics/expressions.md:99 53cce3babeac44c98bbfe68d122e5796 -msgid "`ramMax`" -msgstr "" - -#: ../../topics/expressions.md:100 ed43db0eedef4716800239b9c6c5c9f0 -msgid "`tmpdirMin`" -msgstr "" - -#: ../../topics/expressions.md:101 e4e8d9975aa74847a49060459ace3edc -msgid "`tmpdirMax`" -msgstr "" - -#: ../../topics/expressions.md:102 13713c1adb7f4759b1792bbf3e720c29 -msgid "`outdirMin`" -msgstr "" - -#: ../../topics/expressions.md:103 d8c878c467f34807b98c156ad8705445 -msgid "`outdirMax`" -msgstr "" - -#: ../../topics/expressions.md:104 fb119535e57d4a55b6e9a86deaecc100 -msgid "" -"From " -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../topics/expressions.md:105 dbe84d62840049e7b9ed3498d15847f6 -msgid "`listing`" -msgstr "" - -#: ../../topics/expressions.md:106 6db83a55040447c7903dd5d2d0bb00f8 -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../topics/expressions.md:107 8ff197dd79524f25912ef459fb7b20d1 -msgid "`entry`" -msgstr "" - -#: ../../topics/expressions.md:108 fcea352f4e4246bf8fba2f53665427df -msgid "`entryname`" -msgstr "" - -#: ../../topics/expressions.md:109 120885c8f41e4ad58458699a66b38fc6 -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../topics/expressions.md:110 17cea5e071b0430d901810a76ff224d4 -msgid "" -"From " -"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../topics/expressions.md:111 5e6e3c6614d043e596be33cb9aba75c5 -msgid "`envValue`" -msgstr "" - -#: ../../topics/expressions.md:116 54b20c309ca543df81b8221c6d8f9eaa -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../topics/expressions.md:118 54df5f1a63554bf7989dccf12aa205a1 -msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" -" attribute that allows users to load external JavaScript files, or to " -"provide inline JavaScript code." -msgstr "" - -#: ../../topics/expressions.md:122 8e6566d5b3fd424fa95e77df42ae18ed -msgid "" -"Entries added to the `expressionLib` attribute are parsed with the " -"JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts" -" of the CWL document." -msgstr "" - -#: ../../topics/expressions.md:128 50f2d063d4864db1b051a41769b3d928 -msgid "" -"The CWL standards (versions 1.0 through 1.2) " -"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" -" that the only version of JavaScript valid in CWL expressions is " -"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " -"that any code that you include or write in your CWL Document must be " -"compliant with ECMAScript 5.1." -msgstr "" - -#: ../../topics/expressions.md:135 e2c6c8b5d1b345368e0699a5a2a079cc -msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a " -"JavaScript function inline in `expressionLib`. That function can then be " -"used in other parts of the CWL document:" -msgstr "" - -#: ../../topics/expressions.md:139 1ce74804ca97479fb6bdacbdba2bbc5c -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../topics/expressions.md:146 fbe150d3864e4987ae145a8b7de60151 -msgid "" -"Running this CWL workflow will invoke the JavaScript function and result " -"in the `echo` command printing the input message with capital initial " -"letters:" -msgstr "" - -#: ../../topics/expressions.md:149 7552ea9b4f714fbe8aea6db94fd8894f -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../topics/expressions.md:155 2f3154ec78274b43accde1409c59ec56 -msgid "" -"Let's move the `capitalizeWords` function to an external file, `custom-" -"functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../topics/expressions.md:158 ee2508f7faf74dd3a2928aebd3dc4314 -msgid "`custom-functions.js`" -msgstr "" - -#: ../../topics/expressions.md:164 9ba72aae0ff546e282aaa2518a5cd237 -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../topics/expressions.md:171 e1b9ad0192e44844ab641c883e859510 -msgid "" -"The `custom-functions.js` file is included in the CWL document with the " -"`$include: custom-functions.js` statement. That makes the functions and " -"variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../topics/expressions.md:175 3b40577e79f9432b9bad3fbaf5fc4b78 -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../topics/expressions.md:181 6298a4cf813142e09b35c55fd7077cbc -msgid "" -"Finally, note that you can have both inline and external JavaScript code " -"in your CWL document. In this final example we have added another entry " -"to the `expressionLib` attribute with the new function " -"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" -" the external file `custom-functions.js`." -msgstr "" - -#: ../../topics/expressions.md:186 881975804cc246cdb81af6ad04734a19 -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../topics/expressions.md:193 9369098b680540e2b6ea67f861e193ed -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../topics/expressions.md:200 ec09ac813f3142e9b333428a44bb1244 -msgid "" -"The `$include` statement can be used to include a file from the local " -"disk or from a remote location. It works with both relative and absolute " -"paths. Read the [text about " -"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " -"the CWL specification to learn more about it." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/file-formats.po b/locales/en/LC_MESSAGES/topics/file-formats.po deleted file mode 100644 index 73be3838..00000000 --- a/locales/en/LC_MESSAGES/topics/file-formats.po +++ /dev/null @@ -1,93 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/file-formats.md:1 24ece5b3bfe646268d48b0339ba10e7b -msgid "File Formats" -msgstr "" - -#: ../../topics/file-formats.md:3 a7520d9841f044f8a33d1acf1f6234bf -msgid "" -"Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This " -"helps document for others how to use your tool while allowing you to do " -"some simple type-checking when creating parameter files." -msgstr "" - -#: ../../topics/file-formats.md:8 544fcf8047db45c3aad991cfdf732309 -msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM" -" in our example), reference a local ontology for your institution, or do " -"not add a file format initially for quick development before sharing your" -" tool with others. You can browse existing [IANA file format " -"listings][IANA] and [EDAM file format listings][EDAM] on their websites." -msgstr "" - -#: ../../topics/file-formats.md:14 12d2dc549a684fff9cb46320700143fa -msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` " -"section of the document in greater detail, so don't worry about these for" -" now." -msgstr "" - -#: ../../topics/file-formats.md:17 c362c433ba544d1eaa19781db09aafbd -msgid "" -"Note that for added value `cwltool` can do some basic reasoning based on " -"file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../topics/file-formats.md:20 c1007004cc7a4c408a713c38208574c0 -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../topics/file-formats.md:26 47ec32f1249f48149068417e431a20f5 -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../topics/file-formats.md:32 f99998f5da604c9b827367670cd30879 -msgid "Sample Parameter Files" -msgstr "" - -#: ../../topics/file-formats.md:34 050ec30459884b1581d715038fe2b05a -msgid "" -"Below is an example of a parameter file for the example above. We " -"encourage checking in working examples of parameter files for your tool. " -"This allows others to quickly work with your tool, starting from a " -"\"known good\" parameterization." -msgstr "" - -#: ../../topics/file-formats.md:39 dd49f6afbc754b9083888cf822cc369e -msgid "`sample.yml`" -msgstr "" - -#: ../../topics/file-formats.md:45 7e1974e26afc40568d4e483d20c4b86f -msgid "" -"___Note:___ To follow the example below, you need to download the example" -" input file, *file-formats.bam*. The file is available from " -" and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../topics/file-formats.md:52 46649847e8d440b9b4f6726be286e067 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/index.po b/locales/en/LC_MESSAGES/topics/index.po deleted file mode 100644 index b90b5d6b..00000000 --- a/locales/en/LC_MESSAGES/topics/index.po +++ /dev/null @@ -1,24 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/index.md:1 55452f6967174ff5a1d8cf776874a90b -msgid "Topics" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/inputs.po b/locales/en/LC_MESSAGES/topics/inputs.po deleted file mode 100644 index 03f1b021..00000000 --- a/locales/en/LC_MESSAGES/topics/inputs.po +++ /dev/null @@ -1,313 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/inputs.md:1 03f3a68492ca43bea79742a839864b86 -msgid "Inputs" -msgstr "" - -#: ../../topics/inputs.md:3 9772b8bb0b694b9e9eef5e65b4ffe333 -msgid "Essential Input Parameters" -msgstr "" - -#: ../../topics/inputs.md:5 68cd0cab423c4d10a69989e6a3833e7a -msgid "" -"The `inputs` of a tool is a list of input parameters that control how to " -"run the tool. Each parameter has an `id` for the name of parameter, and " -"`type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../topics/inputs.md:9 2a76b22fc015489b81d6c396f4f8ae30 -msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*," -" and *null*; complex types are *array* and *record*; in addition there " -"are special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../topics/inputs.md:13 ba487511ecd84b37af0796d5159e50e3 -msgid "" -"The following example demonstrates some input parameters with different " -"types and appearing on the command line in different ways." -msgstr "" - -#: ../../topics/inputs.md:16 59dd55e707cd49f385f5763aa54bc461 -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../topics/inputs.md:18 0d05676c671a420b87f3808010ccc207 -msgid "`inp.cwl`" -msgstr "" - -#: ../../topics/inputs.md:24 06e169026a20469cb6b04a216045cc87 -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../topics/inputs.md:26 05dd5f7e9edf4c379e66d8b6cfc1f86f -msgid "`inp-job.yml`" -msgstr "" - -#: ../../topics/inputs.md:33 f02466c6a7bf4795892d14963a8ad22e -msgid "" -"You can use `cwltool` to create a template input object. That saves you " -"from having to type all the input parameters in a input object file:" -msgstr "" - -#: ../../topics/inputs.md:40 5e5a2fe06ad04b2d8969d6cbfed213ec -msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template " -"inp.cwl > inp-job.yml`, and then modify the default values with your " -"desired input values." -msgstr "" - -#: ../../topics/inputs.md:44 fafabc3b11f14bb68c16e3f497e26e40 -msgid "" -"Notice that \"example_file\", as a `File` type, must be provided as an " -"object with the fields `class: File` and `path`." -msgstr "" - -#: ../../topics/inputs.md:47 7e3d42ea93dd417195ab6b5559638326 -msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" -" command line." -msgstr "" - -#: ../../topics/inputs.md:53 0bbabcf2be26490dbe920f52f8cbe9b0 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " -"following boxed text describes these two commands and the expected output" -" from the command line:" -msgstr "" - -#: ../../topics/inputs.md:64 c340c8aa7b80488ba6d16329e1ca2149 -msgid "" -"The CWL reference runner (cwltool) and other runners create temporary " -"directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not " -"explicitly specified" -msgstr "" - -#: ../../topics/inputs.md:70 5c2e148fdb324017a685f5adefadd74d -msgid "" -"The field `inputBinding` is optional and indicates whether and how the " -"input parameter should appear on the tool's command line. If " -"`inputBinding` is missing, the parameter does not appear on the command " -"line. Let's look at each example in detail." -msgstr "" - -#: ../../topics/inputs.md:83 97d14a1cf8fc4b3687281aa93eb1ceb6 -msgid "" -"Boolean types are treated as a flag. If the input parameter " -"\"example_flag\" is \"true\", then `prefix` will be added to the command " -"line. If false, no flag is added." -msgstr "" - -#: ../../topics/inputs.md:95 6c2008aed010466c8e4465c72a4b6d79 -msgid "" -"String types appear on the command line as literal values. The `prefix` " -"is optional, if provided, it appears as a separate argument on the " -"command line before the parameter . In the example above, this is " -"rendered as `--example-string hello`." -msgstr "" - -#: ../../topics/inputs.md:109 95f2a1493e50455ea6e546f70726fab1 -msgid "" -"Integer (and floating point) types appear on the command line with " -"decimal text representation. When the option `separate` is false (the " -"default value is true), the prefix and value are combined into a single " -"argument. In the example above, this is rendered as `-i42`." -msgstr "" - -#: ../../topics/inputs.md:124 3a48173a38904861b9994edddbc2f082 -msgid "" -"File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the " -"parameter is optional. In the example above, this is rendered as " -"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " -"parameter were not provided in the input, nothing would appear on the " -"command line." -msgstr "" - -#: ../../topics/inputs.md:131 54186920b4a14fbfa059779411b20192 -msgid "" -"Input files are read-only. If you wish to update an input file, you must" -" [first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../topics/inputs.md:134 920e8b7d7eee4239b327b0386a872492 -msgid "" -"The value of `position` is used to determine where parameter should " -"appear on the command line. Positions are relative to one another, not " -"absolute. As a result, positions do not have to be sequential, three " -"parameters with positions 1, 3, 5 will result in the same command line as" -" 1, 2, 3. More than one parameter can have the same position (ties are " -"broken using the parameter name), and the position field itself is " -"optional. The default position is 0." -msgstr "" - -#: ../../topics/inputs.md:142 690f556fa0854517a4e3e43747178461 -msgid "" -"The `baseCommand` field will always appear in the final command line " -"before the parameters." -msgstr "" - -#: ../../topics/inputs.md:146 65ae530b9da84e7e98bcf5a5cf516c30 -msgid "Array Inputs" -msgstr "" - -#: ../../topics/inputs.md:148 21f30b0db29c4aa4989c39997b1a720c -msgid "" -"It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to " -"provide `type` field with `type: array` and `items` defining the valid " -"data types that may appear in the array. Alternatively, brackets `[]` may" -" be added after the type name to indicate that input parameter is array " -"of that type." -msgstr "" - -#: ../../topics/inputs.md:154 cefc841cd57c4b19b2be69aa80106c8b -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../topics/inputs.md:160 bae9c79fa8bb42f6922ee937a5c5ff7a -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../topics/inputs.md:166 b756a25aad9e4fcfb68cbe2123cac3c5 -msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../topics/inputs.md:178 0a930f2019b748858ddc5ca5acbde210 -msgid "" -"The `inputBinding` can appear either on the outer array parameter " -"definition or the inner array element definition, and these produce " -"different behavior when constructing the command line, as shown above. In" -" addition, the `itemSeparator` field, if provided, specifies that array " -"values should be concatenated into a single argument separated by the " -"item separator string." -msgstr "" - -#: ../../topics/inputs.md:185 57551982494e4152b2c2c11f04bae126 -msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` " -"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " -"lines, where array values that are not defined with an associated key are" -" marked by a leading `-`. This will be demonstrated in the next lesson " -"and is discussed in more detail in the [YAML Guide](yaml-" -"guide.md#arrays). You can specify arrays of arrays, arrays of records, " -"and other complex types." -msgstr "" - -#: ../../topics/inputs.md:191 30d6b347401d4304b4dcc1ef2268ded2 -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../topics/inputs.md:193 cf8b6d0ed47a4e57a39add29f91f0ec0 -msgid "" -"Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be " -"provided together (they are exclusive). You can use records and type " -"unions to group parameters together to describe these two conditions." -msgstr "" - -#: ../../topics/inputs.md:198 5aa374f61a2a41e383da4b960e3603d5 -msgid "`record.cwl`" -msgstr "" - -#: ../../topics/inputs.md:204 6557427907d0465695aa88f2f27d5bf1 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../topics/inputs.md:215 3f39bfdadeb14b0d8dfb67fe5aad7790 -msgid "" -"In the first example, you can't provide `itemA` without also providing " -"`itemB`." -msgstr "" - -#: ../../topics/inputs.md:217 30829196c2f54dbb9b1c35e462fe4e85 -msgid "`record-job2.yml`" -msgstr "" - -#: ../../topics/inputs.md:233 049396bf53d241cd9d03b9ff81468e0c -msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the " -"first matching item (`itemC`) is added to the command line and remaining " -"item (`itemD`) is ignored." -msgstr "" - -#: ../../topics/inputs.md:236 a9036f0e32ff418482573d23ed074256 -msgid "`record-job3.yml`" -msgstr "" - -#: ../../topics/inputs.md:252 bc0b43accbf9452ca4b7c2d7d69c2984 -msgid "" -"In the third example, only `itemD` is provided, so it appears on the " -"command line." -msgstr "" - -#: ../../topics/inputs.md:255 6cfc57be54f8458ebc9d784bc9ac2555 -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../topics/inputs.md:257 0279c53e41c94ccc9f2de65d057dd903 -msgid "" -"If you use exclusive input parameters combined with expressions, you need" -" to be aware that the `inputs` JavaScript object will contain one of the " -"exclusive input values. This means that you might need to use an **or** " -"boolean operator to check which values are present." -msgstr "" - -#: ../../topics/inputs.md:262 b94737f481d343bfbb6ecf0fd81c9d6f -msgid "" -"Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from" -" an enum." -msgstr "" - -#: ../../topics/inputs.md:265 b5335802dcd148e9bb8f72d75f1ff6cd -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" - -#: ../../topics/inputs.md:271 08b50c80fd024f86ba9c6239895385d0 -msgid "" -"Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you " -"provide a valid value, such as “fasta” (one of the values of the enum), " -"your command should execute successfully:" -msgstr "" - -#: ../../topics/inputs.md:280 77c08d3144b04e58a6733cbd01346102 -msgid "" -"However, if you do not provide any input value, then `file_format` will " -"be evaluated to a `null` value, which does not match the expected type " -"for the output field (a `string`), resulting in failure when running your" -" workflow." -msgstr "" - -#: ../../topics/inputs.md:289 91280fddf3624696b90632ca8466ca59 -msgid "" -"To correct it, you must remember to use an or operator in your JavaScript" -" expression when using exclusive parameters, or any parameter that allows" -" `null`. For example, the expression could be changed to " -"`$(inputs.file_format || 'auto')`, to have a default value if none was " -"provided in the command line or job input file." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po b/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po deleted file mode 100644 index fb846967..00000000 --- a/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po +++ /dev/null @@ -1,70 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/metadata-and-authorship.md:1 e5511fed73914ceeaf73b9ca7020e8d2 -msgid "Metadata and Authorship" -msgstr "" - -#: ../../topics/metadata-and-authorship.md:3 1a4f0cbf7a694f949646c7bfc1d6f5dc -msgid "" -"Implementation extensions not required for correct execution (for " -"example, fields related to GUI presentation) and metadata about the tool " -"or workflow itself (for example, authorship for use in citations) may be " -"provided as additional fields on any object. Such extensions fields (e.g." -" `format: edam:format_2572`) can use a namespace prefix listed in the " -"`$namespaces` section of the document (e.g. edam: " -"http://edamontology.org/) as described in the [Schema Salad specification" -"][schema-salad]. Once you add the namespace prefix, you can access it " -"anywhere in the document as shown below. Otherwise, one must use full " -"URLs: `format: http://edamontology.org/format_2572`." -msgstr "" - -#: ../../topics/metadata-and-authorship.md:13 f1dcef50a880467f82b93f383030501b -msgid "" -"For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to " -"cite your tool." -msgstr "" - -#: ../../topics/metadata-and-authorship.md:16 1af01d43dfd9408ab58a960b62bf44f0 -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../topics/metadata-and-authorship.md:22 ecd7d3e4f19146ef807219add82fff00 -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../topics/metadata-and-authorship.md:28 a8b454c10d484726b194de1f8c0775da -msgid "Extended Example" -msgstr "" - -#: ../../topics/metadata-and-authorship.md:30 0e5960b6d60b4a73837d1ea4b36a896d -msgid "" -"For those that are highly motivated, it is also possible to annotate your" -" tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints" -" at hardware requirements in order to use the tool, and a few more " -"metadata fields." -msgstr "" - -#: ../../topics/metadata-and-authorship.md:35 89713dbe4568459488494cf7f23ee622 -msgid "`metadata_example3.cwl`" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/operations.po b/locales/en/LC_MESSAGES/topics/operations.po deleted file mode 100644 index dd111423..00000000 --- a/locales/en/LC_MESSAGES/topics/operations.po +++ /dev/null @@ -1,73 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/operations.md:1 968848522a1c419e94cdb03a48f7bab8 -msgid "Operations" -msgstr "" - -#: ../../topics/operations.md:3 825f5584a57148e4ba1df435653351a1 -msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-" -"line tool, or an expression tool. It is a step of a workflow that " -"specifies inputs and outputs, but it does not provide enough information " -"to be executed." -msgstr "" - -#: ../../topics/operations.md:7 1c8a712c12b54c26ac8d2d24270390cf -msgid "" -"You can create operations to visualize a workflow during development, " -"before you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../topics/operations.md:10 e0e24f86682447ad88bb59f73f4c272f -msgid "`operations.cwl`" -msgstr "" - -#: ../../topics/operations.md:16 a1448ed2695b4b849c0e2879c38640d8 -msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like" -" a command line tool or an expression. You can also plot it with the CWL " -"Viewer or `cwltool`:" -msgstr "" - -#: ../../topics/operations.md:24 0ed9d93f0ead46fea1f3d5f28d22419b -msgid "" -"The output of the command above can be rendered with a Graphviz renderer." -" The following image is rendered with the Sphinx Graphviz directive (this" -" user guide is built with Sphinx):" -msgstr "" - -#: ../../topics/operations.md:55 4a03e03b140a45b3bfc26d7b0f677cb4 -msgid "" -"If you try running it with `cwltool`, the command will fail since " -"`cwltool` does not have enough information to know how to execute it:" -msgstr "" - -#: ../../topics/operations.md:58 7794ec6d263c425bb423135f4025d2f1 -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../topics/operations.md:66 8c8423c44aec4a619ea9bbce986b3b96 -msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A" -" CWL runner could, for instance, use abstract operations with ID's that " -"correspond to steps executed by a different workflow engine." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/outputs.po b/locales/en/LC_MESSAGES/topics/outputs.po deleted file mode 100644 index 84287200..00000000 --- a/locales/en/LC_MESSAGES/topics/outputs.po +++ /dev/null @@ -1,147 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/outputs.md:1 8b140307638c4baa9261df35f7372240 -msgid "Outputs" -msgstr "" - -#: ../../topics/outputs.md:3 59a76cb3f5b04cf391310d816bdd4759 -msgid "Returning Output Files" -msgstr "" - -#: ../../topics/outputs.md:5 f1e1c91b796e4c4bbb5c8e234852225d -msgid "" -"The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name" -" of parameter, and `type` describing what types of values are valid for " -"that parameter." -msgstr "" - -#: ../../topics/outputs.md:10 aa7076aea7e54d489af848f9523794fe -msgid "" -"When a tool runs under CWL, the starting working directory is the " -"designated output directory. The underlying tool or script must record " -"its results in the form of files created in the output directory. The " -"output parameters returned by the CWL tool are either the output files " -"themselves, or come from examining the content of those files." -msgstr "" - -#: ../../topics/outputs.md:16 7ee8d5efbc2d43c297960a3d851628f9 -msgid "" -"The following example demonstrates how to return a file that has been " -"extracted from a tar file." -msgstr "" - -#: ../../topics/outputs.md:19 ba6fcc05fcdd46f6b1f354295bf124de -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../topics/outputs.md:21 7534fb6a5894438f9da2167e08f4e218 -msgid "" -"In previous examples, the `baseCommand` was just a string, with any " -"arguments passed as CWL inputs. Instead of a single string we can use an " -"_array of strings_. The first element is the command to run, and any " -"subsequent elements are mandatory command line arguments" -msgstr "" - -#: ../../topics/outputs.md:26 3c50004d2d7d4695944015e40bf1f22f -msgid "`tar.cwl`" -msgstr "" - -#: ../../topics/outputs.md:32 cddecc6f8aa640d2b245eef27f5bb87e -msgid "`tar-job.yml`" -msgstr "" - -#: ../../topics/outputs.md:38 3d7918df94094da9b8ecc7ec1c5a1b3b -msgid "Next, create a tar file for the example." -msgstr "" - -#: ../../topics/outputs.md:45 7bf5e274a89048838c9fdf28633a5cec -msgid "" -"And now invoke `cwltool` with the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../topics/outputs.md:51 fce348fc9cce4fdaa699b0d0f6f3b542 -msgid "" -"The field `outputBinding` describes how to set the value of each output " -"parameter." -msgstr "" - -#: ../../topics/outputs.md:62 aa92f3f4f14e4025b874ffec26bff141 -msgid "" -"The `glob` field consists of the name of a file in the output directory. " -"If you don't know name of the file in advance, you can use a wildcard " -"pattern like `glob: '*.txt'`." -msgstr "" - -#: ../../topics/outputs.md:65 1a5ab9a9e91640d48a0cb2c13e691cbc -msgid "Capturing Standard Output" -msgstr "" - -#: ../../topics/outputs.md:67 9896a750508f4a57b128f4e30e718814 -msgid "" -"To capture a tool's standard output stream, add the `stdout` field with " -"the name of the file where the output stream should go. Then add `type: " -"stdout` on the corresponding output parameter." -msgstr "" - -#: ../../topics/outputs.md:71 9345911f55b945eab39897e85e648ea4 -msgid "`stdout.cwl`" -msgstr "" - -#: ../../topics/outputs.md:77 cea8fa310b0c471e8f6f6317b9ffcec6 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../topics/outputs.md:82 ../../topics/outputs.md:105 -#: 5e059fc800fa4f9f93e8a5b07e68de36 d62a95decb134c87a4280ce5526e03bd -msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../topics/outputs.md:89 9d6affcf4fbd4ca2a3f8dbd8d50a5c27 -msgid "Array Outputs" -msgstr "" - -#: ../../topics/outputs.md:91 8c5ad552c70e49b09bdda33cda587fec -msgid "" -"You can also capture multiple output files into an array of files using " -"`glob`." -msgstr "" - -#: ../../topics/outputs.md:93 0558868e3e554b5890eb69b275a6b14b -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../topics/outputs.md:99 4fae0201b0f64c03a134f0bd9aeae9ba -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../topics/outputs.md:112 9f9c8a4a10d444879c7984a95e40fdb4 -msgid "" -"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " -"expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions" -" to mark entries in arrays, as demonstrated in several of the upcoming " -"sections." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/parameter-references.po b/locales/en/LC_MESSAGES/topics/parameter-references.po deleted file mode 100644 index 89399c97..00000000 --- a/locales/en/LC_MESSAGES/topics/parameter-references.po +++ /dev/null @@ -1,279 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/parameter-references.md:1 9f53de1545d2441eaca40a478ab3b2b5 -msgid "Parameter References" -msgstr "" - -#: ../../topics/parameter-references.md:3 86efaeb616844254ac6651e3b312d648 -msgid "" -"In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file " -"we were interested in was called \"hello.txt\", and this was written into" -" the `.cwl` file. This is not the best way to do this, as the " -"\"hello.txt\" filename may vary or be dependent on the input file(s) " -"used. To avoid this we can specify the name of the file we want in the " -"job parameters file (`.yml`). In this example, you will see how to " -"reference the value of input parameters dynamically from other fields, " -"which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../topics/parameter-references.md:13 e19913c8e6bb449aa55959dd82acda2d -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../topics/parameter-references.md:19 7e40643c4a474987aea13be5af260677 -msgid "`tar-param-job.yml`" -msgstr "" - -#: ../../topics/parameter-references.md:25 46112899f2dd46ba828dc57245680909 -msgid "" -"Create your input files and invoke `cwltool` with the tool description " -"and the input object on the command line:" -msgstr "" - -#: ../../topics/parameter-references.md:36 896da20f29e2465fae5555d1f51cb681 -msgid "" -"Certain fields permit parameter references which are enclosed in " -"`$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../topics/parameter-references.md:47 2e0849d53b6b4491a5d779390ea1319e -msgid "" -"References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " -"`$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../topics/parameter-references.md:51 3dab2befe3e840738419f1dedaac04d5 -msgid "" -"The value of the \"inputs\" variable is the input object provided when " -"the CWL tool was invoked." -msgstr "" - -#: ../../topics/parameter-references.md:54 f92b2507989f4836bf33c78326bf8bc3 -msgid "" -"Note that because `File` parameters are objects, to get the path to an " -"input file you must reference the path field on a file object; to " -"reference the path to the tar file in the above example you would write " -"`$(inputs.tarfile.path)`." -msgstr "" - -#: ../../topics/parameter-references.md:59 2a7ca85801a841f2acc94431a2accef8 -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../topics/parameter-references.md:61 737a086da43644b3979fd3ebb16b2696 -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../topics/parameter-references.md:63 fcf3c4392e48496a8776ba9a49a6e867 -msgid "" -"From " -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../topics/parameter-references.md:64 1b2a1714c66d4b2398c7fd614b3099c4 -msgid "`arguments`" -msgstr "" - -#: ../../topics/parameter-references.md:65 -#: ../../topics/parameter-references.md:73 -#: ../../topics/parameter-references.md:86 4458fac137854a9499a9afd221c344ac -#: 96f0d31f8d3549689bdfd4908698eed2 b234d82653a44b4ab1f9532e71e5e962 -msgid "`valueFrom`" -msgstr "" - -#: ../../topics/parameter-references.md:66 e6857e57ba424ec1bd86789a27458c8c -msgid "`stdin`" -msgstr "" - -#: ../../topics/parameter-references.md:67 8544dee0d05a492ca7f7727d277001ba -msgid "`stdout`" -msgstr "" - -#: ../../topics/parameter-references.md:68 a73a304246064187a5ef01aa04c528c8 -msgid "`stderr`" -msgstr "" - -#: ../../topics/parameter-references.md:69 8a86bb148ba9488185ac8f7a621aeba9 -msgid "" -"From " -"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../topics/parameter-references.md:70 -#: ../../topics/parameter-references.md:75 -#: ../../topics/parameter-references.md:82 -#: ../../topics/parameter-references.md:90 26f25bcad002476287ac6597033b3a68 -#: 2911d4b287444e159b2a1cfb9880a977 3657033c01b847febc8d6cdae2cf62b6 -#: 65f8db3faadb4fb59f8f26e7084b7a02 -msgid "`format`" -msgstr "" - -#: ../../topics/parameter-references.md:71 -#: ../../topics/parameter-references.md:76 -#: ../../topics/parameter-references.md:83 -#: ../../topics/parameter-references.md:91 3e57f5d7e1934e19a0f5de1bf11516ef -#: 40e34ff2cf47440a87f6548d3fa0ee65 64382062a5d5464fbf679cc774d0b886 -#: 99c94c256ce444a5a7a2ed4f52498c54 -msgid "`secondaryFiles`" -msgstr "" - -#: ../../topics/parameter-references.md:72 9a7a2dc3b4854f998fe36bd55d062abe -msgid "" -"From " -"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../topics/parameter-references.md:74 9f9ebe1562de4739bdf432fa9f51df65 -msgid "" -"From " -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../topics/parameter-references.md:77 d0ed73eea69a488da98f09b5da9e956a -msgid "" -"From " -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../topics/parameter-references.md:78 153b0efcb519496b89acf861c4cc0af6 -msgid "`glob`" -msgstr "" - -#: ../../topics/parameter-references.md:79 e3ff712139e640b19b06a9270570ac3d -msgid "`outputEval`" -msgstr "" - -#: ../../topics/parameter-references.md:80 4ab6c83d91eb438a972136acae6c128c -msgid "From `Workflow`" -msgstr "" - -#: ../../topics/parameter-references.md:81 d34255008ec94e0cbbf48381fd81a642 -msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../topics/parameter-references.md:84 be964cd5acd74de6bf636baa4299eb81 -msgid "From `steps`" -msgstr "" - -#: ../../topics/parameter-references.md:85 038484e05e724c868a2d1d53cfced2c6 -msgid "" -"From " -"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../topics/parameter-references.md:87 1ee43a5c98f6440e95d688afdb6e4822 -msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../topics/parameter-references.md:88 bf82bae8614f4d3f8e57c20a086ce013 -msgid "`expression`" -msgstr "" - -#: ../../topics/parameter-references.md:89 f708c3a4d3fd404c95285558b8cc6d91 -msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../topics/parameter-references.md:92 fa914a651d5444ebbcff86b1b6226212 -msgid "" -"From " -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../topics/parameter-references.md:93 683a5eb1aa8e41adb89b1e7aec649a36 -msgid "`coresMin`" -msgstr "" - -#: ../../topics/parameter-references.md:94 151709a04a0a455481b9458c535a2e54 -msgid "`coresMax`" -msgstr "" - -#: ../../topics/parameter-references.md:95 93ec484b73bd457b9a34b681e62dba55 -msgid "`ramMin`" -msgstr "" - -#: ../../topics/parameter-references.md:96 3e17671a4aca4443b24bca32b1898bbf -msgid "`ramMax`" -msgstr "" - -#: ../../topics/parameter-references.md:97 b9d4ba2a422542609db7c994b9c89971 -msgid "`tmpdirMin`" -msgstr "" - -#: ../../topics/parameter-references.md:98 fdab43c7a8bb420d84154aa70e24d05a -msgid "`tmpdirMax`" -msgstr "" - -#: ../../topics/parameter-references.md:99 fe3f4e63d6014e34a01243d6e1d54b1a -msgid "`outdirMin`" -msgstr "" - -#: ../../topics/parameter-references.md:100 6db5ab1a64ec40e9a6bc16060657b284 -msgid "`outdirMax`" -msgstr "" - -#: ../../topics/parameter-references.md:101 79f66c8ecf60493697c03d90e111f5aa -msgid "" -"From " -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../topics/parameter-references.md:102 c42fe7e8d1dd4e35a255a5fe1f0dbdd0 -msgid "`listing`" -msgstr "" - -#: ../../topics/parameter-references.md:103 2d14a16d2a354839bcfdbcdd473c59e3 -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../topics/parameter-references.md:104 5545855b55f34682b2a4e78dfa401952 -msgid "`entry`" -msgstr "" - -#: ../../topics/parameter-references.md:105 b267ab6613524236b50e698be4381087 -msgid "`entryname`" -msgstr "" - -#: ../../topics/parameter-references.md:106 6eb7f722fe294d2c81bb97e5bb193c0b -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../topics/parameter-references.md:107 43feefec5bc54adf9340f754e3bbe6fd -msgid "" -"From " -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../topics/parameter-references.md:108 154d6c865631433d89589bd0748c9850 -msgid "`envValue`" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/requirements-and-hints.po b/locales/en/LC_MESSAGES/topics/requirements-and-hints.po deleted file mode 100644 index 380aa5be..00000000 --- a/locales/en/LC_MESSAGES/topics/requirements-and-hints.po +++ /dev/null @@ -1,24 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/requirements-and-hints.md:5 1a39722a112b48beb8cf24e0f5e6ad88 -msgid "Requirements and Hints" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po b/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po deleted file mode 100644 index c5cd86e9..00000000 --- a/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po +++ /dev/null @@ -1,68 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/specifying-software-requirements.md:1 -#: 206f3f103faf4ac19eccdce6e038ed49 -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../topics/specifying-software-requirements.md:3 -#: 4a6f03a974fc4a9e86e260d9bd48b908 -msgid "" -"Often, tool descriptions will be written for a specific version of a " -"software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may " -"also help to avoid confusion about which version of a tool the " -"description was written for." -msgstr "" - -#: ../../topics/specifying-software-requirements.md:13 -#: 8bd36ba850bc4f04bd886ae39e361dbb -msgid "" -"In this example, the software requirement being described is InterProScan" -" version 5.21-60." -msgstr "" - -#: ../../topics/specifying-software-requirements.md:25 -#: 8a5b0083c986452e82183cdc78d2da87 -msgid "" -"Depending on your CWL runner, these hints may be used to check that the " -"required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the " -"[dependency resolvers configuration][dependencies]." -msgstr "" - -#: ../../topics/specifying-software-requirements.md:29 -#: 52df6af7c58b4f099c194b28b0a34de6 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the " -"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" -" looked up in the [SciCrunch][scicrunch] registry, which provides a " -"portal for finding, tracking, and referring to scientific resources " -"consistently. If you want to specify a tool as a `SoftwareRequirement`, " -"search for the tool on SciCrunch and use the RRID that it has been " -"assigned in the registry. (Follow this [Adding a Resource Tutorial" -"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " -"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " -"field of your requirement description. Other good choices, in order of " -"preference, are to include the DOI for the main tool citation and the URL" -" to the tool." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/staging-input-files.po b/locales/en/LC_MESSAGES/topics/staging-input-files.po deleted file mode 100644 index 36848e63..00000000 --- a/locales/en/LC_MESSAGES/topics/staging-input-files.po +++ /dev/null @@ -1,48 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/staging-input-files.md:1 da94c2c9fedf40f789a8afe9ff97abe7 -msgid "Staging Input Files" -msgstr "" - -#: ../../topics/staging-input-files.md:3 57675258a9ef4d948e3ebf0edd7779af -msgid "" -"Normally, input files are located in a read-only directory separate from " -"the output directory. This causes problems if the underlying tool " -"expects to write its output files alongside the input file in the same " -"directory. You use `InitialWorkDirRequirement` to stage input files into" -" the output directory. In this example, we use a JavaScript expression to" -" extract the base name of the input file from its leading directory path." -msgstr "" - -#: ../../topics/staging-input-files.md:9 0cf7fa6cd86c41bf92cd35616a4399e2 -msgid "`linkfile.cwl`" -msgstr "" - -#: ../../topics/staging-input-files.md:15 79ff820bc8d34c3ea37d396d98b56688 -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../topics/staging-input-files.md:20 5f9403a7426941cb806bb76578d53987 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/troubleshooting.po b/locales/en/LC_MESSAGES/topics/troubleshooting.po deleted file mode 100644 index 7658928c..00000000 --- a/locales/en/LC_MESSAGES/topics/troubleshooting.po +++ /dev/null @@ -1,101 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/troubleshooting.md:1 29507aa59aff4e249fcd12240b9fed91 -msgid "Troubleshooting" -msgstr "" - -#: ../../topics/troubleshooting.md:3 fac133f1d79f49599d516794dd45517e -msgid "" -"In this section you will find ways to troubleshoot when you have problems" -" executing CWL. We focus on `cwltool` here but some of these techniques " -"may apply to other CWL Runners." -msgstr "" - -#: ../../topics/troubleshooting.md:6 68f47e9e268248af8a07b4b35080a918 -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../topics/troubleshooting.md:8 4ce1b123ee4745a3aa149e0f98ebe310 -msgid "" -"You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor " -"output files, but created while your workflow is running). By default, " -"these files are created in a temporary directory but writing them to a " -"separate directory makes accessing them easier." -msgstr "" - -#: ../../topics/troubleshooting.md:14 afa8d683568747839d41d2e9051d06ec -msgid "" -"In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " -"World\" | rev`, which would print the message \"Hello World\" reversed, " -"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," -" where instead of executing the `rev` command it tries to execute `revv`," -" which fails." -msgstr "" - -#: ../../topics/troubleshooting.md:20 699bac84262647c7bc091c7cea92a4ba -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../topics/troubleshooting.md:27 c4ce2451329d468a8a5a489eca901262 -msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " -"value (`cwltool` will create the directory for you if it does not exist " -"already):" -msgstr "" - -#: ../../topics/troubleshooting.md:35 31f0242e1c5a4c3bb621ce4414e34add -msgid "" -"The workflow is in the `permanentFail` status due to `step_b` failing to " -"execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. " -"You can inspect the intermediate files created:" -msgstr "" - -#: ../../topics/troubleshooting.md:44 7294bf3bcfd447bf9b894ffef0b2873a -msgid "" -"Each workflow step has received a unique ID (the long value that looks " -"like a hash). The `${HASH}.status` files display the status of each step " -"executed by the workflow. And the `step_a` output file `stdout.txt` is " -"visible in the output of the command above." -msgstr "" - -#: ../../topics/troubleshooting.md:48 a18b5467b1c643d987e494d5a9ced7c7 -msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" -" in the `step_b`). After fixing the typo, when you execute `cwltool` with" -" the same arguments as the previous time, note that now `cwltool` output " -"contains information about pre-cached outputs for `step_a`, and about a " -"new cache entry for the output of `step_b`. Also note that the status of " -"`step_b` is now of success." -msgstr "" - -#: ../../topics/troubleshooting.md:59 7925dcec83bc48cd88eaf2e6860304fd -msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had" -" been cached, and there was no change in its execution or output. " -"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for" -" troubleshooting your CWL documents and also as a way to prevent " -"`cwltool` to re-evaluate steps unnecessarily." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/using-containers.po b/locales/en/LC_MESSAGES/topics/using-containers.po deleted file mode 100644 index 6779614b..00000000 --- a/locales/en/LC_MESSAGES/topics/using-containers.po +++ /dev/null @@ -1,106 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/using-containers.md:1 33c3ff349c68416e8968af39e5e588e0 -msgid "Using Containers" -msgstr "" - -#: ../../topics/using-containers.md:3 5c50f28d3926477e965a32d31e5329ee -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../topics/using-containers.md:5 5cb16dd51c1d41aeb34c4aa1fb2e0940 -msgid "" -"[Docker][docker] containers simplify software installation by providing a" -" complete known-good runtime for software and its dependencies. However," -" containers are also purposefully isolated from the host system, so in " -"order to run a tool inside a Docker container there is additional work to" -" ensure that input files are available inside the container and output " -"files can be recovered from the container. A CWL runner can perform this" -" work automatically, allowing you to use Docker to simplify your software" -" management while avoiding the complexity of invoking and managing Docker" -" containers." -msgstr "" - -#: ../../topics/using-containers.md:15 e0e83e827b734355aa97b19dc4c7e0d5 -msgid "" -"One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the " -"container." -msgstr "" - -#: ../../topics/using-containers.md:18 38f82d201fa2455f94afacae2c1c76b2 -msgid "" -"This example runs a simple Node.js script inside a Docker container which" -" will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../topics/using-containers.md:21 00459eae5fef4f5f907ceb53eee857dd -msgid "`docker.cwl`" -msgstr "" - -#: ../../topics/using-containers.md:27 7e59171b12eb46e98ffa08a05ccebf16 -msgid "`docker-job.yml`" -msgstr "" - -#: ../../topics/using-containers.md:33 d90442f3550f4e9b84905bb76ecb6fc1 -msgid "" -"Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that " -"is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../topics/using-containers.md:44 feb03506a2614ea3a0fc97f3154425c2 -msgid "" -"`baseCommand: node` tells CWL that we will be running this command using " -"the Node Js runtime that is meant for Javascript files. We then need to " -"specify some `hints` for how to find the container we want. In this case" -" we list just our requirements for the docker container in " -"`DockerRequirements`. The `dockerPull:` parameter takes the same value " -"that you would pass to a `docker pull` command. That is, the name of the " -"container image (you can even specify the tag, which is good idea for " -"best practices when using containers for reproducible research). In this " -"case we have used a container called `node:slim`." -msgstr "" - -#: ../../topics/using-containers.md:52 fa521c85542c410ba187c69fe5b3aebd -msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` " -"providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../topics/using-containers.md:55 f3012553a17a42fca78b210ecec92003 -msgid "`hello.js`" -msgstr "" - -#: ../../topics/using-containers.md:69 fd0ad3c4cd904765ae5b043b44078a1c -msgid "" -"Notice the CWL runner has constructed a Docker command line to run the " -"script." -msgstr "" - -#: ../../topics/using-containers.md:72 60fa9a28e9bf4a4fa54289516e22f4cd -msgid "" -"In this example, the path to the script `hello.js` is " -"`/home/me/cwl/user_guide/hello.js` outside the container but " -"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " -"reflected in the invocation of the `node` command." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/workflows.po b/locales/en/LC_MESSAGES/topics/workflows.po deleted file mode 100644 index 9c8321d5..00000000 --- a/locales/en/LC_MESSAGES/topics/workflows.po +++ /dev/null @@ -1,504 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/workflows.md:1 d6acbcdd75704f7b966a49edb8af28d9 -msgid "Workflows" -msgstr "" - -#: ../../topics/workflows.md:3 4d3032eb6fcc4cf8a2a67958877d7850 -msgid "" -"A workflow is a CWL processing unit that executes command-line tools, " -"expression tools, or workflows (sub-workflows) as steps. It must have " -"`inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../topics/workflows.md:13 89e89efbb04b47909df04a046169442c -msgid "CWL workflow." -msgstr "" - -#: ../../topics/workflows.md:41 a6e739c210e54652aa8833825f58e36f -msgid "" -"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier " -"examples." -msgstr "" - -#: ../../topics/workflows.md:51 5b187be9b5314039a7e16d35fe4672e3 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../topics/workflows.md:81 59c9035c8eb94a4984c2fdf66c1cb787 -msgid "" -"A command-line tool or expression tool can also be written directly in " -"the same CWL document as the workflow. For example, we can rewrite the " -"`echo-uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../topics/workflows.md:91 0e790b8a77874eeca2efcdf8254226e1 -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../topics/workflows.md:150 176b128d31d549ec947e2112bda59e10 -msgid "" -"Having separate files helps with modularity and code organization. But it" -" can be helpful writing everything in a single file for development. " -"There are other ways to combine multiple files into a single file (e.g. " -"`cwltool --pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../topics/workflows.md:160 058879c518a24859933efd7c62d2b3e4 -msgid "" -"For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this" -" user guide in more detail." -msgstr "" - -#: ../../topics/workflows.md:165 9e596d54fc074e3dbb622429244304dc -msgid "Writing Workflows" -msgstr "" - -#: ../../topics/workflows.md:167 14760ea2dd594df4a11af3c2b267e2ee -msgid "" -"This workflow extracts a java source file from a tar file and then " -"compiles it." -msgstr "" - -#: ../../topics/workflows.md:170 73d971cacade4ed4893f03978d930b3b -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../topics/workflows.md:179 ../../topics/workflows.md:180 -#: 54719da53e4043758f29194fda1b0448 652551d8f4cf49fbb785e56b9bccf2ea -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../topics/workflows.md:180 84d558ae6abc432695ccb49d050d92c7 -msgid "" -"[![Visualization of 1st-" -"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" -"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../topics/workflows.md:183 9ced46957b8b4f20b2315979aecb30b9 -msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a" -" run:" -msgstr "" - -#: ../../topics/workflows.md:185 bda955c302b2489fa76f54a08f6a4119 -msgid "`1st-workflow-job.yml`" -msgstr "" - -#: ../../topics/workflows.md:191 e57cce93798d4cb3a2e7a50f88549049 -msgid "" -"Next, create a sample Java file and add it to a tar file to use with the " -"command-line tool." -msgstr "" - -#: ../../topics/workflows.md:198 0270321fc2554e318de95a5684e9b6ea -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - -#: ../../topics/workflows.md:205 e7035e4184a14b1bb2a33b9a22e06df3 -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../topics/workflows.md:212 b242d87aa48241c094c78051fd1b4e6d -msgid "" -"The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a " -"workflow." -msgstr "" - -#: ../../topics/workflows.md:221 fef2e2bdae81488bb23e6a63b8fec415 -msgid "" -"The `inputs` section describes the inputs of the workflow. This is a " -"list of input parameters where each parameter consists of an identifier " -"and a data type. These parameters can be used as sources for input to " -"specific workflows steps." -msgstr "" - -#: ../../topics/workflows.md:233 7e9c2fbfcebf45f0a8c906d32ad4ddb7 -msgid "" -"The `outputs` section describes the outputs of the workflow. This is a " -"list of output parameters where each parameter consists of an identifier " -"and a data type. The `outputSource` connects the output parameter " -"`classfile` of the `compile` step to the workflow output parameter " -"`compiled_class`." -msgstr "" - -#: ../../topics/workflows.md:248 f5dd8d4b1e324d7f81b12657f847c040 -msgid "" -"The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second " -"step compiles the file from the first step using the java compiler. " -"Workflow steps are not necessarily run in the order they are listed, " -"instead the order is determined by the dependencies between steps (using " -"`source`). In addition, workflow steps which do not depend on one " -"another may run in parallel." -msgstr "" - -#: ../../topics/workflows.md:256 76d103db569b4ec6ab33fbd3d8c11e79 -msgid "" -"The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input" -" parameters, `tarfile` and `extractfile` and one output parameter " -"`extracted_file`." -msgstr "" - -#: ../../topics/workflows.md:261 36ae3b2a1dab47b18b3896d208393e73 -msgid "" -"The ``in`` section of the workflow step connects these two input " -"parameters to the inputs of the workflow, `tarball` and " -"`name_of_file_to_extract` using `source`. This means that when the " -"workflow step is executed, the values assigned to `tarball` and " -"`name_of_file_to_extract` will be used for the parameters `tarfile` and " -"`extractfile` in order to run the tool." -msgstr "" - -#: ../../topics/workflows.md:267 e0e1cf7c5e86443eaf7717b5c683ed89 -msgid "" -"The `out` section of the workflow step lists the output parameters that " -"are expected from the tool." -msgstr "" - -#: ../../topics/workflows.md:278 91eceaf92e5441ce8b70e57e59fcda75 -msgid "" -"The second step `compile` depends on the results from the first step by " -"connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described " -"previously in [Additional Arguments and Parameters](additional-arguments-" -"and-parameters.md)). The output of this step `classfile` is connected to " -"the `outputs` section for the Workflow, described above." -msgstr "" - -#: ../../topics/workflows.md:285 6112278376cb4e84ba05ebe6db7b039f -msgid "Nested Workflows" -msgstr "" - -#: ../../topics/workflows.md:287 19b5cd110ef149819d91c5bb86f56def -msgid "" -"Workflows are ways to combine multiple tools to perform a larger " -"operations. We can also think of a workflow as being a tool itself; a CWL" -" workflow can be used as a step in another CWL workflow, if the workflow " -"engine supports the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../topics/workflows.md:297 5d4aca9586434f40917c3532ae97bb22 -msgid "" -"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " -"workflow:" -msgstr "" - -#: ../../topics/workflows.md:300 a32ab81c1a4a4150a0cf6fc792104a2a -msgid "`nestedworkflows.cwl`" -msgstr "" - -#: ../../topics/workflows.md:309 a28860105216475ab93a1fcd2b740b52 -msgid "" -"This two-step workflow starts with the `create-tar` step which is " -"connected to the `compile` step in orange; `compile` is another workflow," -" diagrammed on the right. In purple we see the fixed string " -"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../topics/workflows.md:314 b3a4a7cfd77340029137a2cc9462b65c -msgid "" -" \"Visualization" -msgstr "" - -#: ../../topics/workflows.md:322 88aff05f9f3a45b297dd3eda9f52bc91 -msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " -"its CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " -"mapped to become the step's input/outputs." -msgstr "" - -#: ../../topics/workflows.md:336 d5bc4016a294455baef3fe1e32c5c636 -msgid "" -"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and " -"`*.java` filename. This is generally best-practice, as it means it can be" -" reused in multiple parent workflows, or even in multiple steps within " -"the same workflow." -msgstr "" - -#: ../../topics/workflows.md:341 5d59589eef4d44d69d2ef65821aaae45 -msgid "" -"Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar" -" file at `tarball`, which we will prepare in the `create-tar` step. At " -"this point it is probably a good idea to refactor `1st-workflow.cwl` to " -"have more specific input/output names, as those also appear in its usage " -"as a tool." -msgstr "" - -#: ../../topics/workflows.md:347 d39c9aba4eda4252964711369c0ca9d6 -msgid "" -"It is also possible to do a less generic approach and avoid external " -"dependencies in the job file. So in this workflow we can generate a hard-" -"coded `Hello.java` file using the previously mentioned " -"`InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../topics/workflows.md:366 dd9b058b571347deb207200501a54651 -msgid "" -"In this case our step can assume `Hello.java` rather than be " -"parameterized, so we can use hardcoded values `hello.tar` and " -"`Hello.java` in a `baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../topics/workflows.md:383 c2d3d7b3f62344b3841dadd0c2dd4981 -msgid "" -"Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This " -"is generally not best practice, as the tool then can't be reused. The " -"reason for doing it in this case is because the command line is hard-" -"coded with filenames that only make sense within this workflow." -msgstr "" - -#: ../../topics/workflows.md:389 847d59018c6940f0b7248bc82abf4818 -msgid "" -"In this example we had to prepare a tar file outside, but only because " -"our inner workflow was designed to take that as an input. A better " -"refactoring of the inner workflow would be to take a list of Java files " -"to compile, which would simplify its usage as a tool step in other " -"workflows." -msgstr "" - -#: ../../topics/workflows.md:394 f041304d817446d39cd9dd41b00e2e78 -msgid "" -"Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL" -" Tool description, care must be taken to improve its usability in " -"multiple workflows." -msgstr "" - -#: ../../topics/workflows.md:398 a232c586c24045d7ad0813aabe2c62b7 -msgid "Scattering Steps" -msgstr "" - -#: ../../topics/workflows.md:400 f1d87f16200142318d6ec00d19ae9dcb -msgid "" -"Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish " -"to run a tool or workflow multiple times over a list of inputs. The " -"workflow then takes the input(s) as an array and will run the specified " -"step(s) on each element of the array as if it were a single input. This " -"allows you to run the same workflow on multiple inputs without having to " -"generate many different commands or input yaml files." -msgstr "" - -#: ../../topics/workflows.md:411 884b61d0625a4561a963b381fcff7344 -msgid "" -"The most common reason a new user might want to use scatter is to perform" -" the same analysis on different samples. Let's start with a simple " -"workflow that calls our first example (`hello_world.cwl`) and takes an " -"array of strings as input to the workflow:" -msgstr "" - -#: ../../topics/workflows.md:415 35097a2dfc3c421bab46e81a53c34087 -msgid "`scatter-workflow.cwl`" -msgstr "" - -#: ../../topics/workflows.md:421 44c8319f97b242f197f1311fcb2719b5 -msgid "" -"Aside from the `requirements` section including " -"`ScatterFeatureRequirement`, what is going on here?" -msgstr "" - -#: ../../topics/workflows.md:429 839e0cd993b44899a4049b44eb8aacfa -msgid "" -"First of all, notice that the main workflow level input here requires an " -"array of strings." -msgstr "" - -#: ../../topics/workflows.md:441 333b64b5ab4a4078b9189c8bbb5924b9 -msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This " -"field tells the runner that we'd like to scatter over this input for this" -" particular step. Note that the input name listed after scatter is the " -"one of the step's input, not a workflow level input." -msgstr "" - -#: ../../topics/workflows.md:445 73aa0f6708264bc39b0c6398827f1e6e -msgid "" -"For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if " -"you expect that the final output of your workflow will now have multiple " -"outputs to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../topics/workflows.md:450 5f6a3bf1dc314cb8beb9b336fc2c8f6f -msgid "Using the following input file:" -msgstr "" - -#: ../../topics/workflows.md:452 d5808863a44b4a6695e36ac1ae4a22f2 -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../topics/workflows.md:458 2c642b5be9c94763aee4bdf73d8bc2a1 -msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" -" calls the command `echo` on a message. If we invoke `cwltool scatter-" -"workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../topics/workflows.md:466 dcf2a0d97e4a4afa842a971b304e23b4 -msgid "" -"You can see that the workflow calls echo multiple times on each element " -"of our `message_array`. Ok, so how about if we want to scatter over two " -"steps in a workflow?" -msgstr "" - -#: ../../topics/workflows.md:469 2aea56527429469c8af125414e4f4f00 -msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding " -"the following lines instead of `outputs: []`" -msgstr "" - -#: ../../topics/workflows.md:472 a4279d75f660475d82c4bc8f869c17cc -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../topics/workflows.md:480 33ac7f4c0b1040b89811c0445b1f6824 -msgid "" -"And add a second step that uses `wc` to count the characters in each " -"file. See the tool below:" -msgstr "" - -#: ../../topics/workflows.md:483 17b1da21293d40f7b246abb4f3a6fcd7 -msgid "`wc-tool.cwl`" -msgstr "" - -#: ../../topics/workflows.md:489 5aff13d9cf7841b29e2285ce2fdc90ad -msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under " -"each step:" -msgstr "" - -#: ../../topics/workflows.md:491 53afeb0f6b4f405782b0eb2e74d3acfe -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../topics/workflows.md:497 fbab18460296443daddb7bc1bcafe4fc -msgid "" -"Here we have placed the scatter field under each step. This is fine for " -"this example since it runs quickly, but if you're running many samples " -"for a more complex workflow, you may wish to consider an alternative. " -"Here we are running scatter on each step independently, but since the " -"second step is not dependent on the first step completing all languages, " -"we aren't using the scatter functionality efficiently. The second step " -"expects an array as input from the first step, so it will wait until " -"everything in step one is finished before doing anything. Pretend that " -"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " -"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " -"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " -"could finish in 4 minutes, it will actually finish in 8 minutes because " -"the first step must wait on `echo Hallo welt!`. You can see how this " -"might not scale well." -msgstr "" - -#: ../../topics/workflows.md:509 52b2dee5459b4bbdab9f09576ec96f65 -msgid "" -"Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can" -" make an entire workflow a single step in another workflow! Convert our " -"two-step workflow to a single step subworkflow:" -msgstr "" - -#: ../../topics/workflows.md:513 24185616ce374615a6966a70df77693b -msgid "`scatter-nested-workflow.cwl`" -msgstr "" - -#: ../../topics/workflows.md:519 7302c1e575bf4457a04243e9e0ef6f59 -msgid "" -"Now the scatter acts on a single step, but that step consists of two " -"steps so each step is performed in parallel." -msgstr "" - -#: ../../topics/workflows.md:522 6ac74585b69d4197a26c8230f53f75cb -msgid "Conditional Workflows" -msgstr "" - -#: ../../topics/workflows.md:524 f189ba0d5e7547d1a6540abde5c4da78 -msgid "" -"This workflow contains a conditional step and is executed based on the " -"input. This allows workflows to skip additional steps based on input " -"parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../topics/workflows.md:527 257301405fda4c6aa98195f4344b496d -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../topics/workflows.md:566 189ea6307a25445ca573ff93cd8c4f1d -msgid "" -"The first thing you'll notice is that this workflow is only compatible " -"for version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../topics/workflows.md:573 b0701c43575d4dc79c4abe2c932928c3 -msgid "" -"The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when`" -" is where the condition validation takes place. In this case only when " -"`in1` from the workflow contains a value `< 1` this step will be " -"executed." -msgstr "" - -#: ../../topics/workflows.md:587 7de691f8e339422e8b027297e3d16fa6 -msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" -" will pass the first conditional step and will therefore be executed and " -"is shown in the log by `INFO [step step1] start` whereas the second step " -"is skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../topics/workflows.md:607 246e5e7c82aa48c9a7f5f2c3b7b4d707 -msgid "" -"When a value of 3 is given the first conditional step will not be " -"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../topics/workflows.md:627 b28362ad11bb44c9b7247f411e58caa4 -msgid "" -"If no conditions are met for example when using `--val 2` the workflow " -"will raise a permanentFail." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/yaml-guide.po b/locales/en/LC_MESSAGES/topics/yaml-guide.po deleted file mode 100644 index 4b225c2e..00000000 --- a/locales/en/LC_MESSAGES/topics/yaml-guide.po +++ /dev/null @@ -1,193 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/yaml-guide.md:1 153f05199ec24a5da81da49288e2679a -msgid "YAML Guide" -msgstr "" - -#: ../../topics/yaml-guide.md:6 95951c4a95d943c89be9252a898018d8 -msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers " -"and humans. This guide introduces the features of YAML that are relevant " -"when writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../topics/yaml-guide.md:13 60a16d7722724500b0a31194b6958cea -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../topics/yaml-guide.md:16 61f0a8fcfa2044ada7761d35e6ee6bbb -msgid "Contents" -msgstr "" - -#: ../../topics/yaml-guide.md:18 3c5dd09c0fbc4079abff7f8ee9c1bd03 -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../topics/yaml-guide.md:19 c7fa245866d0430fb8fcef9392869999 -msgid "[Comments](#comments)" -msgstr "" - -#: ../../topics/yaml-guide.md:20 dde5f9ad058445d1b0131ddf1fd80b74 -msgid "[Maps](#maps)" -msgstr "" - -#: ../../topics/yaml-guide.md:21 fdb88e5dafea4cb0876cea846eccca7d -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../topics/yaml-guide.md:22 f2ae9d617f274c7eb84a2d87c10a4cc5 -msgid "[JSON Style](#json-style)" -msgstr "" - -#: ../../topics/yaml-guide.md:24 47bffc9bb7b64047a25903eb42bde019 -msgid "Key-Value Pairs" -msgstr "" - -#: ../../topics/yaml-guide.md:26 283f64df8dcf4abc8f00ee515d0cc9bb -msgid "" -"Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the " -"`:` is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have " -"special meaning in the CWL specification and underscored key names " -"otherwise. For example:" -msgstr "" - -#: ../../topics/yaml-guide.md:42 51a3cd8bd6d2403daadc57d0091e99dc -msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, " -"`age_years`, and `home` - with their four respective values. Values can " -"be character strings, numeric (integer, floating point, or scientific " -"representation), Boolean (`true` or `false`), or more complex nested " -"types (see below)." -msgstr "" - -#: ../../topics/yaml-guide.md:51 7d58fe0504534589adfadf74e82de41a -msgid "" -"Values may be wrapped in quotation marks, but be aware that this may " -"change the way that they are interpreted i.e. `\"1234\"` will be treated " -"as a character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a" -" command: in CWL all parts of `baseCommand` must be strings so, if you " -"want to specify a fixed numeric value to a command, make sure that you " -"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../topics/yaml-guide.md:61 35e8c97a24344c7d9933f1910d6bd995 -msgid "Comments" -msgstr "" - -#: ../../topics/yaml-guide.md:63 5ba35d4bbb4644949c37993a77a50bf6 -msgid "" -"You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program " -"interpreting the YAML. For example:" -msgstr "" - -#: ../../topics/yaml-guide.md:76 e63546bf4b144bfba77767ec7248d63d -msgid "" -"If there is anything on the line before the comment, be sure to add at " -"least one space before the `#`!" -msgstr "" - -#: ../../topics/yaml-guide.md:79 25ac6edc52bd484cac8eb4fe4d5b6e1c -msgid "Maps" -msgstr "" - -#: ../../topics/yaml-guide.md:81 20e1be6499d9470fa74dde6da33f2120 -msgid "" -"When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, " -"these hierarchical structures are described in YAML by providing " -"additional key-value pairs as the value of any key. These pairs " -"(sometimes referred to as \"children\") are written on new lines under " -"the key to which they belong (the \"parent\"), and should be indented " -"with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../topics/yaml-guide.md:104 a99731edefb049299d313941156c41a6 -msgid "" -"The YAML above illustrates how to build up complex nested object " -"descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and " -"`inputBinding`, while one of these children, `inputBinding`, contains a " -"further two key-value pairs (`position` and `prefix`). See the " -"[Arrays](#arrays) section below for more information about providing " -"multiple values/key-value pairs for a single key. For comparison with the" -" example YAML above, here is a graphical representation of the `inputs` " -"object it describes." -msgstr "" - -#: ../../topics/yaml-guide.md:127 51d8ad7d937540ee88b46fc790319b4a -msgid "Arrays" -msgstr "" - -#: ../../topics/yaml-guide.md:129 bfeee0ef93e44a0ea50e3970e027b2f1 -msgid "" -"In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) " -"section above, more than one key-value pair can be mapped to a single " -"key. However, it is also possible to define multiple values for a key " -"without having to provide a unique key for each value. We can achieve " -"this with an _array_, where each value is defined on its own line and " -"preceded by `-`. For example:" -msgstr "" - -#: ../../topics/yaml-guide.md:146 297035119d42476e8dbebd1ed2241ac3 -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../topics/yaml-guide.md:167 563dd83823d745b6aebeb956fca51aa3 -msgid "JSON Style" -msgstr "" - -#: ../../topics/yaml-guide.md:169 7edbeea182fe4043be66f02bc5952114 -msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " -"arrays can also be defined in YAML using the native JSON syntax. For " -"example:" -msgstr "" - -#: ../../topics/yaml-guide.md:177 37ddb7add5ea4fde94c97ab2bd2c85e7 -msgid "and:" -msgstr "" - -#: ../../topics/yaml-guide.md:184 ed9f6a7d062c43f099b5181e2c930303 -msgid "" -"Native JSON can be useful in indicating where a field is intentionally " -"left empty (such as `[]` for an empty array), as well as where it makes " -"more sense for the values to be located on the same line (For example, " -"when providing option flags and their values in a shell command). " -"However, as the second example above shows, it can severely affect the " -"readability of a YAML file, and should be used sparingly." -msgstr "" - -#: ../../topics/yaml-guide.md:194 9cb613e445b5429196ced3d66fe95e45 -msgid "Reference" -msgstr "" - -#: ../../topics/yaml-guide.md:196 030fd9aede23463d981faf746e2b070f -msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" -" us while we wrote this guide, though it also covers features that are " -"not valid in CWL." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/tutorials.po b/locales/en/LC_MESSAGES/tutorials.po deleted file mode 100644 index 5222f765..00000000 --- a/locales/en/LC_MESSAGES/tutorials.po +++ /dev/null @@ -1,58 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../tutorials.md:1 99ae22e436b042009833051fac79e2c9 -msgid "Tutorials" -msgstr "" - -#: ../../tutorials.md:5 2ffee614f02343cb94399b8199803149 -msgid "" -"This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to " -"the list." -msgstr "" - -#: ../../tutorials.md:7 1831288df8f14081b13cf52d587c678a -msgid "Beginner Tutorials" -msgstr "" - -#: ../../tutorials.md:9 bc1fd03f560340d68bdcf39455d25c8d -msgid "" -"[Introduction to Workflows with Common Workflow Language: For " -"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" -"tutorial/)" -msgstr "" - -#: ../../tutorials.md:11 47d068326ee34835a7a00ce7e24ef711 -msgid "Advanced Tutorials" -msgstr "" - -#: ../../tutorials.md:13 bcee717d8bf740c49c79200b0c660f3e -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../tutorials.md:15 5e55349fd3d749de964e8fcfca5959f3 -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../tutorials.md:17 77245b1c0ebe437f89dc07b45c5fa95e -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" - From 22702ace6c8a9c71c6bbbb4d83da8a8be4ca6d06 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 24 Jan 2023 18:59:04 +0100 Subject: [PATCH 31/49] Added translation using Weblate (Spanish) (#360) Co-authored-by: Michael Crusoe --- locales/es/LC_MESSAGES/index.po | 57 +++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 locales/es/LC_MESSAGES/index.po diff --git a/locales/es/LC_MESSAGES/index.po b/locales/es/LC_MESSAGES/index.po new file mode 100644 index 00000000..b87c1d09 --- /dev/null +++ b/locales/es/LC_MESSAGES/index.po @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: es\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/index.md:1 +#: a58ca61ccefc401588f91699bc98bd32 +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: 6dcf12053f104cb3a8d23ce8d4f90363 +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 1cc90206170d46119c5756f31a9e8799 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: b54801d84a944dadb4e4637551e3f7b9 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 860afd2eda4847e0a0d8834de3af4aa8 +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: d6046316c84b40ffb5478c90b2604911 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: c3c89ac756a74d9688e179b8718c9bf0 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: 0eb795062b484537b090c4d5c361f7f4 +msgid "Table of Contents" +msgstr "" From c2115d76e07c5015b508db18c19851f15010ea93 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 24 Jan 2023 19:48:24 +0100 Subject: [PATCH 32/49] collapse the translation references --- locales/LICENSE.pot | 36 +- .../what-is-cwl.pot => _includes.pot} | 4 +- locales/episodes.pot | 6 +- locales/faq.pot | 112 +- locales/index.pot | 18 +- locales/introduction.pot | 607 +++++ locales/introduction/basic-concepts.pot | 217 -- locales/introduction/index.pot | 27 - locales/introduction/prerequisites.pot | 257 -- locales/introduction/quick-start.pot | 167 -- locales/setup.pot | 6 +- locales/sphinx.pot | 6 +- locales/topics.pot | 2083 +++++++++++++++++ .../additional-arguments-and-parameters.pot | 62 - locales/topics/best-practices.pot | 137 -- locales/topics/command-line-tool.pot | 62 - locales/topics/creating-files-at-runtime.pot | 77 - locales/topics/custom-types.pot | 77 - locales/topics/environment-variables.pot | 42 - locales/topics/expression-tool.pot | 47 - locales/topics/expressions.pot | 373 --- locales/topics/file-formats.pot | 77 - locales/topics/index.pot | 22 - locales/topics/inputs.pot | 247 -- locales/topics/metadata-and-authorship.pot | 57 - locales/topics/operations.pot | 62 - locales/topics/outputs.pot | 134 -- locales/topics/parameter-references.pot | 278 --- locales/topics/requirements-and-hints.pot | 22 - .../specifying-software-requirements.pot | 42 - locales/topics/staging-input-files.pot | 42 - locales/topics/troubleshooting.pot | 72 - locales/topics/using-containers.pot | 82 - locales/topics/workflows.pot | 374 --- locales/topics/yaml-guide.pot | 157 -- locales/tutorials.pot | 18 +- src/conf.py | 2 +- 37 files changed, 2794 insertions(+), 3317 deletions(-) rename locales/{_includes/what-is-cwl.pot => _includes.pot} (91%) create mode 100644 locales/introduction.pot delete mode 100644 locales/introduction/basic-concepts.pot delete mode 100644 locales/introduction/index.pot delete mode 100644 locales/introduction/prerequisites.pot delete mode 100644 locales/introduction/quick-start.pot create mode 100644 locales/topics.pot delete mode 100644 locales/topics/additional-arguments-and-parameters.pot delete mode 100644 locales/topics/best-practices.pot delete mode 100644 locales/topics/command-line-tool.pot delete mode 100644 locales/topics/creating-files-at-runtime.pot delete mode 100644 locales/topics/custom-types.pot delete mode 100644 locales/topics/environment-variables.pot delete mode 100644 locales/topics/expression-tool.pot delete mode 100644 locales/topics/expressions.pot delete mode 100644 locales/topics/file-formats.pot delete mode 100644 locales/topics/index.pot delete mode 100644 locales/topics/inputs.pot delete mode 100644 locales/topics/metadata-and-authorship.pot delete mode 100644 locales/topics/operations.pot delete mode 100644 locales/topics/outputs.pot delete mode 100644 locales/topics/parameter-references.pot delete mode 100644 locales/topics/requirements-and-hints.pot delete mode 100644 locales/topics/specifying-software-requirements.pot delete mode 100644 locales/topics/staging-input-files.pot delete mode 100644 locales/topics/troubleshooting.pot delete mode 100644 locales/topics/using-containers.pot delete mode 100644 locales/topics/workflows.pot delete mode 100644 locales/topics/yaml-guide.pot diff --git a/locales/LICENSE.pot b/locales/LICENSE.pot index 0460a73e..67ae058a 100644 --- a/locales/LICENSE.pot +++ b/locales/LICENSE.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,86 +17,86 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../LICENSE.md:2 -#: 3d749a78eb3e47c991d603c2cabd1b91 +#: 087fa59ef53947e683e1b0d1097cfa14 msgid "Licenses" msgstr "" #: ../../LICENSE.md:4 -#: 4689ade8475a4c8a9d5e325f072c1392 +#: e134424e12c14d46a8cfa417dbb39dbf msgid "Instructional Material" msgstr "" #: ../../LICENSE.md:6 -#: ef8ec0f072d947fbba997c4b2191abc2 +#: 44fc3047733e40408793ef3438e4a21c msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." msgstr "" #: ../../LICENSE.md:12 -#: 696f3824ca814c9eb314abae51be8202 +#: b2a65a97826d48aa859843a1dbe646a0 msgid "You are free:" msgstr "" #: ../../LICENSE.md:14 -#: 72ebe92edf58434e9d7a4fc6bddf8880 +#: 922b2a5bc70b49e299d0662622aca1b2 msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" #: ../../LICENSE.md:15 -#: 9b403f96d4194ffaab3f309d7d12f360 +#: 51700e62261a4a20a887c6c5ef4d3f46 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" #: ../../LICENSE.md:17 -#: 10b1befd0f834d79880c8aeb70b595d4 +#: f84b26c1e38e46d79fa6b5cdcc7c6434 msgid "for any purpose, even commercially." msgstr "" #: ../../LICENSE.md:19 -#: 9017d0b760bb4370926d511b97a604c6 +#: 435cf52ad40643139c4eaec84b263132 msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." msgstr "" #: ../../LICENSE.md:22 -#: 1faadcaead6748dfb34886e5819af9b9 +#: 4eeaef6ed7304ea8ad815fb8b35f374c msgid "Under the following terms:" msgstr "" #: ../../LICENSE.md:24 -#: 7a49ed3a728349c9b486f3d0b1dbf577 +#: 9295c98517134bc0b8b08e088ad630fb msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" #: ../../LICENSE.md:32 -#: 57da6294edce46eab00e7d15e6f6d4fa +#: c07512980b6a4433944edf2e80a88c6c msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" #: ../../LICENSE.md:36 -#: 8fc8a30cd63c4a0a9d8ba1b913687029 +#: 6a4d80c1331c470facd6ccc060a0cd94 msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" #: ../../LICENSE.md:39 -#: fe59e74a4d024831a6d5cbcfd3e4ee38 +#: d00d862c37ef4371bc40ad101c433199 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" #: ../../LICENSE.md:44 -#: 3ea41d5a14ad46729cabb387a33814b0 +#: 93ba22a55b954a86af163557e05c52a4 msgid "Software" msgstr "" #: ../../LICENSE.md:46 -#: 23751e2552ff450c83e3dd255da56dac +#: 367e01c9a6ad426a83bf5f5374e6a8ab msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" #: ../../LICENSE.md:51 -#: 13fb5eb48a8a434e95dbbb717ccaef8a +#: 565193677802418693fdbc123b34dd2b msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" #: ../../LICENSE.md:57 -#: e262fbd0e7de4f148f31afe39d1cb9e9 +#: a4a99fc7709a49c29482f6e992d9e2bc msgid "Trademark" msgstr "" diff --git a/locales/_includes/what-is-cwl.pot b/locales/_includes.pot similarity index 91% rename from locales/_includes/what-is-cwl.pot rename to locales/_includes.pot index 22d33219..41cc9fb0 100644 --- a/locales/_includes/what-is-cwl.pot +++ b/locales/_includes.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,6 +17,6 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/_includes/what-is-cwl.md:1 -#: 44a9467c5d3b4a128ceade82a521b6da +#: 46f474e1b364495181698bd13ce28a1e msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." msgstr "" diff --git a/locales/episodes.pot b/locales/episodes.pot index 8a04d6ae..ecff4e32 100644 --- a/locales/episodes.pot +++ b/locales/episodes.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,11 +17,11 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/episodes.md:5 -#: 0cbb5e7334a647c3bcae7333ec3ced90 +#: 5b500989fc13480681ecb39954c13fd7 msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 -#: fabb221482cb4ac0a98bbe10943ed025 +#: ff7a3cc03e2048278bcb9af2429b8dee msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." msgstr "" diff --git a/locales/faq.pot b/locales/faq.pot index 7a9282b8..f4ead324 100644 --- a/locales/faq.pot +++ b/locales/faq.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,276 +17,276 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/faq.md:1 -#: 5daa5afac36f46dd8329e5629056384c +#: 38d96ecb6f4f4835a94fce7389f64290 msgid "FAQ" msgstr "" #: ../../src/faq.md:11 -#: 40c8efda3caf4c6089bda3027c522f37 +#: cf04e2bcede444ec84829b20873bb458 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 -#: ee854bcb685941cab45ae7f33b0efe48 +#: 7f5a8ebf64a6457290031a9878fcadb4 msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 -#: a4cdd5ab6fe341a3ad3e3055556d96c3 +#: d2da25aa3d4149c6a839e5a9d260d637 msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 -#: d1f359d47f124dfab23a75b196cd5884 +#: bb7a7c1994c44fd984a3d6daee56ca77 msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 -#: d83ced40605e411c92c4ae38761d7ffa +#: ab649294dceb4701b50840614da498e9 msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 -#: bc8997df2e6746cebc2068534f30ee82 +#: 38a2bfda017f48af91062768c29228d6 msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 -#: 20b6ae57e1cf4410877a60fb3ef87264 +#: 73d6982c5a414307943c5100df766a29 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 -#: 73c66b809e9a4218b624338ccb88a05e +#: 81acda6459354bf08b4f1454b3b2dcc4 msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 -#: 9be72b7d5d604526b125b63148e99320 +#: c06ed26bc9d54aa2803014ba69e9ac78 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 -#: fd96d178901545008a43fa99e3aa6cf3 +#: eb25e79af23e4104b38f6265e677c6a8 msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" msgstr "" #: ../../src/faq.md:97 -#: db58a582e66244468f4d31e9213933d1 +#: b618a3759865456f9ceb02a6a16ccba1 msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." msgstr "" #: ../../src/faq.md:104 -#: 3e70f0da5cd7460b90c1690366f40820 +#: 455b1a1f10044b5c98b7fab451f48ed5 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 -#: db28dc27c82b4b29a7a9a768550bba9b +#: 6b44a7665da14b6aa887224b2fe3c15f msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." msgstr "" #: ../../src/faq.md:115 -#: 4474b16fb3fd4cdc85da931159804967 +#: a05b7978ef76413588e211bd9bf9250c msgid "The second method involves including an input of `type: File` in the script itself:" msgstr "" #: ../../src/faq.md:135 -#: 23c9b2e21cec4ee8ade087e6630f62c2 +#: 6caf0ac2ccad4e449dfe5578ff75ec0e msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 -#: c01309dcd65c4f1080c396e6a9efb75d +#: ffe1586183ab4a3199639b1f9e8062c1 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 -#: 0a36801172fd4e24a04b3ba85cf74e29 +#: a8314e810d564e198e9fad0e32c23117 msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 -#: 433e788ba01141e98ea5a9e73ef71e6f +#: 77c15e3d59c74848b3b6ad85f213b30c msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 -#: b6de2761ce454992904775a06b7ba326 +#: f3d50a6a37494ce9883a4d9cd0ce7870 msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 -#: e36c2d53e8ba40f4a602b489a6688e24 +#: 9d7e8ab5d8864376814d12f10b52c6a4 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 -#: a9310166cb514e4e8824bba7fcfcb277 +#: 93b78d5afe4541eaba53b6ea29150658 msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 -#: f6144f77152e4284963951abaa30adb2 +#: 8bfb650cce844e31a30a6e1773d92a48 msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 -#: 790709dfc2854e4a89fcc4769f84b0f4 +#: 0624c44a35e944c2b463146331c9ba4d msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 -#: 438789c8def549d1b4b8a187d5acc48e +#: 1f4df1cd685e4bd5a695e7ace5a9159d msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 -#: 23ede7dfd5c84492baee1d5bbb9a91d9 +#: 1f057777e7a9430bbbc2036e53a6e4fb msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." msgstr "" #: ../../src/faq.md:229 -#: 37c0474e48164160b23c4094d583d2d3 +#: f64dbbcaac5642cebbd7cbd96d85c40d msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 -#: 3b2be0a4a87041b7a5bda20c6df2ffc8 +#: 71f80d93e08342ad8b6db87ec9c837cf msgid "To make an input parameter optional, add a question mark to the type declaration." msgstr "" #: ../../src/faq.md:247 -#: 886300d2dcff4861aae503d34b0bee44 +#: 7dec6a02cc364c8a9723043a3e8b7d79 msgid "" msgstr "" #: ../../src/faq.md:248 -#: fe393ecdff25428da6cbcd30171c7811 +#: 8a06fc5a9f80481888418234671702cd msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 -#: ebfd4991d917413b858da8b437a55805 +#: 2f3dc891f5b64378abc449947a5117cc msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 -#: 2919ff4f51254e69aea40146e2d911f1 +#: b5324b01d6614202b0fac7026a450caa msgid "" msgstr "" #: ../../src/faq.md:268 -#: 61ed4e87457c41eea31f51740557597e +#: 1198ce319b4847f8b74a14d2ec5248d5 msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 -#: 1e6624104b024eb092682cd0dd0f6a3c +#: d9e2a621f8ae455092120ebb711d1f99 msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." msgstr "" #: ../../src/faq.md:322 -#: b741b8333e104feaa6d1f41fd4476304 +#: 2c4153eb18d94ad7bbad6acab1b5b61a msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 -#: 334673ae870a4dada817857f3a49326e +#: 77b90349be254ceb8de2cf58aa410e6d msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." msgstr "" #: ../../src/faq.md:342 -#: 362f85270df04712b2e2f21c7019e3cb +#: 31e2b62687b84efda4924d7108e23cb3 msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 -#: ad6997f24c7c42fe965b5d7bfd1e633e +#: 8c72738f5aaa4fcd8457a10e799d0e8d msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 -#: 99dce9d60b6a4f99bc39899b7c8c10ef +#: 3a83df07178945d4822e3520674d6308 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 -#: 6b68fe24cbf64624b49ea56fce2eecad +#: 2aca2690fdac4922bfdc9e5a9f2741b8 msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 -#: d23326837eb74e7faf1f54e25f8309c4 +#: 3d072aa6b914445ca8326ffe260b4e35 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 -#: 2e2eabe92670412e95474b25ad9cda4c +#: fb653b6af6a74231904d2d0f850d1116 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 -#: 81f9308adbee4a3c9e585b8e0f0c4844 +#: d3d261dd88a94fa8ae8bf65c39eef6a1 msgid "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 -#: a5d3ed6cac28415288e7fc7fbfc6e8a6 +#: f7125b78a28c4924bdd3fcb37a184ff6 msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 -#: 72f9692803304daf9f846e2b90139660 +#: dc28c1a8e15b4499b4af492ac3cd2c1e msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 -#: a7eb20c817704811b3bcf2f94ec2e51d +#: db57566297534dea82c6f66dd9c14b51 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 -#: 20fa869849ef4b358a11db46111017de +#: 09a115ecb8d2487da88cd31e1bac337f msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 -#: 35032fcd9f23403ca006d62a7d6e7be7 +#: 4537ae8ebd5c49f3857b2cbe81032d29 msgid "The file is here" msgstr "" #: ../../src/faq.md:410 -#: f6d6a4e3691446378c8fb01a2d19f8ad +#: d31aa1c1adf343e8b2b71322511bf7f1 msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 -#: 44608fed1048458e999e13b014327e7e +#: 096f725de9ee4c558d72695a84c40cbb msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 -#: 96ede8a8f1f34786aabd4004bf2e7acc +#: 58316efc7814473383abb738c5c0b5ef msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 -#: 84634a368e704e8d828678785c784595 +#: 2ac3f24fd4074acb8e96542b350d5771 msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 -#: 545c4db9c24f42ee946081254d9ca7a8 +#: ef3c267c3282458f891a76e5d467ec8e msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 -#: 1c1e6d583d5646a8a5c9316dcd743d9f +#: aa97ef90186747f7b9d0aaccf17535d1 msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 -#: cf7d336d444e4f59aa83585b7abb1fe5 +#: bb5bc05d377d441abe02a09e3f1d1a03 msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" diff --git a/locales/index.pot b/locales/index.pot index 1d9fcd30..9000da74 100644 --- a/locales/index.pot +++ b/locales/index.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,41 +17,41 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/index.md:1 -#: a58ca61ccefc401588f91699bc98bd32 +#: 1e479cad716c478689be58d4b4aabd82 msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 -#: 6dcf12053f104cb3a8d23ce8d4f90363 +#: 0afc69049ce0403695a03e30416fd9f9 msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" #: ../../src/index.md:7 -#: 1cc90206170d46119c5756f31a9e8799 +#: 852b4bfd1a374deb803accb90c7fea8c msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 -#: b54801d84a944dadb4e4637551e3f7b9 +#: d702011b81064e65af1fcbd230d9977e msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 -#: 860afd2eda4847e0a0d8834de3af4aa8 +#: 884f157b64ce4787ab8da8f9e674c233 msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 -#: d6046316c84b40ffb5478c90b2604911 +#: fd0133a1a0214ef49b763ba33e282a9e msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" #: ../../src/index.md:23 -#: c3c89ac756a74d9688e179b8718c9bf0 +#: e699c33ef40045528c31d74b2d797742 msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 -#: 0eb795062b484537b090c4d5c361f7f4 +#: 21aacf872e7a444c891c41ca3411ee06 msgid "Table of Contents" msgstr "" diff --git a/locales/introduction.pot b/locales/introduction.pot new file mode 100644 index 00000000..32cc94f9 --- /dev/null +++ b/locales/introduction.pot @@ -0,0 +1,607 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/basic-concepts.md:1 +#: 92c85569d9e746d8a5b7a5e8f9773545 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: 5e501be2f49044c9897f6e8d65186abb +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: a6f5f188f9af4b608b8401996a558e83 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:2 +#: 2ecb1a3a4c7546ba94e560924cfb09a8 +#: 3c0da8bd74824f8b88223c2a9dcc6ec2 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: 7fb9ad094d844047b0d35dc70c295400 +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 303d1a15612846c1b60a4d651f9d1d4a +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: c84c4bde07034846b043c4f281f8e00c +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: d774877d6e4447b7b83d56ebbaf09e96 +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: e8884f39f08c41bab29c4284077fd860 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: 984ac8cee64e4e41957d8c5a4aff0cfd +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 17381e8872414c49b178d91ace2e3e82 +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: c4cdbf2a42644e0eb4eb74512388e9f7 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 7d994284e320413bb8dbb2a42cd16a4e +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: ce92487ca4e3495ebd0693c502773626 +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 0ce512c3cd744652b5feb2d8dcfdb613 +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: dd7d6a1399b04923b25df70abb1becf5 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: ce4c76b46531416bb4006a9c01f45a23 +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 0256a343321447559471d731c86d3546 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: e1235589f24942babe54adaae4f169af +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 81baaa297562452f80afe68657c8099d +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: 0c8bbd88bd8c4c71b19011812e7487c3 +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 3b64da1f14964cea9e5cbf8376578789 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: bf33807babb64befab3385eca4c92131 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: afdb75d374624f4798f358a3dfe7752e +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: bc28744d5fa644218ef55672d726307f +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 24ffb5bfa767424585b6b6c93169de93 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: bd53afe50cc14f2ca428adddb0e60dc9 +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: 35c98c4b352c4f9bb9572c740894dc57 +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: f7fb57fdf9344a7eb0f334aca8d3e85f +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 0dc6a8f19fda4e9eaa80b8e1bd1fc5be +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: ff1224487c35402d8afee6da3803e19b +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 63c2dd9aaec54df088e82febfd7bc49c +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 18f310d11c9b48b4a447b6662446cd3e +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: a3922283fdce4f99832c816626d5f098 +#: 19245373c2e84793a72462b7d2fa1c34 +#: 7c3ea7150c7d41fead10ddf2a6205ec8 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: cf39d3563e344ad9b31d5268c4069972 +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 97b0113a847044b98f79b5e00941f4c3 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 8cf4edbb4b344ac7b3eae86ed52beff8 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: c1dfc170fdf54c9e846539a5170f204f +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: 778babbcfb2648a1ad7a7ad8f80653a8 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: 23abed59f5d44bfb96e8fa13aa213b83 +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: ee93304de4e447c1bd5626e72b99b6fe +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: a79f07e33fc5437c9fa204111d0290d8 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: 3cf08b553a814478b4b2c6c84ebe354e +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 98751950a97f44fdb16e826fece810fb +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: eac153b881fa47ab8bb08074dad8eed2 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: 806ff7b185d74538a9b0e20c6ad84ffe +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: 1f9573b6cd45479bae2481a251132d53 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: c3995fd5588741148e3b2c91ca011ca9 +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: 8a67b172ce524aa09858acd9d1a62762 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: a567e0f952bc46be8b82d0a357f2c209 +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: 21d3bb850bb14fdcb6d4c4a15c9966b6 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 62cbb29459b24e9fa83c7cd7994bdf12 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: aaa319d4446c41ba82bf925f29f7d9dd +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: c49938a0100a4850b67d067a61304d01 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 91e986d0c1f44d7f9c3b32366160da6a +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 301c5a3baaaf46bb81bdc25b53a31f23 +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: 1664589ced314daebfb163e6424f220f +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 1223fecd61f34ad98ebbb7e45eaf4ac7 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 242c496599d84a64959db275ee1e212e +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 9b749d47f48341cb9ac8cd14098e6c47 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: e8ec351d7b79447bb15f4d4518b8de87 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: 58d5613243914dc8bc4ce88676525783 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 731a6c30786f43d88160f9642cbb05d2 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: ca2088eb9565429dbc1ce0b28b2ef1fb +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 5ac9c6bfb50b48878aff52f1194e53c4 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: b8d0c12ff07f4269bba87cd653803345 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 83780c1b43f744b4ae87a917b26293f5 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 2919320c41e94930a0aa9bc6aacb5a87 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b8e799c075214d539aa0a7c04dbc33c0 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: ccbd51a29ca841efb74c5e0a25d1eb87 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 5f3330c1e15a402781c3325f9d3dc779 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: 314fbc9f866a405b86e7bd704781dea1 +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 9434e3680aa9487fab9ddb782c6ff3d0 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: 2ce0bda38d814b248a2c23ebc26bf462 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 105c3be6f5f34f4388b9999603275bb5 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: bd378c8483a14c93b5fe00d76e5b0a06 +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 5ace5416560247c7a3304c41caa000c6 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: 5d7a175b3c5a4f888daf037672211d61 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: 4e0c0c345527412eaf70e8efe67fab8f +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 6dd8379682824d1397c48ac10db4b894 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 57691f7bd87741d68f4e1a963da91654 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: 13a4d71f127b4bd09c12a37752d27c8b +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: a574ed30000541b2816fbfe66b32c314 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 9bb9c9052ad14c7c9fc0275c8f1b651b +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 5afcf2e79ceb424ea0a570797a712321 +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: cc5b91b8c5b14a40bdd09d3bd45fe9bb +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: d5e36c7827334fc69498459db5137d30 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 39d3eff64d004a0f8257d61f2a90b186 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 19946d0d9a6f42d487537273225b91cd +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: 66048204601a439d8245455c48b08826 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: dcc41d0ce48e42a0ba209ca1fa37220a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: e2ebe32f12b74608b35217cea30cd0e0 +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: 37a4f461b82f4e48948c5eab400b14a5 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 371c6801e92448f9875fff60a509f509 +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: e3fb51cd196542008cb16458fdef7c1f +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: d00cd96d47c6450a8c0955765eff9ac1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: e06fdf0744344d0193b99791b9b94c7d +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: 6e2191fbb8794f83a51897028a2e50f7 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 931b6b49a46d4d5581a05446ac2e9a7d +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: 5cb281f4d0ea4163af0f7203c150345e +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: 4e6c4c2b6bae49a2b2d93bc95538c7b9 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: b37ba76e0dd940559e13543ea241376e +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: 22d7ac26f2ca41b2aa141fd4774b6f5c +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 15033ad0574d46b2951bb2121c80c462 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 2b2fc79461674b9ebdef49750f7fb319 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 8b11c9920b97427aa2d29498664e24bb +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: d11de6ee015f46c991fbc8b48cd1fb60 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: 71adfebd042a4820ac533a2e6e07c0ca +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: 8f199e6778a84ba68d385b42169f6b26 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: 28ec66afdad24dfd871ef1a2686f9976 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: cccb84844ce0453cb77ce3db65ffbc1b +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 0c5a431846f241829975552ef8dd9c32 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 8e383a7ea5b54c56adb9cb0c6ed6c179 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 98473d00529345d4989f0f5d2101da1b +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: d105326cb76b455d907c283a509f038c +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d4d00a573e36474f9c915563d4ea8709 +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: aa8195d109974f9da3b9da97479525cb +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" diff --git a/locales/introduction/basic-concepts.pot b/locales/introduction/basic-concepts.pot deleted file mode 100644 index ceeed500..00000000 --- a/locales/introduction/basic-concepts.pot +++ /dev/null @@ -1,217 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/basic-concepts.md:1 -#: 570f94ae2d4d4e19a9cf3a9bbceba835 -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 -#: 67f2ebceccce441caa8279166f8f901d -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 -#: b7c949f867b8475f8969622abc045729 -msgid "The CWL Specification" -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:2 -#: 744c9501df5d47dc93962d217838f312 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:21 -#: 0a0131d9b3be4af484b43fb3d12f804e -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 -#: 6c2f26b24ece4319bc9ecbd147f928e0 -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 -#: 0305e3bc2de04b15a64a1b1c1188da2a -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 -#: 21d7e31a2abf4d36ba5acef1faa76b97 -msgid "Implementations" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:39 -#: 1c7e942576304977954be9ddcc9b2927 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 -#: 920cf7f770054d87807273e8901630b4 -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 -#: a4c286729d884042aa9f6703ae958896 -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: ea9dc3c2e83246508ee111cbeb5e5379 -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: c40f991cf70a4eefbf5b04e4089f809d -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: b3a1d362a96b426992cc37c11e13e09f -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: 201d5104011e4178adf564f969e45951 -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: d2027b38193f4252908c9f1fa8a1999e -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: df6be4b832ac4bbe9ef1eb5fc8cfc1ec -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 521eb59a379444afa0478b4536923f28 -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: b600a21001d24203855b9d972365de5d -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: 60b8285020a34af9b8a22688953899e6 -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: aac2f76a1da1470cab9ff221c35134a3 -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 1adb2eda9c8a4e2493872e33a13bb77a -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: 08847ed6cc8d4b76b23fe54117ecd929 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: d5fa5caa377e4cac9cb9736d54ee312b -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: f1c84c485ad9400aa80dd46eb5c75241 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 500a1a4565f24639ba5e248c382b2c45 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: 1b407a21568b4c4da8a90d3eb33611b6 -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: d715b520274949bf9f9e3e7235f6d3f6 -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: 5c18ffe7e7254167a02be50ebab5e285 -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: b9cdc830853f45bab2876305373f35b8 -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: 6d839e88664f41f0b5d01d38053ede18 -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: 3e4b846a939a43929c4a45af1a7eafe8 -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: b19094f1044648718b9fdea72eda8994 -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: 33191f1525334cc398892bb867135b42 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:180 -#: 6fe0b86d8a3b4bb0ac1f075fbac8988c -msgid "Semantic Versioning - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:181 -#: b206be2c6a5043429a1213b2989a0f53 -msgid "The CWL Specification page in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:182 -#: f45e3dc2b0a74948a0977c47aab8db4a -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:183 -#: afaa1ed8a0b949959992d4f4d7e00356 -msgid "The list of Implementations in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:184 -#: 51073c8b56864cca84600f12048a6036 -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:185 -#: 1215f39220b441a79f56cfe7cd61aa92 -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." -msgstr "" diff --git a/locales/introduction/index.pot b/locales/introduction/index.pot deleted file mode 100644 index f4ae1f30..00000000 --- a/locales/introduction/index.pot +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/index.md:1 -#: 6c33d560fcc64807a04e7a1536b1032a -msgid "Introduction" -msgstr "" - -#: ../../src/introduction/index.md:3 -#: ad616e9a47d14c5bb4532e5266d61ff5 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." -msgstr "" diff --git a/locales/introduction/prerequisites.pot b/locales/introduction/prerequisites.pot deleted file mode 100644 index 519e8ca7..00000000 --- a/locales/introduction/prerequisites.pot +++ /dev/null @@ -1,257 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/prerequisites.md:1 -#: 789e7b95b23d4bdb8398d691587613ee -msgid "Prerequisites" -msgstr "" - -#: ../../src/introduction/prerequisites.md:6 -#: 53432372af8c447cbeb5f05892daee72 -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 -#: 36f42adbc26f42a891d996f8b9730589 -msgid "CWL Implementations" -msgstr "" - -#: ../../src/introduction/prerequisites.md:14 -#: 090df41a03204aac91aa7f663c6a5209 -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 -#: 57ad125f7c2e4f01982acbabb1ff3d80 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 -#: edfd6bf214d042feb6662b1c2d2fa48e -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 -#: a44cd70295f5442fb6651d85794528ba -msgid "Linux" -msgstr "" - -#: ../../src/introduction/prerequisites.md:25 -#: df31f7835d544160be90401bd20993a3 -msgid "macOS" -msgstr "" - -#: ../../src/introduction/prerequisites.md:26 -#: f5e9ef0126f74353bc4c30a6e92bd92a -msgid "Windows" -msgstr "" - -#: ../../src/introduction/prerequisites.md:29 -#: d11b1c901d004a10a7b8cda2e727bae9 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:35 -#: 37e363cb5987436d86e5725a63984e5c -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:41 -#: 1a19bd057d3c48679e2ae844c6b8291a -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 -#: 2a18beeff42d4cf8a4315e4a171cdede -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 -#: 17f353c8e861492d91e51b78b5da3351 -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:62 -#: 5f178532a9004163b795c1433248eb77 -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:65 -#: d2ff1f8e720f4bd49912ccd7040f2ccc -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:67 -#: 77e4e1e5b4764d59a990b43ed93a7459 -msgid "`true.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:73 -#: 22b4c40f082d4bacac051617b617cbae -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:79 -#: 7f97cf170a854ce685bae8f30a16572b -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:84 -#: 11fdbc38c5ed45a4976e16844729a3cd -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:86 -#: c513823812a5423da694e85a20f86506 -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 -#: 7be568d02d7e4593a1c0ef719d0f83ac -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../src/introduction/prerequisites.md:93 -#: 36ee569c74ac4602a51818a92c95f031 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:101 -#: 06defabc17634ceea15e1f4523164a23 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:104 -#: ac847d3d1587499ea6e1b3796e16282c -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:111 -#: a4d5291859bb415b981a7dd6dff3c313 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:115 -#: d80356bf607b4f7d9572b925c69163f1 -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:120 -#: 54ddcf5f932c40c4bbec2f88114e6e20 -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:125 -#: f159836854c14187929cf24f716ccee0 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:129 -#: 728b24fff1f14726b27168dbf46e4e7b -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 -#: 5590cd84de1c4f9382ab37644a5adac7 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:137 -#: 5a066c4dcd034cfd8902ae01128134c5 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:144 -#: 846f1eaf4f81477c84b885f7c17ab030 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 -#: a972f3ea3b5f41f6b78f682a42616197 -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 -#: 3165d673bd7341518d2b259932917b53 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 -#: d23de68e21e1429886b3814af9cc3104 -msgid "Text Editor" -msgstr "" - -#: ../../src/introduction/prerequisites.md:163 -#: 9538d8b0944f4e72bceec9ebf1fb5832 -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:167 -#: 2e710620d21f44a0a036431453ed5e20 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:171 -#: 25c6c7a87e1847f9aec1c32cbc83cf4c -msgid "Visual Studio Code with the Benten (CWL) plugin - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 -#: a90b90e926324cd687a29436e82eef38 -msgid "cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:174 -#: 91a2b9d7d7b642c2904bd55d29690254 -msgid "The CWL community also maintains a list of editors and viewers: " -msgstr "" - -#: ../../src/introduction/prerequisites.md:177 -#: e0cdb48ef04846cd9a39008260b18777 -msgid "Docker" -msgstr "" - -#: ../../src/introduction/prerequisites.md:181 -#: ac55bc8b751d440086043c4af6776d10 -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 -#: be04aba59f3c40f1aa90316090792441 -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:191 -#: 2d4790bd46124cd8be789927c25fbbbd -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:196 -#: af2e128598294dee9330002a2f7bfc63 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/prerequisites.md:198 -#: f4ffd0d89ef1406f9e957a05a4172c57 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:199 -#: 00fa0dd045054fcbbe3322e10e591430 -msgid "The Python `venv` module: " -msgstr "" diff --git a/locales/introduction/quick-start.pot b/locales/introduction/quick-start.pot deleted file mode 100644 index 62c7c9fc..00000000 --- a/locales/introduction/quick-start.pot +++ /dev/null @@ -1,167 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/quick-start.md:1 -#: 1f7df6c4ef354b4284ffca2f01ba7a40 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 -#: 98a2ea8175314bf5b6fbdd2464402c82 -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 -#: 924b8fd198fc487f87a8de4948261bee -msgid "“Hello World”" -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:2 -#: 1d89d9d6798a4e38adc28680ceec1a29 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/introduction/quick-start.md:12 -#: ca24ba5ebb324a90b34fb1b28468fbcf -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 -#: 7a3bbeb141914c0daee451f2bca9a081 -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 -#: cdd3578d507d41539c38a601701e8854 -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 -#: 767cf30acc9d4f81b8d34bfc90a8891c -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 -#: 8acd83b581f2499fb640153186711660 -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 -#: 46d1f843730a4c848a327de9a03c04e2 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 -#: 939e54e81c304d21a4eb33f99407ee50 -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../src/introduction/quick-start.md:47 -#: 4db304a983cb46fe917563a1884659cd -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 -#: 72d657288bf248b6a53080e6295302e3 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../src/introduction/quick-start.md:53 -#: a03263ff919e4777afdca4fc20efc673 -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 -#: 2f6d2f41de974a469babd97d1106608c -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:62 -#: cef66179a76a432c9b0c1a49b0f6bf69 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 -#: 133d0f054f784d7ab5f2fd5f028d80eb -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 -#: 454aec8aa868430da0449434df741b21 -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 -#: 5f7a1d2d705145a58fb37d6b7fe66add -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../src/introduction/quick-start.md:80 -#: 18c580026a2346c8b1e020fa9b2f3f8a -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" -msgstr "" - -#: ../../src/introduction/quick-start.md:82 -#: 0051eb403e43451390f5775976d11818 -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:88 -#: dbbb23a79b1143a7aa7c91a1277851ce -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:94 -#: f0ad9eabc2c04cde941bf78f0bfcb641 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/quick-start.md:96 -#: 0e14c76da55e4501b6fb8ed246a344a7 -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../src/introduction/quick-start.md:97 -#: 6e813c00aa564fc1a407cc7aae77475a -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../src/introduction/quick-start.md:98 -#: 6029a1f35b10455389c63c680a468d3c -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." -msgstr "" - -#: ../../src/introduction/quick-start.md:99 -#: c1312d1ce89e4a48b31597c5a8b2e603 -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../src/introduction/quick-start.md:100 -#: 18cdf73c71574ce9a74c189aeaae971b -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../src/introduction/quick-start.md:101 -#: 5488abc1abcd4aa68e7e8a702834c619 -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." -msgstr "" - -#: ../../src/introduction/quick-start.md:102 -#: 4cf8dc5e58244810866649259ac13f9f -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" diff --git a/locales/setup.pot b/locales/setup.pot index 10900ecf..961f7927 100644 --- a/locales/setup.pot +++ b/locales/setup.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,11 +17,11 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/setup.md:5 -#: 29bb5c68be6042e5aa4a370e9c4024b3 +#: 8395100e210f4ac5a87cc2aeb3d7067c msgid "This page has moved" msgstr "" #: ../../src/setup.md:9 -#: 8bcf31398c34491da1a1590422a72cbe +#: 1e47ac8e393541d19b9499e307fe69e7 msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." msgstr "" diff --git a/locales/sphinx.pot b/locales/sphinx.pot index 0c4554c5..f8448bb7 100644 --- a/locales/sphinx.pot +++ b/locales/sphinx.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:27+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,11 +17,11 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/_templates/sidebar-nav-bs.html:1 -#: b896fd5e11fe4674a7f46ad489476692 +#: 1c343f1abfaa4e14b7f1b645c77c595c msgid "Main navigation" msgstr "" #: ../../src/_templates/sidebar-nav-bs.html:3 -#: acede4e78f7e4aefa0ad9425928cbb42 +#: 3c55f014feb3477889c4df5a158a8804 msgid "Section Navigation" msgstr "" diff --git a/locales/topics.pot b/locales/topics.pot new file mode 100644 index 00000000..1f40bff2 --- /dev/null +++ b/locales/topics.pot @@ -0,0 +1,2083 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 1a006f1604c0405aaa4b93e41edc5184 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: b61b4d7ed53a436486c1429987a2a21b +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: 1bf9e65f1cc249ee93656a53ddd354ca +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: 3329dc69c32f4b9092b196d79ae5d0c1 +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: a003a3d1de0e4dfe8c777905e55fb9fe +#: e2dc24c683054cd785326de2c3f3f136 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: aca6a0cd24a2411c8cfb1ad392f6d315 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: bcf37e403eb041269e351d7f98a19587 +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: c5f68f8a9f34445ebcbd5783f96cb046 +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: 4eca90c659ba43158db373d36ee681df +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 7474eeb128624dc4b1e980dbd0f04ca4 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 0c520e5add334609a1afddc559abe19a +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 125a69207077425fa54f346abc45342d +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 6ca38a04844c403b836942b2f2f1e1e2 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 1da05be0d97d429a84085459ebae54cf +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: fb1b2a8c54f34d78ac61dd4b5ffd9063 +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: a8b1b5caf9904fc5b9eef8c110474b84 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 42a5a8cb3b284549aabb817b73ce5810 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: eddd878eb0324851997de2a69bcbb43f +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: b05c8ff667174f6798feb811cdd3c41d +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: 9dc16d1a6b0546cead6967f5e9b1526a +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: b8bf85e8523a4553a58face698aa863b +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: 6fb9a1a2ffe14f39b01af8736a9698eb +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 0a935aa93e554c0987af7349f94ccd3a +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: cadb5982a13e4621807ad976cf9b1524 +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: bd7ab2cc6234458181e9b99938eba824 +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 7beb72d7dd5a405f9be8b6fb6a310f10 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: e5942c4d4b4d4e1a8c0e9ed3da80960e +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: 5a5dbc9b9d2242ba8d15ecf39123694b +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: dd3016d33b7d4340a09a7c8e5aec4f0b +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 45d110a660b348f58a1107476df18cee +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: 97a5b141592e4415aa4acef4f6228045 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: 85f624f8879348e8bb368ec2749925bf +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 20a851dae87941c7975173ed9cd1e360 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: bb19e1b689564a11bb9e72d5f82cf3d9 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: b14199173add4585be62c4e8278b49f4 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: 9e883f18843a41d7b10102bc11655839 +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: fe3a1468aa864742b92c6e8f4ff1a38f +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: e9dbf14538404cceb02507962a173ee8 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a650a7dacbb547db97158a8ac2c9d0dc +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 501217b98c424a319e70ef963de506f6 +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: 7143809471454e00880ad8faaf43f141 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: 7ad86e42708a465980a56f735644de9f +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a8f29712337b4d1daf3190cc8973b8f7 +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 534843389795437991fad0b5a702b483 +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2052170aa2624feeb2253477895aa838 +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d5ed098a33ae4c1ab2a30eba483ecc6f +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: 2b55c028602f41babb6e535b425ba5dc +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 47408669ae8b4432a43d763dba12a466 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: b2e5e925971849a09a8d54d9c649a32d +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 9a39f53bdcc94904a90effb507767645 +#: f296149bf19947528b134b01a4d7ce81 +#: 965fa9769dea4ac9b3dd252e0a3bc603 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 79d8ea95f0c34585a3dec4f83453de60 +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 4afab699247b4f619702c4086eb1b6f3 +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 693b91423f004118b806bb8ee7952eaf +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: e4a25f04a6fa4001bb1e58cb775cdd84 +#: c771cbc64607412a9164c28934e9e0f5 +#: bdd5a3eac1e3436496e05a13c4f06073 +#: 1e62b28ef0184081b4d6e53f34b753e1 +#: 33edd6deb38740ed98466b6e023b0393 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: a3a8bcdfadc4484ea5e4c13a25b2da85 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 7800570badf149b3bb1f81d470dbf4be +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 496313f8ec67403ca78ba66130df261e +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: f7cc0d1ac5dd47658093cd0360f90329 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 0d563f15c1cc4484b6b2955bdc70e1a9 +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: 06425b6cdaf244b198fdde312e864190 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: 26c3762a637a4492a6c12588544cb0a7 +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: 221433aa39104642af8afb70ebd08576 +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: 197bf36a5d7741b3a9ac56c19d4a7686 +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: d9249cf936d24ab3b3fc508d17d94745 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: 2ff7ce81cd3a492a8549484ba8d1f135 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 2bb45c56e2fc49e094be2cf742222e67 +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: e2a4a531c6164f15bc711618db058f52 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 90f7960bd24d4481bd05da1d61ef146b +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: a51814548e44467c841ca65b2ac63b2c +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: fa13573d9c174ca1accf20a449e5984f +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: f2912b17e3be47b0b7186efdb4c4010f +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 4d9c95d18c1a4880845e7194a99aed3c +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: c656a020978f465b85b8754346ea5b6d +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: ff4d0b6bc0264650a21adc811b8caf4c +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: 77e00be2c0984465af5bf501b4031f32 +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: 3d7b7238be974c0487f219cb5c030149 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 03a62f421c8241779c0e79f4dbad96cc +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 31a85893835748339b6c84fb98fde14b +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 08d9ecd7d3294c5b9dd4db228a1d8d5b +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: d94d6c69aaa64edd9c75624286713c2e +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: 020019b8aedb494fad022d19b7106f83 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: a6b66e0fc0de442e8f72f0d0c37c7e8c +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: 48b7d9ddac2940c0815e5c855bfca6d9 +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 894b843f9c064d56913e1a8c48093314 +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 2319e845caee41a3bc5888c3f1fc28d1 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 9ea661d749db428eacd2207dc7a01e36 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: 4ff76250f28144a4a9d8807a9d4ed3b4 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: 7f9f2df357a740feb89bfbcc44ff4d61 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: 12633ed841dd447a8753faeb4f9e5096 +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 4db64481d38c4896a85a8f6038a9931c +#: 1b4ff3eeddde4a9a8018235b9d706567 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: 50547062ee404e2ebeae7eeb54b9de4b +#: 88933bc02fa84412944673c3463af1ad +#: 4fde39d8a50e49f09bd28a8598760682 +#: b933cbf847d94c5fb8471918ce8cb4ad +#: 0145c520b85a4bc29302bb654f08f23b +#: a3e322ac8a0d4e2ba9bfbece6b5ae64b +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: d9b166225120432f9a2bf2cc7b6ffdfe +#: 28f8ec2fc5c0436aaba19e9d479aa466 +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: b866a0e5897e44329714f4c55eb20d2e +#: e64b5027878346d79f9ab52b3d3b916e +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: ed38ec582fbb48ff9f9cffa7962ef515 +#: 6cc0788250624fd69fa4e3881191ab7f +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 17eefb5f38534c1b87116c3a061ea1bb +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: ce0572fc81b343e6991c88ca0195149a +#: f8b77ad06ebe43d7b03b2135737902e2 +#: c7953486c99d4c7898c0155a6085dfd5 +#: 46d99b1f7f0747479bd58486cf7941d2 +#: cd0a797b3619404f964ba9efb33756bd +#: 528cd5e0d3994230b719fbfb39b1f13e +#: 324241aae8ff4505ab0467f2a7f27fe2 +#: f4086b1ad2e44c2b9de2636f8bc1eb90 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 764d7cf3fb5444d58dc9e0eb6b8fc649 +#: 0450a4b8de3046998d30ce1f09c10daf +#: fd6bf79cbb694dbb89e8731aed733e6c +#: e6048a64e09d46099132fee40a2e0644 +#: 9512391eb96440bd8e48c3754821e3d0 +#: 3e8669bf4a6741f9aba170864b251dac +#: a02ede726d3f4eec9602f72054c0d963 +#: 4ed593dfc39246789f1e4ecdc742323b +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 304de40206cb43d7b651245586cfa55b +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: 7855471c93bc44aabb1a2b9beb52b56a +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: f0452f324bfa451f9f3264f9a55e0e5d +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 6dc476cf8689465ea3993f49a9eead75 +#: 4dfc0be21065471d91def850bc2528fb +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: 09d69778a89044099b3e5d7cf02471bb +#: e3077bdff0dc4dfdae60eb60f3d66d8b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: b28843f7b57745db9cb3648ef23fda0f +#: 6a745fa266dd42849c95410775b690e0 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: be00ed49197f48ecb7cb244ecc214369 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: 90ad2b27f97b4ca089cf23a073cdf17b +#: 38d062892cb04bc7bbf0b56f263079e1 +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: c2d2756d617743b886c67160c2face21 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: 8681600183d1429cbd1b15639e1a222f +#: 1d49cd7337004fc38f4e8e9aa4270481 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: 24b7f85116cc4d2f904600555aa19b8b +#: c401a68b4f384d3eb13ab3e89a4a7195 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: 0e1f9d22d0714bc5b80e420f63b34cff +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: 5fed95f16aaf42d4b41c569d9546b7f0 +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: b539a931f31d4cfe9d72aa5800115fb2 +#: 48e497c024bc4c38a86dd027aaa4fd2d +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: be638c80121948c99cc9fdb67a5d291e +#: 1fd8fe769ba8497eb8a9520af91ea33e +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: b5f3ad78a233411c97520c1fffdec18f +#: 7854e46c7fd24afd9c1942808521bee1 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 211bd57896494fca9ea8aa2fc142eea2 +#: 28ec0718d3114bfdaae4524c009da944 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: c6a421f7a0214d89958d4c258b58aac8 +#: 07bd0bc74ad74187bdc24c26041467ca +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 3afc146cde2e47d5b52e62fbd1f37426 +#: 2225f5acb44a4ce0ad16be5c4f6cba48 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 9acd61d4d67a4d2c82171a79462fb458 +#: cd7e7fea3b8346268618c31b70581326 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 140e449e46a84e3ca1a604176e583f44 +#: 3d8b717d4568458eb53b0b91695b3de8 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 76f35653e34b433d8e9fedc6d12ce856 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 1a2edf61fda8404689e3c0a7389d7d02 +#: 3bced6d84fa6453195be82dbc6d7ec83 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 0b5aceb6c9d24bd9bfe95cc04fdc61ad +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 3523cc46c6324fca9053d6b1dd8c7495 +#: 21eee2c1cb6b430486446d223dcca0eb +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: b4f126415048402ca388c4c63f34ebe5 +#: fdf588cf8cd34d60bfb6cece3ef859e0 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 1b494245c14e4e22918c43ad9f26cc8d +#: df4d781178f2465b8a421651bdd2f66f +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: a88008a23ede4ea49ffcaccba7029d31 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: a256b51f1e944b7d9659b945d8ab05c9 +#: 23bbd631e73147e3af561eb4a14d2d6c +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: a446842e26e44781ad10cdaad73bc49d +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 3cc10263ab2f4dbfb6ccb12612b89cf1 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 995f6af5fc244293b34f5d840f01ce1c +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: b556a1d134764505aa25003d79a53e88 +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: ad23da5452bd46248606f6799ce93db0 +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: c63036ac68344465af6c7756be00b60b +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 2f7f270b0ac24f2f8df506f5dde72cf7 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: f49272e5e4c1491eb59c79d2dfb88a86 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 8b50c892d36d4d178ec4268c7c13887d +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: 9d22117a6f5a434593d5144bf824999f +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 4fbc454a144a466b9dd7ff74903fc5fb +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 281b129a76a24b0a818092acd1038757 +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 4dda6ca233d54c12b6ddceabae198495 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 59d87fecfd7f4438b68e0bcdecdcfb46 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: 0f7e33673ad349e5ad41a078032e5806 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 77a7141f897048139ef3785b5f870b43 +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: 14ed183bc7e346598921445c0dea11e0 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 9406d05bf0ed4774af50fd66d24aa299 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: f5a9048ef9e047528c291505ef9a2c12 +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: 51e8c5a231eb45fb8c15be49b37a7bff +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 860a6f01ebac45938abd220758fd1109 +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 32155f96d47f4d76998a401aa9e9591f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: a62bbb9251794560ace0e52be3d9ebd3 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: e301af8f675444c69cfb6b578c02fdc7 +#: 3da1dec243994409bd764b133d4fc243 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 82c6efcfb5d5410eb316399b7c4f638e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: 29c3d25c657340a1bab7123a166b78c2 +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: ef8e7bd7e944429da78474d2fc5e0348 +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 08dd50bc6a5942ec8f3b6c201fc4497f +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 78c51215a68f40b280cc21d0e412eacf +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: bb8e2203374a4ae7b833c543ecc563b0 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: f34aa1e4d08944c497602b2a35f38a50 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 2932972efc94447987b02a7707c62656 +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: 968f4e83c511425d8faf4c8d0f18097e +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 2eb89bdbaee04a899a961a7b87f0aef1 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: 3781fc7cd22d48bdb5aa4abc0c93b06f +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: f4af4a85efb243728d2ee783393dce14 +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: dbf8350f003a46b984b7432160e6def5 +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: db2993fe83814747a52f9db0b2fcc81e +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 39fe18bf5d4b4539b2f98e3bf0feea2a +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 58e7b0e7d0a149498e846dd2790c0eee +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: 4b78c5437904492ea3e692372d2fc163 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: f2626686125d4ec29fb2338373b54c93 +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 46327aca33cb49d1ba61149e94884991 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 43f2e7020da94f77bce4e1f852ab11f1 +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 8342aa3f84624325aff8f7f4de788187 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: 2d54f11f99b245e5b2802b984bc024a5 +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: 83a357dc06b343549876035b03b8c5d1 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: 0461538fa12a44c5a9d230a928ae930d +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: 2b2552958f404447b711d09650d22395 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: 82c97e60f8634bd6b4d3e88524722412 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 0ae1393a80e94b899023c29f4af6084b +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 74339f624bba49d6b68e1dfc4724f673 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 3a4473864ec04d2e9a0d550b2051f717 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: 575661b36a2040699956f897bd6cc614 +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 3d18a704f5a94e2889e847c32a78aaab +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: fceca2b53d0646b2ae9f1cf9dbefe2fc +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: cba49054785b4ec2a7acd3aaa2e165d8 +#: 647c0e302af841d7b1789447281d7344 +#: d23de44d5d5b4bc7b32f3726afa97500 +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: dd867685663f4728b9fbe446a9b14a3d +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 67bf2c2cbbc44f6eb870af3a3a852676 +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 94d66455bfd04697814495e116176ffe +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: 39a9d3583f29451d8035158c54266ed6 +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: eba6af5cf8224d198fc04f090362307c +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: b48377cceff342e793e982c9fa2095d3 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: b64ef70d944c461b8ec7219e14e47795 +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 73cd08a2226f4cbe99fcde2d3636d640 +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 3c33bffa2c574ef888b041c1e6735b8e +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: 23bd067b32724dad9daba1e924757d86 +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 1be92fc3d0b44ea089273cfcd47318ef +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: 3d08125883b74f49bba042ed58d34648 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 7636c7e8b6e04d7089ba1cb10c4c475d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: e1c95ce96db043eb86ff9b3ae595017b +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: e6588c4b8fa64959b2dcac52403a6415 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: e7f85cb69a5342889525fbb81b44c86c +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: 71756719e0274300a839b38c8b4ea986 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: 88bf75fce3064eaf823b5d88be0ce053 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: 60374713dea84fff92b89b4ebaa8d7ac +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: 7616d5ea746f47ac972183150b97e8b0 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 0ca022c095334ec4a9fe41cb732e11a1 +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 1c807f8fd1c540ae8802092fbcec7159 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: c51956eb3ece432ea0ed5b676b2f037a +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 45e6ab3a53b94f5b90136d68c1c0e479 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 7e05dc23d6be4428b4a414b3a65c4727 +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 96e7266ef25b429da42337c3582cc201 +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 9cb6959a877f4590bccb977416753410 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 7b54a3cd870d4b038dff685064bbca1a +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 0d661c96ac2d41ee94641a397aa3bdf7 +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 94d39b79923a4a65b1a6ce5c464528c6 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 56801121f70b4cb2ab6207e254ec8bbf +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 42418ff882d44c1b9584fb9f7887f744 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 1118de96d202444d9bb4db74ebe4792d +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: aca51d371db84aa79418c79a18310055 +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: 3473e6d2942e4546a2c1590edeb502f8 +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: c210ad12f61047b68302e67da9b5dae0 +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: 1c15cff5a4614d88a62c8d2df97029fc +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: 4beae917368545688c01a4a929685cae +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 4f4f63b7107e4dc194760802c4581c2a +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: d942035c4c914ccb9de75836af9761c7 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 0e9064cf55fe43588053d37100634538 +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: aa1dcfc618e74a53b3c579380e5e1558 +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: 3ec3f4a2d1c547b18780db17fbff060c +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: 21e598983ce94d22b9d40a77577a6608 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 62f79a2c055b455d9626ca5a18d1bd72 +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 19c2b9b13bcc480aa7474301422faab3 +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 17bb520489a74f64b76ddbe2ffedcb5e +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 9e2b97aa3bfe4eae8524b325bf2ea3f1 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: 028c844ef208450f994b3949210ca996 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 2b758e44e4be4fdf89a5897385db6c59 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 16395173b7ee468f85ee8450493504de +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 51e2e929dadc41a78cea98f779e2e2a3 +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b757d4b151ef46fa96897bf00a0d9ab4 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: 2f2f46a81e8946bf8a9b48a5956c82f8 +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: 75177c797c704385bfa5ce86e03266c9 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: 4d05d16c3cb74eb291da7586fa859b90 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: c115b7ed044346d6a9c4c06306ee82d8 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 8f83261e3e91424b9a3c38280c643f02 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 269af269348e4da5b93cb25dcd10374a +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: c376ab464fec4ee78a33d42dfed5dc1c +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 53d468d14703494699478e6847d82e34 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: 32bd7abe387e4999a0864f6e6a48e435 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 0712e952fe2442daa9ceb0cee79a3ebf +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: ef2b8db0c8d64e41b839b47aae34d0ec +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: f9f45dcc2bcb4fd1a1021d2843137fa3 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 4ffbc016a5344e6e9272793d921e4900 +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7118718b98c5488c9d9a54e5ec84c055 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 20fe8fa105a84171972722158bafbc0d +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 836fa2a818854cf9af13d674f5bb859c +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: 5d56e1ac063d48c2b140a72db9f78540 +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: 0166655553ac4d8fb868138936176986 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: e43fe4a9340b458786c51499c75b5556 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: 0ba13966a1364d4e9992b5cfeb6871d1 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: feb8bce610be4a3a92053f2e2e5aab76 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 0f5fd76c57e7412097b4ebdeb074f2fd +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: b645dd17256543b0a42d231171140c95 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: c8d5743769bd4fee93f77a52ba318883 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: af6cbb89b7a84bf78b7443b6746484fe +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: ad9394b163a94340975a66ea2bba7094 +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: 677bce1f24f449beb2bac5ed8469f624 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 4c0d14a24b354feabf4b6ad4852f9543 +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: d407e5c9aa9043b0b6ab234348467db0 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: f06b60c926204ca88b4355803f1b7b11 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 0a7c19b054d2400abd327736b6829670 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: cd1773f336544b3688bc76c28e9d1f79 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 6b7bbca601f04f7183bc75988bd6db13 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: 069d1dd1f03f4cd79e44f2dcd890b531 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 4924b1a69a5f48b0aa6af943b40ffc68 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: e100d8d8f23c4d6996ac59c5ad68acf0 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: a87dfd0dc0274ff4b34354678f2d49d2 +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 772078ff701a477cae9acb8dda16ef1f +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: d2d67048e93e40c4820b805f1ba28cc9 +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 580477152be041a8ae5c5f546ecbf21d +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: 05f8faea082b4fb9b9c22b8eff7eb356 +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 4c107fb18fb34c2dba7743118c51e8c8 +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: 729ea19aa03b49bdadccc6e6f0d2e7d9 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: e849cda9fb1d4a48b5b1f9a4e44213a1 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: bfc20f529d2d4797b87c63c7b2c05e91 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: 761a900275a044f28ddcebe509a4637a +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 59af21cf1ee848e993563ad47f7bb248 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: d711ce1ccdcf427aba25a2ab3d11165d +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: eaaaa01fe0894f479a42a9c3ce199819 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: 92489f186e3f449295b0dc864ebf17f7 +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 1360c3a2d43b48f3b3e1153bb26b3f30 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 2e993e21a3624910b4282bd088694fec +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: df5b4b041dc944be8580e43012339168 +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: 92ac2766d118428ea148094c022a8b0d +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: e4ddaca03eb449eabbf2d2fce752c367 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 0bc50411a4b748d8864305070d11a304 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 74453227279a46cea3644f3ca7df61b9 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 75ce3269886645eda46a6575fca186eb +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 1e7e5b46017a476a80d57ab7eb614758 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: 1ee41e983ca14a959caa199b1ce12700 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: 070e6a00d09e4675b89afec5d066aec1 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: fd37ebe3aad9473891cc764a47363f8e +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: 85176099018c4ae19bed1261e92e6e92 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 952e9a347f444ef496fa0cdf00160ffd +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 2b5ad46ca3024ce1b37e1c92a820aabf +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: ea17d17cd08b4c40a842598c8521af56 +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 6e5f1266974d4a32995aaa69fbbfd648 +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 20be823f70c348bbaad6bfc8b88201a9 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 02311e5310cb49d19bf2998513f73124 +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: ca6e4a3fe04145a9a21cc43cc53a07bc +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 75452467551a46a2b2b3685f1a4aae0d +#: 93efa8e941a7427f949afc794ed16e75 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: 39beed65cb114bd78c79aa4a5d6f4398 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: dd880d0589fe45dbaf9b7d799402f158 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 671d0bd54bb147518c35f0844a76c61d +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 66de58a51b034f6a8d5dbe742046f817 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 564e68d58e364715aa72183cb16b3d72 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: 558739ceb3fe40de8ea87ff1e7d3fe9d +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: fdc601ee1aa54e1f84cd00eed2e44e52 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: e4f4a76cee96473d9da3bc1c9e35324a +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: d524ed5f1e964688af9d74eef8e46e04 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: c646e4714d78437fb450127b119fbd70 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 8351ddfd726c40159d81c017ef221606 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: 456794c7274f4654b54aae8d4073a2df +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: 6485e8d6814144d1bcbe66bfe4fcbdb9 +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: a2b9e47cc923466f8bd2fbc4b33fc4fa +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 698cc640807247fd8d512c59ce32ee48 +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: dd658e10da624918b7dec1ea18bbf432 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: f6bd95a4fbc44ffdbfec7fcac90f6bb6 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: ac7b02a71d3544848d4fb539b2a4f115 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: 4380dbd066a44102a71c7e42ca7de8d8 +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: da946c9d59f44fb995daa6aadc44031d +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: 7c73bc555f604afd8491c1619d6905eb +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: e79ce424410e4682881fe14326955a14 +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: be8d2b89052e4f9d96ff2bf15526e229 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 967b064ec4284d0aaf374509915497e1 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 02d667b922264f8e8021844df0085578 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: db8734e07541495188d9ee97eaaaeff3 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: 22542da60ac24403827e2e2a14595770 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: d10f35716f9c4b878da0f2b4ff3d44aa +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 1fd555d1f8ca499ead8d5601eb62266a +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: f5fc85accf8c4bb9bc701ba0b4ee2e21 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: e69cb5e87f4b4670abbc1606197d804c +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 15d763c45a2749a8926b1f965db9d97f +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: c2aac63fc0c347d9833d253039000fa3 +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: 06a23beb753c4a97b302943f59128d78 +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 45985434cfe9438cb558075e1fd73809 +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: e92da36d865142289b11d245221ff8d4 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 3ed7a2b9f77b4eadae3bf6e4a98d14b9 +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: fd66c4fb9c2a4beea0ed5ed8874fcd61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 65944dc8b32a46a4beb73dbdebb7b01a +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 6250fe161ab0421b8799040b79ce695a +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: cc40c0f1ade34ab3b400a02b59b7ba01 +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 29f53a5d64fa498bad0dbe94b238fd97 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: 037fccb419bc4e9f839c665ae31e28ee +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: fdd4bec90c484a618ed8e4d1199deff8 +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 11afb584f37947358963f6510935c5d5 +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: a77e0bfb589c40b6a61a9ca559961a7c +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: 3f4aa12588204fe5b33db590a9446283 +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 640c67f3bcd740c59f90c361024acbcc +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: 8c4d30cbbea146a584731d164d4ad9ef +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: 5d0fd4f8b58e4a8e8f46902e64e6556b +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: e98ab273645340f9a1446183a642e79e +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 37a83ed92d9e44689cfd3a31c2785418 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 7cebef0a9e1444149b1dc58d30f6c10e +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 0cd2bd98918b4622bc586d50f1ce1fa4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: 92458de979564d19a634bb8d3bf6f586 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: d4ee6cc8903f4e6992439ca2586246ed +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 62b438c4ed8a409f96974f3d59cc5854 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: f0f288aeae4f4649ba3615437b531e97 +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: f35023cb05504d1db0cbee41c4e5f371 +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: 01564f1d2038489685160f03db92085f +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: ad662dce1e4149728b8e17f74d8f975f +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 4f6a57f34f094418b7c13aa07eef95c7 +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: 373a6c24de9144e69f37418d6ce8857d +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: f804a8493c8e40178772d94bdc45b43e +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: b3c504b8ab1a42788ef4e3339d27b0dc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 2c2681fe72e24a5d8d98f0aa8e8c56a2 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 571e5c13552c4381bb6de53c02fe5f43 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: fd789f444d9a4061b4fc61bac70353bb +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 2cef838551994b078e460c63214517f9 +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: 2a3a8a553d3c455e9288f63b9a02898d +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: b0b8def4623a4018b1ac913a9256c0a2 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 3f0d4346f0104cc08c059eed9ab4b3a9 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 22e0ac963278414d8141ce5ce4031029 +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: 49cad54646d04adc8e5ac9f0f3c8f895 +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: c8776a4511b24f46bbe0a34d52cf3c8b +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 401b053bd08a4286b9059cb6ebf8d679 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: 8d48a277f37f458f88c54f362534d7b5 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: de90253a11f24f29a4a57348b4f60941 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: 1e20968f957441c58cabfbc46c21e8ca +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 4cf2e158afb348d7b3fd6274fe888129 +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 44c5c010c97a40068a6b930949dcd8cf +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: c6277b2a7a934f81a91e406ef317a1fb +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: 8b3ece04170c447e9b5a8f76374c4c23 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: 6b952b7369b447bdb0bf1e9ff8540194 +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: a6024fb7ce664896a6858d5ea3562fb7 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" diff --git a/locales/topics/additional-arguments-and-parameters.pot b/locales/topics/additional-arguments-and-parameters.pot deleted file mode 100644 index c447e7c6..00000000 --- a/locales/topics/additional-arguments-and-parameters.pot +++ /dev/null @@ -1,62 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 4ad19837b80f40af88edf443c4d4e743 -msgid "Additional Arguments and Parameters" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:3 -#: a51e98f4fab24b42b225e24b69471869 -msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 78e7111611734004b650bdde36fe8079 -msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 0c5cc374383a4f058a6c8d7a3d83c7d4 -msgid "`arguments.cwl`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:19 -#: 67cfc6cc46764b07a6738691bc1cb1f6 -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 744b2343db934429b7a04b4ab4f84d15 -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:30 -#: abea839860f447f1b767c3a028ce1ca9 -msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 5a44c7cd8feb4593802cdf56254b79d7 -msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d5f29eae1af646d5be22c816c5d1a4fd -msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." -msgstr "" diff --git a/locales/topics/best-practices.pot b/locales/topics/best-practices.pot deleted file mode 100644 index d4460047..00000000 --- a/locales/topics/best-practices.pot +++ /dev/null @@ -1,137 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/best-practices.md:1 -#: e93667d13f1c481c9ffec6bb3062c073 -msgid "Best Practices" -msgstr "" - -#: ../../src/topics/best-practices.md:3 -#: 685dedff3cf54c4b95bc56b30a5d7fce -msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 -#: 2e4c3af1016e4269b6eb3eb7c37b609b -msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../src/topics/best-practices.md:11 -#: ee2f52f0a96449a7b6e49b2c824288d1 -msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." -msgstr "" - -#: ../../src/topics/best-practices.md:20 -#: 426fc5489a1a44d2b037f1456b6556c2 -msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." -msgstr "" - -#: ../../src/topics/best-practices.md:26 -#: ecf6e24373f944a0a3e9453c31e03e8e -msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" -msgstr "" - -#: ../../src/topics/best-practices.md:28 -#: 0ad7fe10c6584f01991d87544f1d5649 -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../src/topics/best-practices.md:37 -#: b589adbe3f324ecc9670c2355be1e308 -msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." -msgstr "" - -#: ../../src/topics/best-practices.md:40 -#: 50184e2a39fb4a2086afbb236efa603f -msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." -msgstr "" - -#: ../../src/topics/best-practices.md:44 -#: f000d979ab914d94bbfe988792cf1629 -msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:47 -#: a11d2c6e1408411d89cf7d434448a414 -msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../src/topics/best-practices.md:50 -#: 3e379d3bd38b40d38a2a448e907918b1 -msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../src/topics/best-practices.md:55 -#: b8eb7c78ffcc4093aea11fa21cef762e -msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:58 -#: ef540052516840638bb7e5bf4dadb945 -msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." -msgstr "" - -#: ../../src/topics/best-practices.md:66 -#: 378f73d8fd864d0bb3ac5d027224ef08 -msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." -msgstr "" - -#: ../../src/topics/best-practices.md:69 -#: fb1fee0d5583488ea2091dbf9b36eded -msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." -msgstr "" - -#: ../../src/topics/best-practices.md:73 -#: 210127c58cd44557b60d603d8d68725d -msgid "Custom types should be defined with one external YAML per type definition for re-use." -msgstr "" - -#: ../../src/topics/best-practices.md:76 -#: 6b657c5d109646f5bf7a38cef1b903e3 -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../src/topics/best-practices.md:78 -#: 14951e1b672248f095c31c4c96bf5183 -msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." -msgstr "" - -#: ../../src/topics/best-practices.md:82 -#: ff9dbfab87a24cfab3734882216d40af -msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." -msgstr "" - -#: ../../src/topics/best-practices.md:85 -#: 444b5580319b4ee69a1439c7ccf703df -msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." -msgstr "" - -#: ../../src/topics/best-practices.md:90 -#: 9ba7fd2784b2430fb6964b9a16d2d553 -msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." -msgstr "" - -#: ../../src/topics/best-practices.md:93 -#: 0e88ebb9e45c41db83482ccf848ca1ca -msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../src/topics/best-practices.md:97 -#: 3b2fe5ca68944df5baf04c7b5705e207 -msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." -msgstr "" diff --git a/locales/topics/command-line-tool.pot b/locales/topics/command-line-tool.pot deleted file mode 100644 index 422115ac..00000000 --- a/locales/topics/command-line-tool.pot +++ /dev/null @@ -1,62 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/command-line-tool.md:1 -#: 595e9cc7e0a448f695e27b1cd0427d9e -msgid "Command Line Tool" -msgstr "" - -#: ../../src/topics/command-line-tool.md:3 -#: ac9188b4b9dc45589f2173a73dc9d3dc -msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." -msgstr "" - -#: ../../src/topics/command-line-tool.md:8 -#: a6dd1084b9b248e08ec2659999f82ac6 -msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." -msgstr "" - -#: ../../src/topics/command-line-tool.md:19 -#: 9119bb87ef4b48e7946f5412d197ce0a -msgid "CWL command-line tool." -msgstr "" - -#: ../../src/topics/command-line-tool.md:50 -#: 312c6373a25b498db63c67abed6c6289 -msgid "`echo.cwl`" -msgstr "" - -#: ../../src/topics/command-line-tool.md:57 -#: 84b6964c9cbb4d67af2794624de86337 -msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../src/topics/command-line-tool.md:68 -#: c276e21332454452bc814d33f007a670 -msgid "Network Access" -msgstr "" - -#: ../../src/topics/command-line-tool.md:69 -#: 1321360b42da4f65975569e2b7314bf0 -msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." -msgstr "" - -#: ../../src/topics/command-line-tool.md:83 -#: 70739268c7674a99834cf6c166231149 -msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." -msgstr "" diff --git a/locales/topics/creating-files-at-runtime.pot b/locales/topics/creating-files-at-runtime.pot deleted file mode 100644 index c427c32e..00000000 --- a/locales/topics/creating-files-at-runtime.pot +++ /dev/null @@ -1,77 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/creating-files-at-runtime.md:1 -#: d4e5cee7a82447a696e1e9516ccc2e38 -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:3 -#: 6121650880d4447e9b5a6b66e0f3367c -msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:7 -#: e81edd66cbb2461e905a7adf6bff23fa -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:9 -#: cb4602ae814b4b47abe61ab3bd88b046 -msgid "`createfile.cwl`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:15 -#: f6f5c6dc8ff74db3b1c5aa2403ee12d4 -msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:20 -#: 87abe95ca4054b48a8fb76d7916db1d4 -msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:27 -#: de2366c1d2d1459ba23fe1410f2b86f4 -msgid "To test the above CWL tool, use this job to provide the input value `message`:" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:29 -#: 28906471c2fb41358706f624e3c8bd8f -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:35 -#: 449fdfe14172498fb80e2f57ca0c05f9 -msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:40 -#: 9a9ce102e4ed4dc68eeb161746ab4689 -msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:51 -#: 447b2199a76646be8afacb72203e9719 -msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:54 -#: aaae789101c742b292ebdcec727b1762 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" diff --git a/locales/topics/custom-types.pot b/locales/topics/custom-types.pot deleted file mode 100644 index f338bd21..00000000 --- a/locales/topics/custom-types.pot +++ /dev/null @@ -1,77 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/custom-types.md:1 -#: e1169af9b1ed419b80cd7b2ee432c37d -msgid "Custom Types" -msgstr "" - -#: ../../src/topics/custom-types.md:3 -#: e297aa8753564accac64cbad1be99d0b -msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." -msgstr "" - -#: ../../src/topics/custom-types.md:9 -#: aa76f57cb1eb4a81ba6560ca7b7d47fa -msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:12 -#: 7644b22f9154413cb88f46e9a2a1a9fb -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../src/topics/custom-types.md:18 -#: 1d259a15f1884950953d8536b74d437a -msgid "`custom-types.yml`" -msgstr "" - -#: ../../src/topics/custom-types.md:24 -#: db1612c92c3c4d63869aa3d589960ab9 -msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/custom-types.md:30 -#: 4c7038e3a8d6484e9eecb348e825605a -msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../src/topics/custom-types.md:46 -#: 960610e43cd247dfa5921477558f6a2c -msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:53 -#: cd7d7cb81be74acd81bd3af2ecbeba8c -msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../src/topics/custom-types.md:55 -#: b0b4eb8206f54104a7fe02492cd3c0c5 -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../src/topics/custom-types.md:61 -#: 2d0fc88b5d524b4e814f47a147b7e555 -msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" -msgstr "" - -#: ../../src/topics/custom-types.md:76 -#: 8e99e8e00d3340e6bf7025622bdfbf47 -msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." -msgstr "" diff --git a/locales/topics/environment-variables.pot b/locales/topics/environment-variables.pot deleted file mode 100644 index 294a71e7..00000000 --- a/locales/topics/environment-variables.pot +++ /dev/null @@ -1,42 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/environment-variables.md:1 -#: 201d52b060fb44e3b988d1cf08b32569 -msgid "Environment Variables" -msgstr "" - -#: ../../src/topics/environment-variables.md:3 -#: 5438cfdc5df24a2098fc3014731bceb2 -msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../src/topics/environment-variables.md:7 -#: 295b041049874673b1c4f93e3c8932c8 -msgid "`env.cwl`" -msgstr "" - -#: ../../src/topics/environment-variables.md:13 -#: e2076a2e3c4e43228e69f9b4ee535e3a -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/environment-variables.md:18 -#: 74c67839550148b98f8a681f53baae9e -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" diff --git a/locales/topics/expression-tool.pot b/locales/topics/expression-tool.pot deleted file mode 100644 index 329b21fd..00000000 --- a/locales/topics/expression-tool.pot +++ /dev/null @@ -1,47 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/expression-tool.md:1 -#: a1a763367700488eaeeeeb6c1d4aaf3f -msgid "Expression Tool" -msgstr "" - -#: ../../src/topics/expression-tool.md:3 -#: 1baaf7f3bda34cabb4081708f8eb676f -msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." -msgstr "" - -#: ../../src/topics/expression-tool.md:8 -#: cf8f9f21b8bc4cba9e947b631e0452d4 -msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" - -#: ../../src/topics/expression-tool.md:17 -#: 01ad0d7c0c9d4051906424dceb702361 -msgid "CWL expression tool." -msgstr "" - -#: ../../src/topics/expression-tool.md:48 -#: af1958ad56b64631a111aaaa41413a09 -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:67 -#: f50a9dc71c7f4beab2525ce6e6fca385 -msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." -msgstr "" diff --git a/locales/topics/expressions.pot b/locales/topics/expressions.pot deleted file mode 100644 index 012628cd..00000000 --- a/locales/topics/expressions.pot +++ /dev/null @@ -1,373 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/expressions.md:1 -#: 6b0faa9c10ad4da783e2155070095a8d -msgid "Expressions" -msgstr "" - -#: ../../src/topics/expressions.md:3 -#: 9e44e4e737b545a2b10b97e923027bd9 -msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." -msgstr "" - -#: ../../src/topics/expressions.md:9 -#: ad6d3dddfda445a5bfce2665cb195605 -msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." -msgstr "" - -#: ../../src/topics/expressions.md:16 -#: f487ea31d38142839ce5667701b894cd -msgid "`expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:22 -#: 47d7f42a657a4547af1be1e13662effc -msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" -msgstr "" - -#: ../../src/topics/expressions.md:25 -#: c331468453dd4e60a76bc753417b72ce -msgid "`empty.yml`" -msgstr "" - -#: ../../src/topics/expressions.md:31 -#: 6b9b7057eb154a95847ec56652de07d9 -msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." -msgstr "" - -#: ../../src/topics/expressions.md:35 -#: 6facbcd083f04a60941589da7e21621f -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../src/topics/expressions.md:37 -#: a08110192e264a109ee6a568351135e4 -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:47 -#: 1a260934cee04059b4765d154f6388e1 -msgid "Note that requirements can be provided with the map syntax, as in the example above:" -msgstr "" - -#: ../../src/topics/expressions.md:54 -#: ebee54b00af643aba0d53e774b0ac188 -msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." -msgstr "" - -#: ../../src/topics/expressions.md:62 -#: 02ad120e9a72482780f062ae3cadcce7 -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../src/topics/expressions.md:64 -#: 8bb623ae7a9646ff992d7a79856aac8a -msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../src/topics/expressions.md:66 -#: 4437b8ae6fb04a1fa06f494ead97b1c7 -msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/expressions.md:67 -#: 145b4d4cbfaa4c5d914455b0b5b6ef1b -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/expressions.md:68 -#: ../../src/topics/expressions.md:76 -#: ../../src/topics/expressions.md:89 -#: b187028dafc040e8ab04d2a69c547874 -#: ecb148c1da01445a8149b500b5ea50f5 -#: 87f7f23e14e54b87b6f1b4f8c148bf8b -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/expressions.md:69 -#: 9132968dd34f4a9c99ebabcae48a4a3f -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/expressions.md:70 -#: 34b31b4554b442ab9d9bac1e95cc3029 -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/expressions.md:71 -#: 33e3e471fafb4f609694af59556dedcb -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/expressions.md:72 -#: 941720c894bd45a895e3a8e682b7e884 -msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:73 -#: ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 -#: ../../src/topics/expressions.md:93 -#: e2c648a9a5794879b74cf02e489f0c5a -#: 15692bd5c6204aa9b72259e6dae69bec -#: 1a506a3ea7614043a67dd4d93015b19c -#: 166fd96ec8b64db88e1837feaf65df1c -msgid "`format`" -msgstr "" - -#: ../../src/topics/expressions.md:74 -#: ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 -#: ../../src/topics/expressions.md:94 -#: 8c65f558109142048b8831f800264bb4 -#: a4e5f9d5354d483392c157f736cd8c20 -#: 9ec2e908459a468b837b572a426bcd8d -#: 2d82125ff94c441ea29b3da5ff5dbb08 -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/expressions.md:75 -#: 6eecf3fa29d9465882a2b6be02504ac0 -msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:77 -#: 92267f3d8f4e4b3fa129e3bec3b16413 -msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:80 -#: b9b5551681d046e7a0071eee29987b04 -msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:81 -#: b148af79351e4ba49604e24861388496 -msgid "`glob`" -msgstr "" - -#: ../../src/topics/expressions.md:82 -#: 4c48b367e5494d559484c5395af3a5a4 -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/expressions.md:83 -#: 5541a07628174dd6a843afa2c37f4973 -msgid "From `Workflow`" -msgstr "" - -#: ../../src/topics/expressions.md:84 -#: bf6e4a2101654e15bc27ac3db0c6bb6d -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:87 -#: a295cb00ea034ce7820897606999ae4c -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/expressions.md:88 -#: 5fd2e9df08404efa9d24d8bfccf91a18 -msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/expressions.md:90 -#: 51f8b42f4e7d4c8484133a18f83be491 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/expressions.md:91 -#: 73fef9b1b2074077a2525f72b2efaf62 -msgid "`expression`" -msgstr "" - -#: ../../src/topics/expressions.md:92 -#: cf19b246bc20476899a83e68113dd3d1 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:95 -#: dfe56b4ea35a440d91f579efcc2c039b -msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:96 -#: 918bc6b265a549f28f027da29368cac4 -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/expressions.md:97 -#: a9182179ebce4c99b4eafe59ba122799 -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/expressions.md:98 -#: 984ceb05b6b24e4986a28436bdca88e7 -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/expressions.md:99 -#: 9a3f6db0d7f64468bbf2f6f861eab96a -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/expressions.md:100 -#: b7557357360d454dba7ab3c3471b5a23 -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:101 -#: 839ac0ddca374746972ead6d22427edc -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:102 -#: 89bfd53638504c7aa437c2140afb6035 -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:103 -#: f0af6b4cfc23480aae61f42422ad3afb -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:104 -#: 67ccc10e77d644078b170a28a8ebed3d -msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:105 -#: fcb8b8003fc84ab890ce241e63d43b5d -msgid "`listing`" -msgstr "" - -#: ../../src/topics/expressions.md:106 -#: 584682d4db424108b89ea8e315838de3 -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/expressions.md:107 -#: 77439e7f4f214db781edc777a8a03b78 -msgid "`entry`" -msgstr "" - -#: ../../src/topics/expressions.md:108 -#: 4ba274f6d9c44ad7a05891725299a759 -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/expressions.md:109 -#: 1b751542a9f34fe19ae5f91174e01cb7 -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/expressions.md:110 -#: aca9ad053f5441caa5cd51170e35532d -msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/expressions.md:111 -#: 37c96fdc52c443faa1d1e462ff034425 -msgid "`envValue`" -msgstr "" - -#: ../../src/topics/expressions.md:116 -#: 4bcf5cd130b148f7b3f601902ad0b7b4 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../src/topics/expressions.md:118 -#: d6f0074d025742a6b3fe7f91f1dff335 -msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." -msgstr "" - -#: ../../src/topics/expressions.md:122 -#: c664d4710c404ed0af90dc22c8f273b1 -msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:128 -#: bd8dfef3aa934750bdd790e1de6bced6 -msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." -msgstr "" - -#: ../../src/topics/expressions.md:135 -#: 1ae20d38a1574d828ca7cb8e955906da -msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:139 -#: bcda020047784e4191d4de456afc7449 -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:146 -#: a9ccc2da748644dfb28b590eae974f63 -msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" -msgstr "" - -#: ../../src/topics/expressions.md:149 -#: aede8f2c722c49f18cd2a86c051bb1d4 -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:155 -#: 7d1bd9bfba9c496a90fc45f575505e22 -msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:158 -#: 8b906fa3b98c48c68de46f80667d4d2f -msgid "`custom-functions.js`" -msgstr "" - -#: ../../src/topics/expressions.md:164 -#: daa9689f15c746a38dcd22a3f169a4c6 -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:171 -#: d0d8193fbb304f0281db0c6c1147545b -msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:175 -#: e5e1179082c14621bafbd14d887db62a -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:181 -#: 193379258f254ac5a25fcfb61b1c3540 -msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." -msgstr "" - -#: ../../src/topics/expressions.md:186 -#: ec0d1c972b9942f8a55b7b68fc9cfe07 -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:193 -#: 63ff0565300a493f8c84935139c23552 -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:200 -#: f8bb29ee047e407ea226599bccd86196 -msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." -msgstr "" diff --git a/locales/topics/file-formats.pot b/locales/topics/file-formats.pot deleted file mode 100644 index 86733f1a..00000000 --- a/locales/topics/file-formats.pot +++ /dev/null @@ -1,77 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/file-formats.md:1 -#: f2a1cf1e81e54737af8d81bcef76d88a -msgid "File Formats" -msgstr "" - -#: ../../src/topics/file-formats.md:3 -#: f81bab33b2ad46d3a852e15d88858879 -msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." -msgstr "" - -#: ../../src/topics/file-formats.md:8 -#: c1dd91bf59804358be63bcde0614bd31 -msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." -msgstr "" - -#: ../../src/topics/file-formats.md:14 -#: 785ed7d362824bb99887694670aac50e -msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." -msgstr "" - -#: ../../src/topics/file-formats.md:17 -#: c3f54f4d6df44e628c59c1e70124667f -msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../src/topics/file-formats.md:20 -#: 6c3942038fd3446db254260530291732 -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../src/topics/file-formats.md:26 -#: db9222078ef04bd29ac45af0cf8a4ebd -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/file-formats.md:32 -#: 3b17d233095a40cfae0540e678088860 -msgid "Sample Parameter Files" -msgstr "" - -#: ../../src/topics/file-formats.md:34 -#: a7900a2fa76c46e6854d09a7b31df272 -msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." -msgstr "" - -#: ../../src/topics/file-formats.md:39 -#: ac34d1ad2274499f9ea1413b5648f7dd -msgid "`sample.yml`" -msgstr "" - -#: ../../src/topics/file-formats.md:45 -#: 04198e0858a6415a8e3235c29d15c5f1 -msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/file-formats.md:52 -#: 265ff7e37ebd4e9fa85b26a6deb1cd74 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" diff --git a/locales/topics/index.pot b/locales/topics/index.pot deleted file mode 100644 index 9f895c55..00000000 --- a/locales/topics/index.pot +++ /dev/null @@ -1,22 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/index.md:1 -#: 8ecce715c6084f74acf91e896775f6b3 -msgid "Topics" -msgstr "" diff --git a/locales/topics/inputs.pot b/locales/topics/inputs.pot deleted file mode 100644 index 6ec07f47..00000000 --- a/locales/topics/inputs.pot +++ /dev/null @@ -1,247 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/inputs.md:1 -#: 9a97be0420e54706a7c73bc1eb856b96 -msgid "Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:3 -#: d4b396558d594c84b82369a138358fd6 -msgid "Essential Input Parameters" -msgstr "" - -#: ../../src/topics/inputs.md:5 -#: a3966840a8844e1999e21bcecc96a6f7 -msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/inputs.md:9 -#: ebeb58f7ebd541f581415a43d790811c -msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../src/topics/inputs.md:13 -#: 95cf3ab046b44241ba399c56d4b0c6eb -msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." -msgstr "" - -#: ../../src/topics/inputs.md:16 -#: 6e6066facc2141739cac77bf9792572a -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../src/topics/inputs.md:18 -#: e257868f6c6646e6a0d1feef62de079d -msgid "`inp.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:24 -#: 2f2885adf6214b9a8f770097bb02b1e5 -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../src/topics/inputs.md:26 -#: 01ec3e60c2f24f9c912d44d3d5dac4c5 -msgid "`inp-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:33 -#: 8c803c9f11414a9f9b92643923a79c65 -msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" -msgstr "" - -#: ../../src/topics/inputs.md:40 -#: df2b1f41e3e149309ae8b19aaf6034ca -msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." -msgstr "" - -#: ../../src/topics/inputs.md:44 -#: df5bd15a6b084bce879270be669f2923 -msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." -msgstr "" - -#: ../../src/topics/inputs.md:47 -#: e73d20dd91574bcbb7b24932d9ff04e4 -msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:53 -#: 56461c62effc487c9e73d1e82ddd3390 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:64 -#: df42caf04d5f48baa8e5734d6100cdf4 -msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" -msgstr "" - -#: ../../src/topics/inputs.md:70 -#: f8db1efc2092415387e4e16dc24775dd -msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." -msgstr "" - -#: ../../src/topics/inputs.md:83 -#: 859f5479b2cd4e919e3ba19a3f084b01 -msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." -msgstr "" - -#: ../../src/topics/inputs.md:95 -#: d04258dca228411ab16f82585ee53985 -msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." -msgstr "" - -#: ../../src/topics/inputs.md:109 -#: 760c0af7e36d48d1b1681928ad195eaa -msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." -msgstr "" - -#: ../../src/topics/inputs.md:124 -#: 4e5d3fb805f04593b34d5ae88dd6fa83 -msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:131 -#: 7b97d452561c4c158a835fd308feafb8 -msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../src/topics/inputs.md:134 -#: c63782e8b8524857a1683578534f8382 -msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." -msgstr "" - -#: ../../src/topics/inputs.md:142 -#: fe66dc3c9aa743e0a2060a8280e6a59d -msgid "The `baseCommand` field will always appear in the final command line before the parameters." -msgstr "" - -#: ../../src/topics/inputs.md:146 -#: 04993bbb8c7b488d8b1b2517f4333f8d -msgid "Array Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:148 -#: e33e6fd2e8a8472e88c9333c7b44fc2c -msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." -msgstr "" - -#: ../../src/topics/inputs.md:154 -#: adc2cd5bd81b459b996ff65de5d25436 -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:160 -#: 67da943c4d6d49cab1931606fb6938d9 -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:166 -#: 0be87de7fd5e41da895dfc9369da7b5a -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:178 -#: 535a8e26cc3b4e3db43680f030d57879 -msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." -msgstr "" - -#: ../../src/topics/inputs.md:185 -#: 61c26186c1734233bb7d9e5cd3056506 -msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." -msgstr "" - -#: ../../src/topics/inputs.md:191 -#: 66ec7048099f4720989c8de5be49ea2a -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:193 -#: efa9d841028c4135a513f3226b37bdfc -msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." -msgstr "" - -#: ../../src/topics/inputs.md:198 -#: b3543061283e4bf286ed9fb7127238df -msgid "`record.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:204 -#: afeff005e15d49edbd8222e95b4d6388 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:215 -#: 0eb5e94bf86a4c84bb112d612c290bce -msgid "In the first example, you can't provide `itemA` without also providing `itemB`." -msgstr "" - -#: ../../src/topics/inputs.md:217 -#: 3d1f591442f54f9fa8effb98f4cc4f7f -msgid "`record-job2.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:233 -#: 1a8735c689ff4e13bd207eed62d0bc1b -msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." -msgstr "" - -#: ../../src/topics/inputs.md:236 -#: f802a2e638764c95bef8889b958f6872 -msgid "`record-job3.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:252 -#: 54ffe9e897ff4682aa9d17e9239a5b40 -msgid "In the third example, only `itemD` is provided, so it appears on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:255 -#: 892a899a9365419c8cdc95e9f05f9e3d -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../src/topics/inputs.md:257 -#: 2cca4db8543145c0a59da034c82db1fd -msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." -msgstr "" - -#: ../../src/topics/inputs.md:262 -#: 1f42c1eba9f44397942d6bf2dd37855f -msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." -msgstr "" - -#: ../../src/topics/inputs.md:265 -#: 1c0caf1fd3a4411f83dfc4866edeecfe -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:271 -#: d0a92fe266614a5db77f32b0fc40ee83 -msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" -msgstr "" - -#: ../../src/topics/inputs.md:280 -#: e3a608fbb7e14213831c564128421cc2 -msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." -msgstr "" - -#: ../../src/topics/inputs.md:289 -#: a24cd12cc01b4e23b0ed878a27fcaa46 -msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." -msgstr "" diff --git a/locales/topics/metadata-and-authorship.pot b/locales/topics/metadata-and-authorship.pot deleted file mode 100644 index 2d77396e..00000000 --- a/locales/topics/metadata-and-authorship.pot +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/metadata-and-authorship.md:1 -#: c79f6e6491bb4b6b9f1b2677b79c0ce1 -msgid "Metadata and Authorship" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:3 -#: 73dd0c3f814b4b77a9fe0ad09be7e00a -msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:13 -#: 9dbb204051604ffc8b40ff902f1d6c7e -msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:16 -#: a4bd38b9be374a9da651b4c8a876f57f -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:22 -#: 6d6d2685e0a74c8ab242594fff8885ff -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:28 -#: d8261a4cdde0456db33aa7e6bea9774d -msgid "Extended Example" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:30 -#: 11af70cc279a4cb29135aa440d560999 -msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:35 -#: 5a3a6d2577544ff1a996b7b7d15693e0 -msgid "`metadata_example3.cwl`" -msgstr "" diff --git a/locales/topics/operations.pot b/locales/topics/operations.pot deleted file mode 100644 index ea3332ce..00000000 --- a/locales/topics/operations.pot +++ /dev/null @@ -1,62 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/operations.md:1 -#: 8766c4065dfa467f9001aa50564f4812 -msgid "Operations" -msgstr "" - -#: ../../src/topics/operations.md:3 -#: b37c530cac0a4d18b50271b5b5ec4d1b -msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." -msgstr "" - -#: ../../src/topics/operations.md:7 -#: 54e76a0465cf40bf8b76896643cc521b -msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../src/topics/operations.md:10 -#: 9e16b384ac494d07951ad589a0413d2c -msgid "`operations.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:16 -#: cfd13e0311104c95b7de0510f0fb54ab -msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" -msgstr "" - -#: ../../src/topics/operations.md:24 -#: 468b0b4219a84df49286a95115c5d3fe -msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" -msgstr "" - -#: ../../src/topics/operations.md:55 -#: 362bd499ed6b40b8bbf3237a9a08895e -msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" -msgstr "" - -#: ../../src/topics/operations.md:58 -#: 24454b17abae4cd9a8a17cfc5bd79e39 -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../src/topics/operations.md:66 -#: f33e158f449e4594b4f0f1c4660e2be2 -msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." -msgstr "" diff --git a/locales/topics/outputs.pot b/locales/topics/outputs.pot deleted file mode 100644 index eaaa0c37..00000000 --- a/locales/topics/outputs.pot +++ /dev/null @@ -1,134 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/outputs.md:1 -#: 30d1617ac85d41a0956ef5f7eb30c112 -msgid "Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:3 -#: 13aaa50a038f460f829a5554ea950a8b -msgid "Returning Output Files" -msgstr "" - -#: ../../src/topics/outputs.md:5 -#: e26db82dbb934d4aac5a7918c39245f4 -msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/outputs.md:10 -#: 747f0575223f42cd90157c2ec684ab4e -msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." -msgstr "" - -#: ../../src/topics/outputs.md:16 -#: c251eb8f22c54cdbb8683e98d4e527a7 -msgid "The following example demonstrates how to return a file that has been extracted from a tar file." -msgstr "" - -#: ../../src/topics/outputs.md:19 -#: e0fc3bde9de84b2ea5e2b9d7d1491ed1 -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../src/topics/outputs.md:21 -#: cbc068a7d2bc4c1682577ef6b854309a -msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" -msgstr "" - -#: ../../src/topics/outputs.md:26 -#: f2923e674d574ea1a52dab96a12e38a7 -msgid "`tar.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:32 -#: ebe4a9bec6cd42c089e790108b0ddbff -msgid "`tar-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:38 -#: 89c371e54934472e9c09681be5f1ecc3 -msgid "Next, create a tar file for the example." -msgstr "" - -#: ../../src/topics/outputs.md:45 -#: 508663424d2f4eb494ca8611cca4073a -msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:51 -#: 1ee12d2ed35a414d818127ebaaac2364 -msgid "The field `outputBinding` describes how to set the value of each output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:62 -#: 0e0fa84bee1042d88386826c22466619 -msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." -msgstr "" - -#: ../../src/topics/outputs.md:65 -#: 9a37679c41eb4287b43d254a8fd823e2 -msgid "Capturing Standard Output" -msgstr "" - -#: ../../src/topics/outputs.md:67 -#: 7041b9a7b7034bf881bccccc2b691a44 -msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:71 -#: 53075db7e4ca436594d4fd3f3e00917d -msgid "`stdout.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:77 -#: 0860836ece81420dba1b2a080e825f6c -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 -#: 40d221f9b5b642648b918aa0e6902f1c -#: 7ad8f592f52b4aeeaa703a85e79f6356 -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:89 -#: 6f6a26ee1ade4b4f9ed3a82ed44030f8 -msgid "Array Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:91 -#: 61a149a84abf40e7ace2248dc0119838 -msgid "You can also capture multiple output files into an array of files using `glob`." -msgstr "" - -#: ../../src/topics/outputs.md:93 -#: 1322f83871ee49b3a87aa71a0ec5a79f -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:99 -#: 6f92d0458a924c88aaba9e7336eef87c -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:112 -#: ce294dbd94ee4624915c398389eaf1f6 -msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." -msgstr "" diff --git a/locales/topics/parameter-references.pot b/locales/topics/parameter-references.pot deleted file mode 100644 index b17a5e7a..00000000 --- a/locales/topics/parameter-references.pot +++ /dev/null @@ -1,278 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/parameter-references.md:1 -#: 0d925f42133646899f4bb3367057e07d -msgid "Parameter References" -msgstr "" - -#: ../../src/topics/parameter-references.md:3 -#: 473a89b059e14f649354a76bf882142e -msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 -#: 4c57e8c446a0441c810493d34311ace7 -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../src/topics/parameter-references.md:19 -#: 014e74e995bf49eca1c3b09ca011619f -msgid "`tar-param-job.yml`" -msgstr "" - -#: ../../src/topics/parameter-references.md:25 -#: 0d475fd8c50c4dc986643c14b82d0576 -msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/parameter-references.md:36 -#: ff886a60af2b49499ef0a0d31386998e -msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../src/topics/parameter-references.md:47 -#: d1e080ff809946919ed35e2b1055b6e5 -msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../src/topics/parameter-references.md:51 -#: 52e0d66811bc433b8c21b91e5ac6945d -msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." -msgstr "" - -#: ../../src/topics/parameter-references.md:54 -#: 6252fd49bc814c1c97c2a825a6b1b49f -msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." -msgstr "" - -#: ../../src/topics/parameter-references.md:59 -#: 97abdf2838c444f684629c0578a8ed31 -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../src/topics/parameter-references.md:61 -#: 3fd741db4c014ea6a53b6bc2fad63e21 -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../src/topics/parameter-references.md:63 -#: 986da8d3c56b4227a9481c9e2b0ea0a7 -msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:64 -#: 1beb8e88637545b8ad365441de547b59 -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/parameter-references.md:65 -#: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 -#: 8349b7acc74346e0ac0d18dddafe2205 -#: 9b2e0b712ec146e1a636ed8d1f408c56 -#: eac9f2c8f0c0424ca5e70425fa60f677 -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/parameter-references.md:66 -#: cb1036ef7aa449dc8728bf72cf7281e9 -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/parameter-references.md:67 -#: 713a83cfde5e4d4181ec8477f20ac2c4 -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/parameter-references.md:68 -#: 8d666991bcc94c83b1259746ced7e43f -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/parameter-references.md:69 -#: 7ce52aad9f624afeb40e9829ab150651 -msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:70 -#: ../../src/topics/parameter-references.md:75 -#: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 -#: 4207d80deafd4b12a944b4b61e7494bf -#: 0b9493de338a4717bdf643991c72d92c -#: 489bac6cabeb4aeaaf90112969f0bafb -#: 34de0217785146c4ac0130e52319581e -msgid "`format`" -msgstr "" - -#: ../../src/topics/parameter-references.md:71 -#: ../../src/topics/parameter-references.md:76 -#: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 -#: 026108b0d1c344df883689be95db8fad -#: 0b32cdfd79ee469e83a629285223cc0b -#: fbe04046dc744f72b3a88da56f15b483 -#: 9065d837c83d4dd78cd3d664f882300a -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/parameter-references.md:72 -#: 7f5bdccc51a14535891b13d8e787251b -msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:74 -#: daff49176fca4fd8b12369f4f92eb22d -msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:77 -#: d0208c0307b04cf384c7a9334046bb9b -msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:78 -#: b384a85509344ad5bbc3873684a19b9a -msgid "`glob`" -msgstr "" - -#: ../../src/topics/parameter-references.md:79 -#: 83d6911ab8994e55a87871c8a238f4fa -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/parameter-references.md:80 -#: b0298c96113742f6981316ad0e33b018 -msgid "From `Workflow`" -msgstr "" - -#: ../../src/topics/parameter-references.md:81 -#: 636f6c50ac274d88a7ca32f7bafbaca4 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:84 -#: d72570d062e54cfb89c82a1ce1a286b8 -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/parameter-references.md:85 -#: 5b8e3e7c420c4490ac4a5905189cd166 -msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/parameter-references.md:87 -#: 22c6afe7aab84038a74f8478f8d97d64 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:88 -#: 88877e67206e48b3b10e30ddead266fd -msgid "`expression`" -msgstr "" - -#: ../../src/topics/parameter-references.md:89 -#: e763d3be7c3347718bb851b0e601d466 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:92 -#: d7837cc8e8064348b2698f80e4bf47b5 -msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:93 -#: d87be82c3bcb4e1fb33946573d62037c -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/parameter-references.md:94 -#: 2362c7e8e16240e288fbaa49521951a6 -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/parameter-references.md:95 -#: f9d381b7bf2c4caeb6a5a3bace39b6a3 -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/parameter-references.md:96 -#: f957b015fbb64e448083a5a9b4ff4b0b -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/parameter-references.md:97 -#: be4bb996b5954fb8a90c57e5e6456ec2 -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/parameter-references.md:98 -#: 00eb0fff1cc64e41bcbcf63ebb58ee11 -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/parameter-references.md:99 -#: 073bb4a51bcf4447bde792e41e876bbd -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/parameter-references.md:100 -#: ed9e837c60a14da0879a309194213033 -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/parameter-references.md:101 -#: 160c7ce007564ee2825517bc29750c65 -msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:102 -#: 24755cdacd024d949fc6015b43983e22 -msgid "`listing`" -msgstr "" - -#: ../../src/topics/parameter-references.md:103 -#: 4ad1d82ee80844c581197cb14eab518a -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/parameter-references.md:104 -#: 6542359022cd4a1ebfb08e8c104620b4 -msgid "`entry`" -msgstr "" - -#: ../../src/topics/parameter-references.md:105 -#: fa4a51155be34b10aa8c1eaecd2cdbbf -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/parameter-references.md:106 -#: c51af125685146dea16c2dcd7f290aef -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/parameter-references.md:107 -#: e31fc3370fd948c79e945ab30dacf99e -msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/parameter-references.md:108 -#: 7982f559dcff4178b222cdba267d1283 -msgid "`envValue`" -msgstr "" diff --git a/locales/topics/requirements-and-hints.pot b/locales/topics/requirements-and-hints.pot deleted file mode 100644 index a566fb29..00000000 --- a/locales/topics/requirements-and-hints.pot +++ /dev/null @@ -1,22 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/requirements-and-hints.md:5 -#: 15273fbf009b4036a2574d157740db98 -msgid "Requirements and Hints" -msgstr "" diff --git a/locales/topics/specifying-software-requirements.pot b/locales/topics/specifying-software-requirements.pot deleted file mode 100644 index d65ed83d..00000000 --- a/locales/topics/specifying-software-requirements.pot +++ /dev/null @@ -1,42 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/specifying-software-requirements.md:1 -#: b34314bdb71244f2a263427f22172b5a -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:3 -#: c8609548e7904e65a5c395bfc07ad808 -msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:13 -#: e4c1c25793884b5aaead1fb15c2e6bbc -msgid "In this example, the software requirement being described is InterProScan version 5.21-60." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:25 -#: 91586b8767734e0ab01903f2562a7cf2 -msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:29 -#: dd7c487024b44a67a26765e59b5bf64b -msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." -msgstr "" diff --git a/locales/topics/staging-input-files.pot b/locales/topics/staging-input-files.pot deleted file mode 100644 index f9d75eff..00000000 --- a/locales/topics/staging-input-files.pot +++ /dev/null @@ -1,42 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/staging-input-files.md:1 -#: 3064f17a9bae442aaef41b9434cb71fd -msgid "Staging Input Files" -msgstr "" - -#: ../../src/topics/staging-input-files.md:3 -#: 09bb659a5cbe40948b59208f0fb77ddb -msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." -msgstr "" - -#: ../../src/topics/staging-input-files.md:9 -#: a1bcfead8f7f4270945e5512dfa9aea6 -msgid "`linkfile.cwl`" -msgstr "" - -#: ../../src/topics/staging-input-files.md:15 -#: cc0cd8765dac4baab9072a90e82e4f8e -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../src/topics/staging-input-files.md:20 -#: 77ac403083ff41e0a94b4376d57c4310 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" diff --git a/locales/topics/troubleshooting.pot b/locales/topics/troubleshooting.pot deleted file mode 100644 index cfd4aa74..00000000 --- a/locales/topics/troubleshooting.pot +++ /dev/null @@ -1,72 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/troubleshooting.md:1 -#: 628f6b4dad6d4b2e87d3c34d99b3bc9a -msgid "Troubleshooting" -msgstr "" - -#: ../../src/topics/troubleshooting.md:3 -#: c2f444d8af5b47b389a53f047f42f7fc -msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." -msgstr "" - -#: ../../src/topics/troubleshooting.md:6 -#: b4d58509c2874a3a9a4aca8b0eb54b8e -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:8 -#: cf0d233ea286443d9b4cd7b8e9b03090 -msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." -msgstr "" - -#: ../../src/topics/troubleshooting.md:14 -#: e742b4b7517a4461ab38cd572fd02412 -msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." -msgstr "" - -#: ../../src/topics/troubleshooting.md:20 -#: 8d0d5c4374ff4659b0a34f86a106915e -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:27 -#: 2c4194ab026e41cb807e7cb15bc37e34 -msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" -msgstr "" - -#: ../../src/topics/troubleshooting.md:35 -#: 0d287a4115ea4e34b239790ceee5d9be -msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" -msgstr "" - -#: ../../src/topics/troubleshooting.md:44 -#: b72ee99d9aee4c88bf4ae1a493b40415 -msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." -msgstr "" - -#: ../../src/topics/troubleshooting.md:48 -#: 6541e0afd1784cdd890cae031fc6b13e -msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." -msgstr "" - -#: ../../src/topics/troubleshooting.md:59 -#: 3881a8c9e89c42c3a4a9fb99dffd6de8 -msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." -msgstr "" diff --git a/locales/topics/using-containers.pot b/locales/topics/using-containers.pot deleted file mode 100644 index 03e278eb..00000000 --- a/locales/topics/using-containers.pot +++ /dev/null @@ -1,82 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/using-containers.md:1 -#: 3a1cb28acbf64b36b328af24b8ad3896 -msgid "Using Containers" -msgstr "" - -#: ../../src/topics/using-containers.md:3 -#: b0788dc4a9694fcface9c2d1122053ee -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../src/topics/using-containers.md:5 -#: fdb03600e95f43248a8841308892f95f -msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 -#: 7e27ca6ce9974ef8a68e4955c377a7cc -msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." -msgstr "" - -#: ../../src/topics/using-containers.md:18 -#: 7162dac152a344b78a196ab9b304ff96 -msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../src/topics/using-containers.md:21 -#: 7ecf64fbdd774b298455e9cdf5be38df -msgid "`docker.cwl`" -msgstr "" - -#: ../../src/topics/using-containers.md:27 -#: 7ec954f8c1cd4ba3946ed2b3bd675083 -msgid "`docker-job.yml`" -msgstr "" - -#: ../../src/topics/using-containers.md:33 -#: b80d058d42c2414299eca96c4edd908b -msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 -#: c6ddaf94bc9f49e2b507a3eedaf597ee -msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." -msgstr "" - -#: ../../src/topics/using-containers.md:52 -#: d0770aeb8b0546ed943d60a3ae3b9f9a -msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/using-containers.md:55 -#: d8c679b90ba14cf29280c1f1d271358d -msgid "`hello.js`" -msgstr "" - -#: ../../src/topics/using-containers.md:69 -#: c10409c624084be79a3378ae056d50c8 -msgid "Notice the CWL runner has constructed a Docker command line to run the script." -msgstr "" - -#: ../../src/topics/using-containers.md:72 -#: 28514dd1b76648eb9bcec48290d7b66e -msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." -msgstr "" diff --git a/locales/topics/workflows.pot b/locales/topics/workflows.pot deleted file mode 100644 index 9847836f..00000000 --- a/locales/topics/workflows.pot +++ /dev/null @@ -1,374 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/workflows.md:1 -#: f87317cca4ba43af87f6a19b8fff6751 -msgid "Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:3 -#: 00756723cfea4c79ab17ae39e400fd4c -msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../src/topics/workflows.md:13 -#: ee41e057c6be476e9c56ac3c1f4aefad -msgid "CWL workflow." -msgstr "" - -#: ../../src/topics/workflows.md:41 -#: 4e06945e9d794db58ebf5953a7bfc169 -msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." -msgstr "" - -#: ../../src/topics/workflows.md:51 -#: 3bb6bd3fa9a241b18f725f765f6d8f89 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:81 -#: bd0042b64ca14e5fa4abe0b696ed8cc0 -msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../src/topics/workflows.md:91 -#: f640b8cc119544ddb698828751335eef -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:150 -#: ef0a22597b7b43a09b9d930eb733b181 -msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../src/topics/workflows.md:160 -#: 08e47d409fad4688b3fa893aac699505 -msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." -msgstr "" - -#: ../../src/topics/workflows.md:165 -#: 979f0abe51a7435991c062b239ab77ce -msgid "Writing Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:167 -#: 9e7ebb3fd64e4d9b89d10aab7ff6ef5a -msgid "This workflow extracts a java source file from a tar file and then compiles it." -msgstr "" - -#: ../../src/topics/workflows.md:170 -#: a8bb6a54010c4563af5dd0e287e19ea9 -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:179 -#: ../../src/topics/workflows.md:180 -#: 3ca49084a67e48e196a29fce16266ebe -#: 2e5e721e9dcf477aacc5fd7970c8965f -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../src/topics/workflows.md:180 -#: cd69af46dab64758a7eeb25b8dd5ada4 -msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 -#: 1370172b5e4d41dfa0f00268853c4a0c -msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" -msgstr "" - -#: ../../src/topics/workflows.md:185 -#: df872d487e3d4e35b68bebcb27948577 -msgid "`1st-workflow-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:191 -#: 5039994944944010990efb63a1423bd2 -msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/workflows.md:198 -#: ce1bf8dbbe3c448b8d413993b986bee1 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:205 -#: a72841d1fc594789adca91a6cec6b4c8 -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../src/topics/workflows.md:212 -#: ab3448be251d454fbaf3e2e40e2a6179 -msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." -msgstr "" - -#: ../../src/topics/workflows.md:221 -#: b24bc7e75b5e45a6b40f99122f7a46c6 -msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." -msgstr "" - -#: ../../src/topics/workflows.md:233 -#: 9eab201c6c314cf682f7623de820f007 -msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." -msgstr "" - -#: ../../src/topics/workflows.md:248 -#: 7aee0e6910f841eaad08091daaa43819 -msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:256 -#: ad9e578cb5154c06b323ed8934f70359 -msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." -msgstr "" - -#: ../../src/topics/workflows.md:261 -#: 6edc6273c5e84842a74b8921875481e9 -msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." -msgstr "" - -#: ../../src/topics/workflows.md:267 -#: 1d4faf0025bc4fc7bf53b87e4b3477e9 -msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." -msgstr "" - -#: ../../src/topics/workflows.md:278 -#: 2185db6e6c9c470abc4e9a4dc95a921d -msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." -msgstr "" - -#: ../../src/topics/workflows.md:285 -#: 91c1093736ea45e59fafba7d071bfda4 -msgid "Nested Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:287 -#: 17955d02a70d484f8b2654feffc3f853 -msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../src/topics/workflows.md:297 -#: 4e9524ce607243b9a6bd749bc436d796 -msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:300 -#: 6d24477bbd3245a9be26954768605af8 -msgid "`nestedworkflows.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:309 -#: 5525e4fa9a1e4245b5cd3a5465952fa8 -msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 -#: b9dc7d7eab974749953065c7b7a92077 -msgid "\"Visualization \"Visualization" -msgstr "" - -#: ../../src/topics/workflows.md:322 -#: 268089a26de840e8a01026a3d4ad93c8 -msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." -msgstr "" - -#: ../../src/topics/workflows.md:336 -#: 1523ed6264e84a0ea3a2c00857a71bb2 -msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." -msgstr "" - -#: ../../src/topics/workflows.md:341 -#: 125add3880f84620bc124f21096e1d1a -msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." -msgstr "" - -#: ../../src/topics/workflows.md:347 -#: 423dd287ac0c4cc4a39b17dcc380fe45 -msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../src/topics/workflows.md:366 -#: d0fb2fada3c74bc2bb81928891b284a3 -msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../src/topics/workflows.md:383 -#: 27e720818d69436d8c85931749918ad7 -msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." -msgstr "" - -#: ../../src/topics/workflows.md:389 -#: efe03781d801470db0950ca5c33e10b7 -msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." -msgstr "" - -#: ../../src/topics/workflows.md:394 -#: f21f8ee263e043a1b57dc8148a502b85 -msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." -msgstr "" - -#: ../../src/topics/workflows.md:398 -#: 5c91e32bd51045ec8442b28875e914a9 -msgid "Scattering Steps" -msgstr "" - -#: ../../src/topics/workflows.md:400 -#: dbef641be8bb4a18ae974357ecb32f78 -msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." -msgstr "" - -#: ../../src/topics/workflows.md:411 -#: e86d663e2c39446b8c20c5eaf94a8802 -msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:415 -#: 19ae2b52a9ab4b6ea4d8d8e57f40c170 -msgid "`scatter-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:421 -#: b711df1f3b1b4456b015701700c3c818 -msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" -msgstr "" - -#: ../../src/topics/workflows.md:429 -#: 60fb4221648d40968e1a0965a3b6693c -msgid "First of all, notice that the main workflow level input here requires an array of strings." -msgstr "" - -#: ../../src/topics/workflows.md:441 -#: c249bd4f52b348faa46918dee778a75d -msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." -msgstr "" - -#: ../../src/topics/workflows.md:445 -#: ba039b00b2ea4de693b3358a036fd993 -msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../src/topics/workflows.md:450 -#: a50560beb0f84c59b52a03b755e4e028 -msgid "Using the following input file:" -msgstr "" - -#: ../../src/topics/workflows.md:452 -#: b1bde49eb1d6496a8d54094076e9c0f2 -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:458 -#: 18d238a1bba943778f951b22e777af50 -msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:466 -#: 1fef76f43e2048718f82b67f66f48197 -msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" -msgstr "" - -#: ../../src/topics/workflows.md:469 -#: 6c2c8927cadf49858e0e1b3033c22168 -msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" -msgstr "" - -#: ../../src/topics/workflows.md:472 -#: 7482860af6ec4b519585837fee90289a -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:480 -#: b9a64729a3c34bb2aaf4d9f780b29022 -msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" -msgstr "" - -#: ../../src/topics/workflows.md:483 -#: f3ad56146ff3429db2018fcdcef05724 -msgid "`wc-tool.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:489 -#: 4050c846b1144a5985b37c76bb24670d -msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" -msgstr "" - -#: ../../src/topics/workflows.md:491 -#: fc2512823ca24060992b321fcf0d56db -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:497 -#: 2eae7d61ffcd485aac22fc1fbbe7093a -msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 -#: 39971661faa74b58bf2f64c18a27fa76 -msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" -msgstr "" - -#: ../../src/topics/workflows.md:513 -#: b36f484b8f904da58838aac09e7c14ff -msgid "`scatter-nested-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:519 -#: 0db1e2093f8645df8f13fe394e8bf018 -msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:522 -#: 38a16292b8bb4ec48ae169292db7a2f2 -msgid "Conditional Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:524 -#: 2c07c2968b53407686a8dd3f869b4fc4 -msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../src/topics/workflows.md:527 -#: 61f0704412654df781833ffb6d5f33e3 -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:566 -#: d6634b5ec49e4113a90faec6b8de482d -msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../src/topics/workflows.md:573 -#: 9e6488eb6e60434eaf3148208a31a8aa -msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." -msgstr "" - -#: ../../src/topics/workflows.md:587 -#: 3fe08f086e374050a89a39fcb3db0b78 -msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../src/topics/workflows.md:607 -#: ec35b97546eb42c28cc9bbdbf2ac2067 -msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../src/topics/workflows.md:627 -#: 22cf017e76d74584991ded94417c19d8 -msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." -msgstr "" diff --git a/locales/topics/yaml-guide.pot b/locales/topics/yaml-guide.pot deleted file mode 100644 index eb8a5519..00000000 --- a/locales/topics/yaml-guide.pot +++ /dev/null @@ -1,157 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/yaml-guide.md:1 -#: c28a6abcd8334321b7d1c84192b42caa -msgid "YAML Guide" -msgstr "" - -#: ../../src/topics/yaml-guide.md:6 -#: 3e16eeaccec8491dacfde122153d5bd0 -msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../src/topics/yaml-guide.md:13 -#: 363eb3871f5d4c1288138dbd5f89be62 -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../src/topics/yaml-guide.md:16 -#: 31d7b17c34e0405b94f95e273bb22ac5 -msgid "Contents" -msgstr "" - -#: ../../src/topics/yaml-guide.md:18 -#: 60197a7f2b7c40c48ede3d59626a09d8 -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:19 -#: 7b76a198bd154da99e38146a74ecec6c -msgid "[Comments](#comments)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:20 -#: 024a6818d1b9492bb6e1f1c11d932953 -msgid "[Maps](#maps)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:21 -#: d0c550b003fa48c8b1b16888c7e9bc5f -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:22 -#: 7c2f8ceba9a141f097767ae8c3688aee -msgid "[JSON Style](#json-style)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:24 -#: 5cfa92e1509e41cf9dec646d3a5dad86 -msgid "Key-Value Pairs" -msgstr "" - -#: ../../src/topics/yaml-guide.md:26 -#: f76bccaee68c4eec96822d00013395a9 -msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:42 -#: 5591f710f08a4e8c8d974224cdf018b5 -msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." -msgstr "" - -#: ../../src/topics/yaml-guide.md:51 -#: e383736713e243d487b883e669fb7065 -msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 -#: c50eafc65e8b4b8a81318694098a42e5 -msgid "Comments" -msgstr "" - -#: ../../src/topics/yaml-guide.md:63 -#: 3d8de32c3f3448e5beb19d395099e27d -msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:76 -#: 20edeb5c184f4df2ade328131365d751 -msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" -msgstr "" - -#: ../../src/topics/yaml-guide.md:79 -#: 7f436640365249568802a846d4ad896b -msgid "Maps" -msgstr "" - -#: ../../src/topics/yaml-guide.md:81 -#: 7514de6b828f44b1b1d8683d8324a1da -msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 -#: 01288d81ae2e466d94bbee33751b3bd6 -msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." -msgstr "" - -#: ../../src/topics/yaml-guide.md:127 -#: 3e6ba9083cdd4ed586110f76cd071896 -msgid "Arrays" -msgstr "" - -#: ../../src/topics/yaml-guide.md:129 -#: 2c23b44142ba4969bd30c33c97142aed -msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:146 -#: 5956220b3839466aa491e84d2d0a5757 -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:167 -#: 0ff275ae871b49449ec789b1bdc814c6 -msgid "JSON Style" -msgstr "" - -#: ../../src/topics/yaml-guide.md:169 -#: f5215b7de4994cc5890886ac2914be23 -msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:177 -#: 48dec799be364824a5dcbf5329f1f0ce -msgid "and:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:184 -#: b4d3a3a2823147c9aa7a37ad2fe5ce06 -msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." -msgstr "" - -#: ../../src/topics/yaml-guide.md:194 -#: 6998b8bd38a944f19c9ca758b14babe8 -msgid "Reference" -msgstr "" - -#: ../../src/topics/yaml-guide.md:196 -#: bcc40a813d344c0abd960add8685e132 -msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." -msgstr "" diff --git a/locales/tutorials.pot b/locales/tutorials.pot index 7864fea7..f989fb64 100644 --- a/locales/tutorials.pot +++ b/locales/tutorials.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,41 +17,41 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/tutorials.md:1 -#: d32522e2993f4b48a789f46537fa5ebf +#: b963a4be60544dec9a0c34e04aa43371 msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 -#: 63a51dccb29045fd8f78d5e396c6e050 +#: f9246ba9313948f7b8547822aae2305d msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." msgstr "" #: ../../src/tutorials.md:7 -#: cb5f8748a5544be2835467ab07eb7a1c +#: 9a3d1f4c2d0b438188e84b692f831dc5 msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 -#: 685d0cb2faa04703bcef408ecc2b92f4 +#: 3c4d6087706b4c90ac69005cebed9adc msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 -#: 20f45705145d45fc8420c4119b06a49f +#: 585908b83f854dd7a28715a4a0f6b1c4 msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 -#: 2bccd19d542d4458a1ba8616236f1840 +#: 8934504b3c924a7d812014c344d58dce msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 -#: c491c73e4c00476980438ffc79c6e4d3 +#: 0c6b1dbd9f464c698322783bd55d6d6c msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 -#: b8485449206542e097584eca7363c8ce +#: 9a767964b3cb4f619f0b7a7d5d08a97d msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/src/conf.py b/src/conf.py index c5000204..60ece96c 100644 --- a/src/conf.py +++ b/src/conf.py @@ -236,5 +236,5 @@ } gettext_uuid = True -gettext_compact = False +gettext_compact = True locale_dirs = ['locales/'] From 230d934d45eeed062b6c02c94b5c9011db4d8fd7 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 24 Jan 2023 19:58:36 +0100 Subject: [PATCH 33/49] refresh ES --- locales/es/LC_MESSAGES/LICENSE.po | 120 ++ locales/es/LC_MESSAGES/_includes.po | 28 + locales/es/LC_MESSAGES/episodes.po | 31 + locales/es/LC_MESSAGES/faq.po | 307 +++ locales/es/LC_MESSAGES/introduction.po | 746 +++++++ locales/es/LC_MESSAGES/setup.po | 31 + locales/es/LC_MESSAGES/sphinx.po | 28 + locales/es/LC_MESSAGES/topics.po | 2577 ++++++++++++++++++++++++ locales/es/LC_MESSAGES/tutorials.po | 58 + 9 files changed, 3926 insertions(+) create mode 100644 locales/es/LC_MESSAGES/LICENSE.po create mode 100644 locales/es/LC_MESSAGES/_includes.po create mode 100644 locales/es/LC_MESSAGES/episodes.po create mode 100644 locales/es/LC_MESSAGES/faq.po create mode 100644 locales/es/LC_MESSAGES/introduction.po create mode 100644 locales/es/LC_MESSAGES/setup.po create mode 100644 locales/es/LC_MESSAGES/sphinx.po create mode 100644 locales/es/LC_MESSAGES/topics.po create mode 100644 locales/es/LC_MESSAGES/tutorials.po diff --git a/locales/es/LC_MESSAGES/LICENSE.po b/locales/es/LC_MESSAGES/LICENSE.po new file mode 100644 index 00000000..a9655e9f --- /dev/null +++ b/locales/es/LC_MESSAGES/LICENSE.po @@ -0,0 +1,120 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../LICENSE.md:2 385524707375429989b7b4fc7e4c7aa5 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 7682a147e3f74921948bde67ac684338 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 7273f384601c4f18a4cc33c833f05e56 +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 2cd9327d0e2e43aaa963633db1320b96 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 793123b1e0ba4603a0c54c952ea4a590 +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 151178e4c9a9444fb65dbf926edad28d +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 e44aed84ff0d48b3aea3946b3a7c85fc +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 d8bb44ca55b642d6bb4a88eaa8292204 +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms." +msgstr "" + +#: ../../LICENSE.md:22 6859f286e52c417096b072c923b9f235 +msgid "Under the following terms:" +msgstr "" + +#: ../../LICENSE.md:24 ee4ea8e1fd044924b34b2d96ca158257 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" + +#: ../../LICENSE.md:32 7598558aee3244b6b7892b06df94a393 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 a83123e7ae79486c80107d176ea951c7 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 0cc05e8ed5274019998b1dfd6ab76824 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." +msgstr "" + +#: ../../LICENSE.md:44 d70e680300524c8583f1e7fd361ad2ba +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 d17e76d478354904b679b4f5ebde418d +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 015fba86005946eebc5959cc3b0493d0 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." +msgstr "" + +#: ../../LICENSE.md:57 524088befae04f5485dc731d505c769b +msgid "Trademark" +msgstr "" + diff --git a/locales/es/LC_MESSAGES/_includes.po b/locales/es/LC_MESSAGES/_includes.po new file mode 100644 index 00000000..ed23c04f --- /dev/null +++ b/locales/es/LC_MESSAGES/_includes.po @@ -0,0 +1,28 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/_includes/what-is-cwl.md:1 66189f9a18df470791d7e6ab690b3475 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + diff --git a/locales/es/LC_MESSAGES/episodes.po b/locales/es/LC_MESSAGES/episodes.po new file mode 100644 index 00000000..1dbd9f7b --- /dev/null +++ b/locales/es/LC_MESSAGES/episodes.po @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/episodes.md:5 49382fe02e4f4aae96ce4d1b666d649a +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 ebd3b75bc9a347029e9e164e94b43374 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "" + diff --git a/locales/es/LC_MESSAGES/faq.po b/locales/es/LC_MESSAGES/faq.po new file mode 100644 index 00000000..ba1f01be --- /dev/null +++ b/locales/es/LC_MESSAGES/faq.po @@ -0,0 +1,307 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/faq.md:1 e53c79b325b749a691434bf2f7825a5a +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 d95bfefa6344474d9820a266922831f8 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 991a77ca372d4324843ed340ffbfbae7 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 4654eac499464be4845a59bc281ec242 +msgid "" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 4fcb9907771940d8857fab5b8211d337 +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 9f3ed67bcb13459d9e7196e9d82cb58f +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 af6d80606de6412a8fe63ee379702eac +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 fc7c21e08e8e45adb8f1265af494160e +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 e37343ad3edd412f981397b995e6c841 +msgid "" +"The first method involves adding the folder containing your scripts to " +"the `PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 2b7e94e816fa46f4a221b5ce6b2214b2 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 0fd0fd13672d48cda0f3ef7f2b0701da +msgid "" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 a21be18c313d430a8986760ee3725198 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "" + +#: ../../src/faq.md:104 404295b5792747c8a87306181d078cbc +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 92582f3845b446d08ca9cbc4ad76a0a7 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 2d62b6e5d7944818acd0f43b7d37ce67 +msgid "" +"The second method involves including an input of `type: File` in the " +"script itself:" +msgstr "" + +#: ../../src/faq.md:135 c72fa80f79594d479cb99dc6bfcb207d +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 5f2b7881a7c64cf29b05b4d78158e176 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 eb11641ac17e496384a60e4aacc5209b +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 c0aee2cf9ee046128002b09a8aa397d8 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 34a04d6d09e94fd796a5ee13c6b9856a +msgid "" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 b1ee951a6e6e4f4c8e88de4dc93bd616 +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 1664807c6b264fc3b58e9f2c40a9543c +msgid "" +"Using " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 a7ab83c7f31e4e8d83fbfba1abadef2b +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 908451dc6990489e88edc1012899c440 +msgid "" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 30947198b46d4151a5d92076c30659c0 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 0b320fb2e40442608137ed9d6f2a74cd +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." +msgstr "" + +#: ../../src/faq.md:229 a143590b23384ed79fc37b17a0abd46e +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 6b36effcb80040c79396a1df241f635e +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." +msgstr "" + +#: ../../src/faq.md:247 2873af63ee324fab948d16a9e14db5a7 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 a11f170a082a4df2b4a0c068dd0573ed +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 bd2ccba5ac7e486c9af1d906ad96b07a +msgid "" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" +msgstr "" + +#: ../../src/faq.md:267 3f1d8cf3390c43f8b78ce33fc020f1a0 +msgid "" +msgstr "" + +#: ../../src/faq.md:268 89626d59c2164bb99d0b123def33f701 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 028c6179803b4dc8a718669312804101 +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 23d9d603d4d44880aea5ebfd86e02d8d +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 06ae9317c6af481bbf4fd70236ca10a9 +msgid "" +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 0c6c0af33a274a8cb64ae3111c014338 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 1139a2f4e58046f9aac4c64b7d5a2e4d +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 ca97418a37bb4ae99bce1b44eebefbad +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 7a5d2d6c6474492fa65ffd8a5048c733 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 2549c8887b204ddabe4221978dce7e57 +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 d15ae28e932446b48bfc1dbdc34d8eab +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 925a0bb31c5f428b93232e42d96bddeb +msgid "" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "" + +#: ../../src/faq.md:371 591dd97f12ca4b8ca263b17abe674fd6 +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 3ccdf1a970c14cbe8e1d269dc4ae77b3 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 4cefff22947f4d9eb2f66d1b6bca2a8f +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 bfcbe4003ccb4e59baeed0b631871970 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 d729277d8bc0488eadddf507ba63202f +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 ca99353cf8f94d11add95ba36408ee46 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 deb9ae92120d4e30aebd6e4d0374a0a2 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 7f4054de28a243c89bd3aca1e2764b93 +msgid "" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 29658fd7b5724addb5074891942f79fe +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 2dd0d8092e5640e3a930478497b78efd +msgid "" +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." +msgstr "" + +#: ../../src/faq.md:450 0d385ebff8c14cbfa418fa45c9b42e51 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 67d82ee82a184ed3921da6fd1928e83e +msgid "" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + diff --git a/locales/es/LC_MESSAGES/introduction.po b/locales/es/LC_MESSAGES/introduction.po new file mode 100644 index 00000000..3452a5bc --- /dev/null +++ b/locales/es/LC_MESSAGES/introduction.po @@ -0,0 +1,746 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/introduction/basic-concepts.md:1 7d238c155d6a40df8c8471ebb448a41e +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 4af76ab7bd674e6ab73765ddcc81d5bf +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 4fafbbbfec734215872f455f1c7e62e9 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:2 7250962d9fcc4338a7c9e64e0c2b3868 +#: f8759274ac67447ab61551060918d9bc +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 106e3e4dd19b42beaa90908e17529869 +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 eb85aefcc6824c028479e299f3477c5a +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 59a0083e4e594253b5eb0a6d2756f271 +msgid "" +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 19dbee8336704859b5bd9f232879e81e +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 947d98768fef4c3cb5b87208303b5712 +msgid "" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 de6edc23dc9b4759b2aaa0954050b6be +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 ccee7288b79745d9a6a4bb32e9249594 +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: 10b787163c2e418291616a7bc1caf0bd +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 0176badcaff14e79ba00f1f26c40f42d +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 36e1e02745a44b4ab7f80f593eb3c408 +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: c3e19102cf7d44c795dbd57897e4ad8a +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: 288483391ca742e18ed19cd89666c4a1 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 5f5df951ffd6414eb054ca3af83a1abe +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 430425889a4c4f0a9f774d1b2e67debb +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: 9e42047299834ec6b41edf6c1b6d6513 +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: f6d4657261e042fd8bd9782047d19ea9 +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: fb8fa26ade2e4555bc5904a680d4de23 +msgid "" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 1eb86d0cb6c74685829e7f978b177212 +msgid "" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: dda24aff00964493ae997f36dff74c04 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: e696bf67d6d04416b3f9c43f12376a10 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: b9746c3e3e554c2684be3917a31c7d10 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 8605fc09a1a04ab7ad271ac2bea9a17b +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input " +"directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: a1fb5f8dd8964b6fb8990f7e877f8e3f +msgid "" +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: 8fe3e01579524ef2badf284092ce00de +msgid "" +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c0ca689a49334564baf49359b582c491 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: fa9a58da83a04493bee1d1e6c1cba8e1 +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows support the creation of FAIR data " +"and adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 93e390de3c1445e5afa0a8bc8ee99480 +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 4b5b1dfad3aa4fee9a41463d5feeb8ea +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 6c0621375a704ed0a79d4ae65538bb31 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 357ae9a25a644caab49ddb3c9ead1028 +#: 646006005df94092ac1134bc194d5fe7 e495fae55ee1480c88438ec4dcc1fc5c +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: ab4a78d72dfa43b180615e565080d07a +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: ba8d7155363b4ed59912fc426b207ffc +msgid "" +"The CWL Specification page in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 37fc683fd3564bd698e3a8843ed7e401 +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: e6af1cb1c3484a1db8fa8577dd5684c6 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: fe7682c04d344a71a2d1de3586f83f38 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: caf02d5ff6c04255a2144ff453884b0b +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 a22112574264441eb4b775ce72f7ee62 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 fe9e792085024abb95180662bf0657a9 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 23849325192045f5aa48c9f3d9a2080a +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 c7c0e1cd18d54dcca7062d7d053dcc35 +msgid "" +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 5d7a4a2cccbb47bbaa9ba2ca2de1eff2 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 a0ebb398fd1944858fde855a37938446 +msgid "" +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 83d90d246db24c07a73bcd73a3c6bfb6 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 c2fd09dd72af46ca8e3284d0c1c7dffb +msgid "" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 00694f21c8bd435f9de10785d2a829dc +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 3cd6a5a0a9754a678ec4eb5a9569a2ab +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 2b0d2a5dc85c4216840c2ce406e10413 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 0f8ab0f07c9f4e92b6907685a21e0d09 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem" +" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " +"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" +"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " +"details on installing WSL2. Your operating system also needs internet " +"access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 eb1b97c2f64c43c78cf620f0b3197707 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 b0fff1b3d67e4e01b7140def8004924a +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 dfad9ccfdc5949adb5785e57a3f0a345 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create " +"and activate a Python virtual environment using the `venv` module, and " +"install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 229d3b94015c46f89a7fcf3035a06e38 +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 bede33df513b4ff0bf31a1c4a1b76304 +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` " +"and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 f20e6ae025fc48cf82b490aa1e45d978 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 10c729f31bd94b2580a494a07e8c8c06 +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 55571e0099af459bb38ef2cbb5ce3720 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 436d10464d0540da9227bff0e7721928 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 db76c196cff7476c9f0059410071109e +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 5c34965d08704905af72df2d02f399ea +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 c4b1c6f7a6214a2a8cda037dfd1ce5e7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 22b70a1995e24ae1a5e688b08d69be78 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 2b078afe85c9496ebe7c4fd5fa849506 +msgid "" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 edb107bbbef94363a531344862b0646b +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 c92da002f02148e485fccabfb80f78c6 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 5ff5383fffc646cf860b9e6adffe0d4a +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 3fb6539b1da24c6d8cab103ebaa728e9 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 56f8f92a8e4e46de9def7d33926a9354 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 f024c312097941cc838f6e4684709e2d +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 27eb4624fa6a4fbca5c842bc69e277ff +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 a086a591e5034a768d6ed9f95ccffb41 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 dacb4f334ee64afa9da1418b806fbb8a +msgid "" +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 64cb2e80ed554f75aa64bc856c011e74 +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 7c008d7286b242c4989809773075e369 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env ` rather than" +" using a hard-coded location, since `/usr/bin/env ` looks for" +" the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 3d0c3d9473b64745aaadd1c97f86e6bd +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 f87429becda74bdab6e9e8956da16786 +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 40faebbbe3974365adbf4190ac9571af +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 24ce76cffa4c4dc3b1471c932ce34d28 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 1a14a5c5c15941ff8f957be9b7e346fd +msgid "" +"cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 6fccaea992b74740b91aa4dea1e9b6f6 +msgid "" +"The CWL community also maintains a list of editors and viewers: " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 ff2d02dada844e349ce39147eaec02a0 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 756d50a22d9944989e83fd49691b7dc1 +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: " +"." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 208ae40269d64a95922c3b6b88fa7af0 +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models " +"with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 676cbeed9ecf468587f88adf03f088f2 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for " +"pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 97048cb2351f4408946828ff46cd513e +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 28810c389a8f480d8af7af37580fba6e +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 6eba770f0a494294ada23cdfe563ada6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 bc84e8e2bd7b4e2eadf8e09b64f8b11e +msgid "" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 244007c12d0e4c11b5bc5a50fbb7b263 +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 1b7f68f5a3214f4da4f1887d14ced464 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 aab574ceba8348b7a62c1c645c7ae300 +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 e3e88da22e65425292b19d8159e6bcdc +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 fbdbaead418f4246b4216acce9c6a51f +msgid "" +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 008fc4481f1c4c7bb215fa3b6096048f +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 31d3ab3f31c44729989ee72a756c7242 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 069fa8bae74d4c24b680c4199d714277 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 62cacbc189d0440ebe4a8dde4878450c +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 f208e50c0089409aa7463c915be80092 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 6c551e9af341475496b7b6b104330183 +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 da2c9a63648342aab3f3b8a34660a4bc +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 1217d999216f47aa8f1903e2417fc57a +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 3559a76a1fc64f3eb61a503bf7c77757 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 21386999503341408b798efa9fc4f262 +msgid "" +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 215e425a5ae64cd0ac5e8d34d7f47b58 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 963c003c4a334dbe874edc0ab38ea92f +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 83921375eed44fc695cbc172d9317032 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 9795092d234e4fa5a2bdfc4c9c02460f +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 8846a5ff35b64859b8ec7b16be9f8f6b +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 785c9e2330b045b39bf02f77ab6513f6 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 b6d05398bca648b8ac25755fbaab91c0 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 2ccf7e847e0b476493ae514381ca3612 +msgid "" +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 d7168eb1f7384733be6316fe72f486eb +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 14bbd3ce1f2a488ca919d4f26c8f1e5a +msgid "" +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 86f1fc65d2d14a41ac282eb63fd9de86 +msgid "" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + diff --git a/locales/es/LC_MESSAGES/setup.po b/locales/es/LC_MESSAGES/setup.po new file mode 100644 index 00000000..68494d21 --- /dev/null +++ b/locales/es/LC_MESSAGES/setup.po @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/setup.md:5 715f40c8e3f544e4805ae2b456b9d699 +msgid "This page has moved" +msgstr "" + +#: ../../src/setup.md:9 c9641546c55a44eab9ae40ec272d5df8 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." +msgstr "" + diff --git a/locales/es/LC_MESSAGES/sphinx.po b/locales/es/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..1c2687a9 --- /dev/null +++ b/locales/es/LC_MESSAGES/sphinx.po @@ -0,0 +1,28 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 ada5c93414a84374b3eaea93dc11ae74 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 a3cc1c498bad434ebadd4a2e92dbf5f0 +msgid "Section Navigation" +msgstr "" + diff --git a/locales/es/LC_MESSAGES/topics.po b/locales/es/LC_MESSAGES/topics.po new file mode 100644 index 00000000..80ee8dd9 --- /dev/null +++ b/locales/es/LC_MESSAGES/topics.po @@ -0,0 +1,2577 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: be1d17fdb27345ffb7fe0cbe92002434 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: 82ff1f5ebb0647e886d131f7a8c4f5c3 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: 4dbbc91d876746b59f53d3ba49df43f8 +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: 82f4844017ec4f609c8f0f5bf9812f75 +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 afb24d50c0a94693ab9ef9271068e58d +#: ca7a2bce1de34dd2ad8f77095854037b +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 23f9dcf2c7344a40aa2d512f1349135a +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 3d26cfb6a1204ba89ac812bc4fe3df4f +msgid "" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 317f82f2a0d54af29baaf5e3fca1558e +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: c5f85db684c842a5a2d55afb8ea44e94 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 92154668e72240e48268a3dc593f65c5 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 df0c80b10cde412c901b9bfa235b4521 +msgid "" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 93e66f6c1c9643a3944ad3c7651464a1 +msgid "" +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 7b54e111b9a2485d912b9c1dde0e6816 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 c58100a01b034441b247e761df1f6a12 +msgid "" +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 53c3357a75df4704a96848aebc093327 +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 a9ae73ef4d3447038d1180032b41255c +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 a2a654e113d64f37bb3bfcb8828301ce +msgid "" +"For more examples of providing metadata within CWL descriptions, see " +"[the Metadata and Authorship section of this User Guide](../topics" +"/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 66ad30cdce23481d90042b63c3bf8d16 +msgid "" +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 f3c0be3d1a3249288a8cd3053bc1cdcf +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 07ad1cf2508d4cb780a6e703c07d5a5b +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 f0931e33e50a495aabd1c58daca72c3e +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 3da4c1e61c53469e8e313553130a5b28 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 8d3930c2039347beb1383b0dab7ea1d5 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 275a541a634345d2b88a7e982d3a84cb +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 23e3e58d1b5245919d1be053b0c53ddc +msgid "" +"Each `CommandLineTool` description should focus on a single operation " +"only, even if the (sub)command is capable of more. Don't overcomplicate " +"your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 0a7b19343ab34220a615f9d5735f62f3 +msgid "" +"Custom types should be defined with one external YAML per type definition" +" for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 fbb538cc258a445a938333315248a4f8 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 dee070dbc0c54210a3b276dcd1e3b151 +msgid "" +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 0d5c1c5e50de42809afdf4bcddeb86e0 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 63a5664bb6f043529e753fa27faa9104 +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 e3832fa90bc540dd9c92dc606c8a3d1f +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 8a2e36ed7ae0486b9a569b8a7c336fe9 +msgid "" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 00dd50adbb734f0ab7e08d005cf30487 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 eb2ea54b83304757ba4b835d4ae45642 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 ad6f136a690e4c4d9320cbff4b1a3469 +msgid "" +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 3018247f156c470ca7b9c7801a6f59bd +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 7c07c9401a3d424089828def1d272842 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 d5300fa60ee942cc961594a504b0d08d +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 f56c8f69d71f4f4da40fbb007008500e +msgid "" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 4621ef6fe81a4048944814aff22f508f +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 1d3f1abb81ff4186843df880dc732ee2 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. If a command-line tool is written manually in CWL v1.1+, there is" +" a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 93f0719b3b2c4c5297bf925801c93b45 +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " +"Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: 46b4df81014846aea9e0fe7c5caade0d +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 722ed10f0fed4ff59852fa09c45a92f1 +msgid "" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 20b151c8c270433ab74288011f2ad47d +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: 0625cac27fdc4127b50bd7f195117189 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: 2035501f61434c339a5abdf693696c84 +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: f6e00a5502ef4bb386ee5f88b0085527 +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 4fbbc941c4f7412b936446fbf9115363 +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 9f546d2c6a454542a860ead319642479 e6c179499aee4824a5c02babbf26a869 +#: eb2052144d844cdaa0e9e4b3bc487628 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: d9ea213b07e64d04b53cdb32a3650322 +msgid "" +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: fcc7a6d59f8a4e13bf821d488fa17db7 +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: f7c967a182734c8ca47f873a0cb28093 +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: 20f1807303474b5c8c18cede5df322a3 2c41b94f3196446ea483c630af9eea67 +#: 5735865bd655415a9a136f441eebafaf 7364d5ebf81e4949b3212b06788e2381 +#: f1195863b1b345f9a718776763466533 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 d2e58b004bfb4c6cae7c69658de21321 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 484ff45699964c2996a0cdfea0fdb329 +msgid "" +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 c30f12911bb649c6b71e7ad73edd0b4c +msgid "" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 c8ecf2ef21fa4b8ba562625355ba8a65 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 3f328356740644a582ca21d5fa60b2f6 +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 b9569867a46745268f37ff47c18079fb +msgid "" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 636449effdeb481da9ada5d283db2ab9 +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 d6d41dc3bbd746bab0a5905a8611a356 +msgid "" +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 e742d68f3a994b9595bae07ee2099831 +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 f338008e7fb646038a7dcec456d9dce6 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 e69fcaf1f01049d6824058969e87e0f0 +msgid "" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 31abe821b66643d098ecdb4e207ed064 +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number " +"of cores required for the tool to run successfully, as well as details of" +" the version of the software that the description was written for and " +"other useful metadata. These features are discussed further in other " +"chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 b2a8bdbc4e4347389dc9e2c34e7c71ca +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 8de1ffb0a81547f7a616d5ea912998c3 +msgid "" +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 9596b81e881549fba7910947a202ba5e +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 8473228fc0104b4c940a967294276542 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 75f469063959433a8ed459c2b09cd61f +msgid "" +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 6676f841711d43f682e18d954438fc65 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 d6d043d8ce9a41c59ad0d3239f8f306e +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 f3378c740b854b9695ea6ccfb0ab434a +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 c9d5c0dd3eeb4617891f90d1a081a3e7 +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains" +" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 08240053421545288788e84dec6d6614 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 cf3ebc8d28d2443ca0e67b5974a963ab +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by " +"the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 767a6dc8370b4f9aad42e07a657e3e1f +msgid "" +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 f38d9e8192614ba689d17c1cc48ac848 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 ce88970e57f2427a905e1bc66c20ffe8 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 e7238751e3604a34a15fff753136eada +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 ff81d45c3f124c738871b40e5b717d7b +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 f92515a70adc4366bc46e2eacf49e47b +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 dcefffb5ecdc4ec3bcc216c21df896ec +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 bdb0a61e53cf4521bc0f16593eaa5fdd +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 80c3b1fb37aa40038f0bc98905604c47 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 22a6a66f05c94b988789edfc7acb7951 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 f09db29f329141e6b3dc3bf348e62b92 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 ae0f7e0009944da58df73fbc70600fc4 +msgid "" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 3c17c559cfbb4fbcabd0dd57afd0f710 +#: b2c2a86928eb40a18e72586ca43ac3f3 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 0042cbd326484bc985f48f469bedff14 +#: 447dcc99dc59453ca560d6c54bf8d7bb 996a1497269345569208c861d8bcba6b +#: ab62eac4484146cb83f26c5bc74a92e7 ac9c83c8605d47818cd2eceaa107e44a +#: ee13a1bcafb0428abc6f97816476b8a5 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 2054a8bc6ed643129482f73bd0b53823 +#: 4bcda5432fe74135ae0d31b4eb0d5d7b +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 4e5551d884b74e5caa0cad273883fa11 +#: c37ea64ad4f54949b17e442698e25a49 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 28453a745d8f468b94157409007415de +#: 7b476f5cb3f64cafadbd962d465eacee +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 12c9aeec38514f7193d41be7d2b81976 +msgid "" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 280eea3ba89e4d84a5a8bbb14c74e36c +#: 447f71c801564eefa5b04659c834ea23 69f163066cc04c30a34d7b97ac7a4bc2 +#: 6a5d8d98b190442f9aadc2c074227835 89fba2d03ddd4cdc943e9175bd0ece33 +#: 9a9fa9f67e434ddeb38b339d004aec53 c533a40746e44835a82b1cc6461576b4 +#: cca5748633ab4899beddd115e0178db6 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 05182018082a474384e29c2ff90cb060 +#: 30217d1193e142729205e28e4cde49d7 308e0245ba0b48fc8f665d12ce5fa0c0 +#: 64bef9a598ed4adab4b517bb8f23fb25 7f7bbf1a07684e54b97ca1950c34930b +#: c3ae98ea21e244e3a76d06b87aa8bfae d4f067c6c06c4059b133c18affdac280 +#: dae8990502254aa99cc1ba44bd42bc89 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 88c61f4dc48f457b828143b1f0e86168 +msgid "" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 2473f34317664da3888f6696f1bce0e7 +msgid "" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 ced207b70446434bbe64d228a34c825d +msgid "" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 9b6ddcbbd00c4f5fa4088674586b8b60 +#: d02b26eba3b44df5bcc65436f66248f9 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 38ebe3bb55484f61be01dbd31274b05c +#: c6018e429f30454cb30a33a92c39bda6 +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 a13cf40c0af743dea7589c4186465d1f +#: f51dc811ec154fd6a0b60d637ae42f06 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 a115dab301e34a958a9acea03c2b76a8 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 1540eea771934469b6b092c7eba2c223 +#: 6876d25a0d324dcabc7ae2e6202378a1 +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 927df10417db4669916e08b9e4e37641 +msgid "" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 75ec03ffd3e64fabab680a2fcc66e0a4 +#: fa2635bff88c49b38401e2c87035d023 +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 cbe310d7612e4f68b4832692cc0d145e +#: fa897f1a899141fc9e6be1b6af9c01ce +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 ba5b5e8410df4acab9ad6459df2ff061 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 935d707d1e31415e806b2bbcb851e322 +msgid "" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 89f051a47b99491b9ce17ded769ad1a3 +#: 9d59f22a9e734f8982b89830b4e7e6fc +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 182e1b73426e4367bf8fe430a415a9c6 +#: 5b5d3f05e6c647a38af612c10b2b8b71 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 3fa480e44ffe473abb3af953f2d000f9 +#: 6375ee37a7fd4fa19be33c6f0ae75196 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 b6d5c6ff972a4607873daa53817a6860 +#: d0a0be70585842d8b17a8ddc7fabfc3e +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 0d558c8e126f427ca9862d7dae8a2cb7 +#: 293d592f29e34a5aa4f7420368d2f24b +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 43f37d9ec9b5429ab811039d1e8211d0 +#: b3a9149a14d346fbbc844d4de2cb3acb +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 5dbe9152fa2b4554a4ceae0b5163a7f8 +#: e137a1254667427f816aa6b5219e7f26 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 7af83d9455a944c180349d9f3123901c e8219f72a0854febb800511e2897cea1 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 f3f205c655eb4a2fb8c34407ee02fe76 +msgid "" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 0f3325af2b674d07aba8d1b254b7bb67 92c818fc42b64e94b8a3bae737df6ac6 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 a8bc743f7dc648889ce51d8a787597dd +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 04b9cd485e1342d0870c341321089d15 a07dc02fe7bd416994f9755934e6a524 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: 69d9c547532644408b14655f50175684 df87b2c504dc4ae8865a0f4c94a84dff +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: d248acde95024c94b3921e290276a2d1 f77892ff017d48fa833343150cdad6ca +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 c0909df1820f40d599151a7b45db2f04 +msgid "" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 2d62117b8b824035916716cc818348d4 9f0237a087b5445eb0a8fe474d3e3869 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 bdbae4965a344e778ed0e80a8e23845d +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 1af8bb96001e43d9b649044d9631f360 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" +" attribute that allows users to load external JavaScript files, or to " +"provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 303ce6bcd17d4a219d2c3f4079e9b332 +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 d4e0acefb25d458982b37167431c8364 +msgid "" +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 b43add5b2d72451db8eee00a03b347a2 +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 0908315609f1413392b2ed9b5769a62b +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 d8aac17a8a9c4c209695ce760fc4cffb +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 2deae9db0d394245bf21ba3e469fb64f +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 6849411091ab422f8ebffc27e68c3286 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 a74d3576acbc4694bbf75d371c57c4b0 +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 330e32b4188141c083465fd77ac0d962 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 61fae30939644f2e830107bb6815659a +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 8e057a368eae43f892cdfcf1492fefae +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 108a176667a74331a9c634537c6073be +msgid "" +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 dc1a23ba61fe417aab857a2cf3b87d09 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 683b69656c23424d9a171f72cc1ee355 +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 a2d926603ed24b13a77a64606b72f7db +msgid "" +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 f00b6549fb2b40c7a0930fa2d70f78e9 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 02364803949047ddbad575b3f7ed27a3 +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 8f25e0b9d6564f089bc07050eecd2cbe +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 051d96f1784a44478c888a692a43020e +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 c0b16138c24243f7882de4ea02ef14e4 +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 05c4a830b7084575bfd35263d9226104 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: 1af1e2ed821a435088471aa1d28c039c 441a574563f246118f24fc1ab8324b2e +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 241dfed53c39469d9e340a2494f97572 +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 c377cf86598d4ca4bf5311a47978e302 +msgid "" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 53ff3c58049a4096ae894c4b0214d5cb +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 6c6c380437634412900e3f8dff4558f6 +msgid "" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 4ca0f8c05d9e451387a1eda0e6a04dad +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 339cc31ba40c4d2cba0ff21d668701b6 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 802f62184fd545eabc2afb78d90930c1 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 9b641ae58d834dcc8a79fc547ead64a0 +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 8886c014968d4e32b0ce1cc44a9068a0 +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*," +" and *null*; complex types are *array* and *record*; in addition there " +"are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 f40f938f5ac140cea72a4146a3329579 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 415298524e35434ea19a25c31e9ae649 +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 e8b631d0d4e64779aa7333b8e756fcbe +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 c5f3fddee0734d2da9207d64e268463f +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 fed45d1ab5574bd889af14787ac2cd20 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 1654a2e9bca0443c8fb46f7191beb81a +msgid "" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 b22b453eb5d0497e88243bcfc4d3cb1b +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 c136e4badbf3429b8c9c9efbc91d7f65 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 31ddeb567d744c21bbfa76e8cdf95e6d +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 b19099fa3f3a4b5491e094f1ababc4a2 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 685e49311ba547f697fc90073168041b +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 d31fc4e804a34097ab506fa3aa469b1d +msgid "" +"The field `inputBinding` is optional and indicates whether and how the " +"input parameter should appear on the tool's command line. If " +"`inputBinding` is missing, the parameter does not appear on the command " +"line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 26ca8366924a442d9a3fb26f7223b028 +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 e9ba36f7d5ff4776aad272c9a0a7a81b +msgid "" +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 bde0dfcb13ea4ac8bab41a8c3fa024ec +msgid "" +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 0a38fa331eaa41ad9d61c869e5b73574 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 afe9f6fca7314610b25aa519d145f1c8 +msgid "" +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 e976913dca354fd1b027ceba53e279fd +msgid "" +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 3f5437225c06473ca6d99f256b735771 +msgid "" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 e0a6c25648394dc4a06c1a1ab11656d1 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 895ca55530674398af4f3ab0a2ff8295 +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 2c9f27b7c4534f5087194653288fc473 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 2f54898bb89b4f24abcbb9e032b14fac +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 07e7e4b0f9d047aba2b860033e9c939c +#: 12a54ad82e994ce485e2996d4e804373 5fb5d18d006242c2ad4cd143c6e6b5c4 +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 36d386d92a7a47099dff930b89063d26 +msgid "" +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 eb22abf9766e441f835aaad0d12fe198 +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 dad1426793764a71ab0a71c8f6872da4 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 22c9fdaebc8c4e0f9e1e8b72ef87003a +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 c1e21b305da34c6b8960ebe5ca0d60bc +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 5f3e64b47249408c9a1e006d27826a48 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 76984af8223c45688a49ca7082b24cc3 +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 ff1dff0c91ac4324acc01188f2ef2bab +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 951aff2f38bc43c8bd1086a9e62243fe +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 ac93b8f5dd1646b8bbb7f5edc86ad2c7 +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 baa943e150554186ace37f310442a8a0 +msgid "" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 53f7e15ad5dc472faf409f30d902d4ce +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 1c455770202547a0bc3c62c063a0b3ed +msgid "" +"If you use exclusive input parameters combined with expressions, you need" +" to be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 918873fedf60421f9e3713f82ac0c207 +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 4999688d5c954eb48fc42524e7a33176 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 294545640c6148dc8043027d4e4ea7d4 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as “fasta” (one of the values of the enum), " +"your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 258d3d9ec6bb410eb012f89b44bf4072 +msgid "" +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to a `null` value, which does not match the expected type " +"for the output field (a `string`), resulting in failure when running your" +" workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 6470c55fcf5e45b09534705df1fb4e7b +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript" +" expression when using exclusive parameters, or any parameter that allows" +" `null`. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value if none was " +"provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: 0bf3128f26ef41f7b31418f506dc83d4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: ef7ddf8716214cfbb8a411a13967198a +msgid "" +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/) as described in the [Schema Salad specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 913df947afb7420097be3f15caede947 +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 4c773c6b1db9460ba58d5d276781d6e7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: c593b5d1f7e1469da7e97ca737632bc2 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 28f6bc9a1465450ead788703b8329902 +msgid "" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 84b37f20f8cb4136b274ecef284039fa +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 391ca127d3594bf0bd12a3ed29a85fc7 +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 e58e02c974ca451ca7e52d4a7e14ad99 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 b725956dd0ff4906b54a002afacafd09 +msgid "" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 42e684d404aa4715a538bc209e84b469 +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 3bc2f8d60cce460788cff24274fee913 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like" +" a command line tool or an expression. You can also plot it with the CWL " +"Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 910029acb5864b919b452e62a365c789 +msgid "" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx Graphviz directive (this" +" user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 edcbb0fc660840f29309e24a1f934d25 +msgid "" +"If you try running it with `cwltool`, the command will fail since " +"`cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 14bf9940996647ac91ea2de9e95dbe13 +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 71459c6b3efa47a1856c8f22f1b529da +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 77937377da354c46afb8c7d4988cf964 +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 7dbd814741e4452e95af2bddbbd41c73 +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 10965b18de5841eda0658840d0e726c4 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 d1ebab8483744101b29a095067495897 +msgid "" +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 030b920fe9ee445f9f996aef68087129 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 81f1b2d425f244728504cab01a06dfeb +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 d23514327fbd476d87e9a3308cac38e4 +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 ebae564b85824cd1818837689b134af5 +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 94a88afd7acc4576b8cc22780991d629 +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 a4dc894fe82e4b779771b512424ce70c +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 dfd9feebfc7049498f807dfeb91e70e3 +msgid "" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 343cba8708a14ff9bd281fdff790bf39 +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 485a5a4cba354640a53832e4c7460fcb +msgid "" +"The `glob` field consists of the name of a file in the output directory. " +"If you don't know name of the file in advance, you can use a wildcard " +"pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 bafc8ef1a46b4f97af05a146a8903e2f +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 3fafdc8d21344bceb8262e8534e34afe +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 14fff0b709774a4cbb9213dc97ae9d42 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 ae07eb32467f40189765939c2fb4f6ae +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 98aa9d49f5b14429b5fb9e38ab9c594d +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 ddb1cc7a7f6f44cd96748c88753b5bdf +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 af69c5bbfac241809fd6e882dc1cafdd +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 7910b5ce6997467096db8d432cfb2088 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 11452076e78d4ccd9773b301d831d350 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 f8227a94ae9544a189886f90e9a3433c +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 38a045a2b8614cbba3a02d4f27b50127 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 13529a4cc80a4070b85bf29829c762b1 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 da5a588a3155445098b7ad81b78f1fa4 +msgid "" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 9e91e38ca0e4473384498c6e28b1f116 +msgid "" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 a0e0270144df4b6aa3bf0ad261938b17 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 a4a0147041724445b7ab3459cbc786b0 +msgid "" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 ea5153744a3d41dc883c4bb7df4e16de +msgid "" +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 84270504a1c445d2917825b8e854a80d +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 9616d24145e74d17ac76cbe80ee4972a +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 fe869638aa4a4cd3a43bc071ed66cb37 +msgid "" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 1e3f77c12d1c48a7b2df7cdccfe92d41 +msgid "" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 2b86b2eb9a2e4310923aa3e3c16fac1a +msgid "" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 6ad56ee119684a83b42821f3b366cc73 +msgid "" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 11b45dd3f4a644b2b6175fb9bf4219ad +msgid "" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 c5446e59a6bd4a3cbfc0ed2cd21783f4 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 3fefaf0fbde94a85be6db02643d0a5ec +msgid "" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 3911b95f4a72415f968ed640f445bd00 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 841837a2edca4aff8231a0b955def3a4 +msgid "" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 665c8d7b622441cda2c1f6b20da5d664 +msgid "" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: cb71700c69694a53a62a43ef11a62595 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 6be0e1471d164c5099c0ccc2824cf038 +msgid "" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: 5984d3f30ab14197bcc03ce556bad3ab +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: 5357d8f77e504324a2904e7dc327e46a +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 1bbff970e33144148c394d7f18ebfd96 +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may " +"also help to avoid confusion about which version of a tool the " +"description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 0774b6bc9c8f4ab0acf943ed07f4b0d4 +msgid "" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 5cadc31694ee45d99ffa369983971756 +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: a8a0b7191ce9404292df0699b96c51d6 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a `SoftwareRequirement`, " +"search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 86c81fb6d34b4b36ac8778c79cbc0306 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 4bd8293be25d401a868df24fabfc6538 +msgid "" +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use `InitialWorkDirRequirement` to stage input files into" +" the output directory. In this example, we use a JavaScript expression to" +" extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 05c39f514e234bd88895716c99eabcda +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 83fa50745b7e486db93f4d7883a778cc +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 d8d67e5238d049479e9c1a1c4b9b62c3 +msgid "" +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 60e89aea0d634296a9753910a55a4493 +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 7ff74ba8fd9443cc9e1cdda32e38ca7c +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 1c8afaa3ef0c41b2a1ebc57d329d6ed4 +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 b540a4f7a25148098a369350e22c247a +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 1cda8c6f9ed6421bafb39554bdc9b5f7 +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 93b8b99518474d709a90f5442c0d2b65 +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 059deec3f12448b8a673e1d957595d7d +msgid "" +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 9c40b03256274b43a484b2a1108186c5 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 45314aa766a5479f9855cbc054ad17b9 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 8289b75b054040e5bfa71f482554eb4e +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 333b0ee71bde4ce8aacf4ff8946dfbfe +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 54ef32fbf91a4edfa0006f62b51bcbb9 +msgid "" +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 de34c8de4fda441d80abb9990e75b494 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the " +"container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 fbd75c368e6444d89978f010a235709c +msgid "" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 88ba9fb9da1d493ca8a4e37982ff27dd +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 76dc921551ac44de9f07583d304bde3a +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 20b169511e734f0fb8b047b06e442146 +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that " +"is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 bb3199ee47b746529f088a323a72a434 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 562109bed3cc4da896d8307f74244552 +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 417e5bfea2ac485b880ee544984996ea +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 ecd67cff285a43b5b66777032c7f690c +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 e5b8c1e93fda4043839ef0dc204f2ec1 +msgid "" +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 d09c4c6d692548d4b317e5c74445795f +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 9e3bc00a91f948eeb26624078dce6823 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 177aaf8abaf940d1ac006423998974fa +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 28308117076d4adcaf0f923c3f52d666 +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier " +"examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 c851029a3fa542b6ac21e00675661ca1 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 30cb988a8f814823a5dfb2f6ca3928fc +msgid "" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 a7c8734f60664e619c63b98e5d3399b9 +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 f4bb9b7b6ada46a4a1701daaac993798 +msgid "" +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 f4da934d636f4455a63f5ecbda2cfdea +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 529d327e58f64544aa02b075976aee32 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 a4207261aa314fd98cbfdc368d96c1b6 +msgid "" +"This workflow extracts a java source file from a tar file and then " +"compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 7571eba01bc44d0a97d8f283f19a8b49 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 8e58b0c4e12e4a1183fe7b33e8ee39e6 c8833b0a5dc04e35a48575713bed3f24 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 6a0e9118c6ee49fbb9111504dcebe190 +msgid "" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 87e0059d86b64212a1cceee185fe264d +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 77943b217ba34d409ed4a18fd262388f +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 aceb3bee46034a94bdb6784a8c1a484c +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 916621f2ca5d47c4935d68d20c5ea616 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 4a0ceee7f9ac4e80994ac8a750d77855 +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a " +"workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 3408935eb4f945349e00486a8df27c39 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 c0790bc2b8a34016b2eb3d64f0b8903e +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 5ad0adb359db4652a4b7ebd98369190e +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 753f0dc2fa3a45358dfc66e7a86fb65a +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 7eb328b2d93d4ee3b47ec26340bd3e98 +msgid "" +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 9b2cdf146f3d4906931ec9be50a194e8 +msgid "" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 b48d08c1caa241e68a758934f6d934f9 +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 cac7f881e9984afcae77afd99b049334 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 2a60f236d6194b2daebed0fa094edc30 +msgid "" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 6cc53ff3acef4bbc87a5124a4f473b52 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 635696160b8d4b2b9607986a761a0fa0 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 4511d99ea12f4389a18f9fd061e207ce +msgid "" +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 dbd710aa7bd049018af5a693a16f93c6 +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 f9f192f956eb47d7a4fa47c80f1b56c0 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 711bc01e2e5c47f293abe478f43c1b92 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 68509d8627a14073aabfe2071faf5214 +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 0744ac6efec34b61a4a7c3d1060bdb42 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 2f6f5592fb5d44eb8c9998d8d9e9b9f1 +msgid "" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 af8995565822455388c9e32b59f7319b +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 a71808fbee3349079bb3a4fd4382662c +msgid "" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 3684b45ee2b146c2a1470712375b8fb0 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 882cda0615624d7e94c1a8708c35733b +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 3f5af7cf008446f3ad18a7ea5e8aab5b +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 d927b215d2e3400c941e490f1a102c97 +msgid "" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 52466df4530640d8bf65fa8f8dac87b1 +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 15488985c612469d80d9c20b00f1569b +msgid "" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 ccc00c4b29134214ac79fc6815ba15e0 +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 93cf2c2587394b00828a7f944d201c84 +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 5151bd4448314e7c9aac6d4841539613 +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 9154dd4987ad44e3bcb227324179a854 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 636ad7e5c8ec4b8b9f9ea1e70f166695 +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 c3f371626c2f49da9092cd5aabc8e075 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 5b186b36c71d42d19b8ef294384a0365 +msgid "" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 67f8b32d49284698ad5248f7960cb95b +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 e49cbede4a4942e99b6f90e878898362 +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 168b8b8983f84a49ab94c09be99753b4 +msgid "" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 9d2f8b5fc572494e8e1ff54be1ba146e +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 0448518b8c514ec18fea6b32676528ce +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 315b8d60537c4e1b98136ffed099df1e +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 fc4d347151574b95907c3db531b3467d +msgid "" +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 235259da671547188634a55a5616b32c +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 8621d777883f41dead6ec6de0bb01094 +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 87f8702d0b88446ca01018b08b42e5d7 +msgid "" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 c5dacc8526fa4341a13ce9872c1fcba1 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 9dfd2c7d475245d68052fc30d44b90d3 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 c48070836d1a4e53a9256f4e40716f3c +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 88fc7b9654734d838aaf202083a6dcd1 +msgid "" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 2fc5956dbad1411f86aeefe5b8655b07 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 e8a7a80a070148e4958af6b4d70250a1 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 6c2980f728e44c82bfad95316f405be8 +msgid "" +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 8d0fbfb49a3a4aefa3ec7d71e782dbab +msgid "" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 b847adf4f9b343518c45eec4b5fb881b +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 51d36eca415b4040ae7cd2dea438b829 +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 12816605aedd40e5babe852973366a9d +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 9a5c688b2c584362b78fe3041832ee6d +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 b9c062f153ae40f8ae59164f6096a0fa +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 2bd3b6f3998a461f9b4f5babe423242e +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 6a7a52d67e954928b57731d64f9962d5 +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 c0fe4464296e448d89fba9adae04ab71 +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 c5f7a9a163884b18a7dfd3cccbf6bfae +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 5ebef4a028ef4f0dabd3caae4a0b0bfe +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 08f3b7b52d0d48499445fd30cd71640c +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 888ae81b155f41a6860428e200948950 +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 4aa3831e2b9f4fb5b4161c198b9f6419 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 952c18ae0fb24c3ab42ae3f7b7db0844 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 bd5835e2b35349679b1e69a50b958ee6 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 2d36d90d86c3484c9f767e3fcdb29b25 +msgid "" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 48ca1f4243e343c2a3da3c9b5596097d +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 5d15caab19694c58a78d566b2897f6cc +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 42cb06c103784fb087a44e55f570cc79 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 90b1474dba5442a48f9fdd07b07ed9fd +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 76a1a131ac7648f9aa14ce14b09d17fe +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 f04cae70233848f7bd051fd553a89b9b +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 b6b1ad435b13428cb56c22fc135b303f +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 4a45ba50729c42ec949780bbcf495ef7 +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 57fa577b531645ae890c634c6549d680 +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 0cef0765d01e4525878389bb5ae8f6c5 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 1730e578bf2f4a7b8836d0a41e059de8 +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 f5e7fb0d74924c9e9b4ca1434f724ff0 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." +msgstr "" + diff --git a/locales/es/LC_MESSAGES/tutorials.po b/locales/es/LC_MESSAGES/tutorials.po new file mode 100644 index 00000000..9aee982a --- /dev/null +++ b/locales/es/LC_MESSAGES/tutorials.po @@ -0,0 +1,58 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/tutorials.md:1 cba829ebca95427ca72b0c259e199cc1 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 413874a8cfb84860b7bce0ee5f4e6022 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to " +"the list." +msgstr "" + +#: ../../src/tutorials.md:7 5242c591a9814c9793856f432d06adc1 +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 4a3e41ee134d491eafc9a7b07776b926 +msgid "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 207a4a90ec2f406b8541f687540a71a5 +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 ead7b80dc37647289f83036eef8ca959 +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 95a0dd8e5c354219a3eb3140565aa853 +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 82e0cb6989494cef91c464d45cc64728 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" + From 76b24797c7b78de3304f5e3baeed90c9513325e1 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 24 Jan 2023 20:20:37 +0100 Subject: [PATCH 34/49] Translations update from Hosted Weblate (#361) Co-authored-by: Sarah Wait Zaranek --- locales/es/LC_MESSAGES/LICENSE.po | 75 ++++--- locales/es/LC_MESSAGES/episodes.po | 7 +- locales/es/LC_MESSAGES/faq.po | 157 ++++++++++----- locales/es/LC_MESSAGES/setup.po | 9 +- locales/es/LC_MESSAGES/sphinx.po | 3 +- locales/es/LC_MESSAGES/tutorials.po | 18 +- locales/pt/LC_MESSAGES/LICENSE.po | 102 ++++++++++ locales/pt/LC_MESSAGES/episodes.po | 27 +++ locales/pt/LC_MESSAGES/faq.po | 292 ++++++++++++++++++++++++++++ locales/pt/LC_MESSAGES/index.po | 57 ++++++ locales/pt/LC_MESSAGES/setup.po | 27 +++ locales/pt/LC_MESSAGES/sphinx.po | 27 +++ locales/pt/LC_MESSAGES/tutorials.po | 57 ++++++ 13 files changed, 761 insertions(+), 97 deletions(-) create mode 100644 locales/pt/LC_MESSAGES/LICENSE.po create mode 100644 locales/pt/LC_MESSAGES/episodes.po create mode 100644 locales/pt/LC_MESSAGES/faq.po create mode 100644 locales/pt/LC_MESSAGES/index.po create mode 100644 locales/pt/LC_MESSAGES/setup.po create mode 100644 locales/pt/LC_MESSAGES/sphinx.po create mode 100644 locales/pt/LC_MESSAGES/tutorials.po diff --git a/locales/es/LC_MESSAGES/LICENSE.po b/locales/es/LC_MESSAGES/LICENSE.po index a9655e9f..87af7480 100644 --- a/locales/es/LC_MESSAGES/LICENSE.po +++ b/locales/es/LC_MESSAGES/LICENSE.po @@ -19,102 +19,117 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../LICENSE.md:2 385524707375429989b7b4fc7e4c7aa5 +#: 3d749a78eb3e47c991d603c2cabd1b91 msgid "Licenses" msgstr "" #: ../../LICENSE.md:4 7682a147e3f74921948bde67ac684338 +#: 4689ade8475a4c8a9d5e325f072c1392 msgid "Instructional Material" msgstr "" #: ../../LICENSE.md:6 7273f384601c4f18a4cc33c833f05e56 +#: ef8ec0f072d947fbba997c4b2191abc2 msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." msgstr "" #: ../../LICENSE.md:12 2cd9327d0e2e43aaa963633db1320b96 +#: 696f3824ca814c9eb314abae51be8202 msgid "You are free:" msgstr "" #: ../../LICENSE.md:14 793123b1e0ba4603a0c54c952ea4a590 -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: 72ebe92edf58434e9d7a4fc6bddf8880 +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" msgstr "" #: ../../LICENSE.md:15 151178e4c9a9444fb65dbf926edad28d +#: 9b403f96d4194ffaab3f309d7d12f360 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" #: ../../LICENSE.md:17 e44aed84ff0d48b3aea3946b3a7c85fc +#: 10b1befd0f834d79880c8aeb70b595d4 msgid "for any purpose, even commercially." msgstr "" #: ../../LICENSE.md:19 d8bb44ca55b642d6bb4a88eaa8292204 +#: 9017d0b760bb4370926d511b97a604c6 msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms." +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms." msgstr "" #: ../../LICENSE.md:22 6859f286e52c417096b072c923b9f235 +#: 1faadcaead6748dfb34886e5819af9b9 msgid "Under the following terms:" msgstr "" #: ../../LICENSE.md:24 ee4ea8e1fd044924b34b2d96ca158257 +#: 7a49ed3a728349c9b486f3d0b1dbf577 msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." msgstr "" #: ../../LICENSE.md:32 7598558aee3244b6b7892b06df94a393 +#: 57da6294edce46eab00e7d15e6f6d4fa msgid "" "**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" msgstr "" #: ../../LICENSE.md:36 a83123e7ae79486c80107d176ea951c7 +#: 8fc8a30cd63c4a0a9d8ba1b913687029 msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." msgstr "" #: ../../LICENSE.md:39 0cc05e8ed5274019998b1dfd6ab76824 +#: fe59e74a4d024831a6d5cbcfd3e4ee38 msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." msgstr "" #: ../../LICENSE.md:44 d70e680300524c8583f1e7fd361ad2ba +#: 3ea41d5a14ad46729cabb387a33814b0 msgid "Software" msgstr "" #: ../../LICENSE.md:46 d17e76d478354904b679b4f5ebde418d +#: 23751e2552ff450c83e3dd255da56dac msgid "" "Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" #: ../../LICENSE.md:51 015fba86005946eebc5959cc3b0493d0 +#: 13fb5eb48a8a434e95dbbb717ccaef8a msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." msgstr "" #: ../../LICENSE.md:57 524088befae04f5485dc731d505c769b +#: e262fbd0e7de4f148f31afe39d1cb9e9 msgid "Trademark" msgstr "" - diff --git a/locales/es/LC_MESSAGES/episodes.po b/locales/es/LC_MESSAGES/episodes.po index 1dbd9f7b..897540f7 100644 --- a/locales/es/LC_MESSAGES/episodes.po +++ b/locales/es/LC_MESSAGES/episodes.po @@ -19,13 +19,14 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../src/episodes.md:5 49382fe02e4f4aae96ce4d1b666d649a +#: 0cbb5e7334a647c3bcae7333ec3ced90 msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 ebd3b75bc9a347029e9e164e94b43374 +#: fabb221482cb4ac0a98bbe10943ed025 msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" - diff --git a/locales/es/LC_MESSAGES/faq.po b/locales/es/LC_MESSAGES/faq.po index ba1f01be..4b38c453 100644 --- a/locales/es/LC_MESSAGES/faq.po +++ b/locales/es/LC_MESSAGES/faq.po @@ -19,61 +19,73 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../src/faq.md:1 e53c79b325b749a691434bf2f7825a5a +#: 5daa5afac36f46dd8329e5629056384c msgid "FAQ" msgstr "" #: ../../src/faq.md:11 d95bfefa6344474d9820a266922831f8 +#: 40c8efda3caf4c6089bda3027c522f37 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 991a77ca372d4324843ed340ffbfbae7 +#: ee854bcb685941cab45ae7f33b0efe48 msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 4654eac499464be4845a59bc281ec242 +#: a4cdd5ab6fe341a3ad3e3055556d96c3 msgid "" -"This example demonstrates how to change the name of an input file as part" -" of a tool description. This could be useful when you are taking files " -"produced from another step in a workflow, and don't want to work with the" -" default names that these files were given when they were created." +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 4fcb9907771940d8857fab5b8211d337 +#: d1f359d47f124dfab23a75b196cd5884 msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 9f3ed67bcb13459d9e7196e9d82cb58f +#: d83ced40605e411c92c4ae38761d7ffa msgid "" -"This example demonstrates how to change the name of an output file from " -"the default name given to it by a tool:" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 af6d80606de6412a8fe63ee379702eac +#: bc8997df2e6746cebc2068534f30ee82 msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 fc7c21e08e8e45adb8f1265af494160e +#: 20b6ae57e1cf4410877a60fb3ef87264 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 e37343ad3edd412f981397b995e6c841 +#: 73c66b809e9a4218b624338ccb88a05e msgid "" -"The first method involves adding the folder containing your scripts to " -"the `PATH` environment variable. This allows you to run the shell script " +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 2b7e94e816fa46f4a221b5ce6b2214b2 +#: 9be72b7d5d604526b125b63148e99320 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 0fd0fd13672d48cda0f3ef7f2b0701da +#: fd96d178901545008a43fa99e3aa6cf3 msgid "" -"After that, make the script executable with the command `chmod +x " -"scriptname.sh`" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" msgstr "" #: ../../src/faq.md:97 a21be18c313d430a8986760ee3725198 +#: db58a582e66244468f4d31e9213933d1 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " @@ -81,117 +93,138 @@ msgid "" msgstr "" #: ../../src/faq.md:104 404295b5792747c8a87306181d078cbc -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: 3e70f0da5cd7460b90c1690366f40820 +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 92582f3845b446d08ca9cbc4ad76a0a7 +#: db28dc27c82b4b29a7a9a768550bba9b msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" #: ../../src/faq.md:115 2d62b6e5d7944818acd0f43b7d37ce67 +#: 4474b16fb3fd4cdc85da931159804967 msgid "" -"The second method involves including an input of `type: File` in the " -"script itself:" +"The second method involves including an input of `type: File` in the script " +"itself:" msgstr "" #: ../../src/faq.md:135 c72fa80f79594d479cb99dc6bfcb207d +#: 23c9b2e21cec4ee8ade087e6630f62c2 msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 5f2b7881a7c64cf29b05b4d78158e176 +#: c01309dcd65c4f1080c396e6a9efb75d msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 eb11641ac17e496384a60e4aacc5209b +#: 0a36801172fd4e24a04b3ba85cf74e29 msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their " -"input binding makes use of `self`. Below is an example workaround for " -"this, pending a more sophisticated fix." +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 c0aee2cf9ee046128002b09a8aa397d8 +#: 433e788ba01141e98ea5a9e73ef71e6f msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 34a04d6d09e94fd796a5ee13c6b9856a +#: b6de2761ce454992904775a06b7ba326 msgid "" -"Below is an example showing how to specify different strings to be added " -"to a command line, based on the value given to a Boolean parameter." +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 b1ee951a6e6e4f4c8e88de4dc93bd616 +#: e36c2d53e8ba40f4a602b489a6688e24 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 1664807c6b264fc3b58e9f2c40a9543c +#: a9310166cb514e4e8824bba7fcfcb277 msgid "" -"Using " -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" along with [`linkMerge: " +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 a7ab83c7f31e4e8d83fbfba1abadef2b +#: f6144f77152e4284963951abaa30adb2 msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 908451dc6990489e88edc1012899c440 +#: 790709dfc2854e4a89fcc4769f84b0f4 msgid "" -"The input must be an array consisting of exactly one entry for each input" -" link. If \"merge_nested\" is specified with a single link, the value " -"from the link must be wrapped in a single-item list." +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 30947198b46d4151a5d92076c30659c0 +#: 438789c8def549d1b4b8a187d5acc48e msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 0b320fb2e40442608137ed9d6f2a74cd +#: 23ede7dfd5c84492baee1d5bbb9a91d9 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " -"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" -" destination step." +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." msgstr "" #: ../../src/faq.md:229 a143590b23384ed79fc37b17a0abd46e +#: 37c0474e48164160b23c4094d583d2d3 msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 6b36effcb80040c79396a1df241f635e +#: 3b2be0a4a87041b7a5bda20c6df2ffc8 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" #: ../../src/faq.md:247 2873af63ee324fab948d16a9e14db5a7 +#: 886300d2dcff4861aae503d34b0bee44 msgid "" msgstr "" #: ../../src/faq.md:248 a11f170a082a4df2b4a0c068dd0573ed +#: fe393ecdff25428da6cbcd30171c7811 msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 bd2ccba5ac7e486c9af1d906ad96b07a +#: ebfd4991d917413b858da8b437a55805 msgid "" -"For command line flags that require a specific input as the argument an " -"enum type can be declared in CWL. **Specifying null here is known as long" -" form style. It does the same thing as the question mark on the other " -"inputs.**" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 3f1d8cf3390c43f8b78ce33fc020f1a0 +#: 2919ff4f51254e69aea40146e2d911f1 msgid "" msgstr "" #: ../../src/faq.md:268 89626d59c2164bb99d0b123def33f701 +#: 61ed4e87457c41eea31f51740557597e msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 028c6179803b4dc8a718669312804101 +#: 1e6624104b024eb092682cd0dd0f6a3c msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " @@ -199,109 +232,127 @@ msgid "" msgstr "" #: ../../src/faq.md:322 23d9d603d4d44880aea5ebfd86e02d8d +#: b741b8333e104feaa6d1f41fd4476304 msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 06ae9317c6af481bbf4fd70236ca10a9 +#: 334673ae870a4dada817857f3a49326e msgid "" -"To properly set fields in a record input type, you need to pass a " -"dictionary to the input to properly set the parameters. This is done by " -"using inline JavaScript and returning the dictionary with the key of the " -"field you want to set. The source field is set to indicate the input from" -" the workflow to be used as the value." +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." msgstr "" #: ../../src/faq.md:342 0c6c0af33a274a8cb64ae3111c014338 +#: 362f85270df04712b2e2f21c7019e3cb msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 1139a2f4e58046f9aac4c64b7d5a2e4d +#: ad6997f24c7c42fe965b5d7bfd1e633e msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 ca97418a37bb4ae99bce1b44eebefbad +#: 99dce9d60b6a4f99bc39899b7c8c10ef msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 7a5d2d6c6474492fa65ffd8a5048c733 +#: 6b68fe24cbf64624b49ea56fce2eecad msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 2549c8887b204ddabe4221978dce7e57 +#: d23326837eb74e7faf1f54e25f8309c4 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 d15ae28e932446b48bfc1dbdc34d8eab +#: 2e2eabe92670412e95474b25ad9cda4c msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 925a0bb31c5f428b93232e42d96bddeb +#: 81f9308adbee4a3c9e585b8e0f0c4844 msgid "" -"For example, the filename `a space is here.txt` includes 3 space " -"characters." +"For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 591dd97f12ca4b8ca263b17abe674fd6 +#: a5d3ed6cac28415288e7fc7fbfc6e8a6 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 3ccdf1a970c14cbe8e1d269dc4ae77b3 +#: 72f9692803304daf9f846e2b90139660 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 4cefff22947f4d9eb2f66d1b6bca2a8f +#: a7eb20c817704811b3bcf2f94ec2e51d msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 bfcbe4003ccb4e59baeed0b631871970 +#: 20fa869849ef4b358a11db46111017de msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 d729277d8bc0488eadddf507ba63202f +#: 35032fcd9f23403ca006d62a7d6e7be7 msgid "The file is here" msgstr "" #: ../../src/faq.md:410 ca99353cf8f94d11add95ba36408ee46 +#: f6d6a4e3691446378c8fb01a2d19f8ad msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 deb9ae92120d4e30aebd6e4d0374a0a2 +#: 44608fed1048458e999e13b014327e7e msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 7f4054de28a243c89bd3aca1e2764b93 +#: 96ede8a8f1f34786aabd4004bf2e7acc msgid "" -"If it is not possible to change the input identifier, then you can use an" -" alternative CWL Parameter Reference syntax:" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 29658fd7b5724addb5074891942f79fe +#: 84634a368e704e8d828678785c784595 msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 2dd0d8092e5640e3a930478497b78efd +#: 545c4db9c24f42ee946081254d9ca7a8 msgid "" -"The CWL standards are built around (optional) Docker format containers. " -"The reference runner and several other CWL implementations support " -"running those Docker format containers using the Singularity engine. " -"Directly specifying a Singularity format container is not part of the CWL" -" standards." +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 0d385ebff8c14cbfa418fa45c9b42e51 +#: 1c1e6d583d5646a8a5c9316dcd743d9f msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 67d82ee82a184ed3921da6fd1928e83e +#: cf7d336d444e4f59aa83585b7abb1fe5 msgid "" -"You can use the --js-console option of cwltool," -" or you can try creating a JavaScript or TypeScript project for your " -"code, and load it using expressionLib, e.g.: " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" - diff --git a/locales/es/LC_MESSAGES/setup.po b/locales/es/LC_MESSAGES/setup.po index 68494d21..6b6fd9db 100644 --- a/locales/es/LC_MESSAGES/setup.po +++ b/locales/es/LC_MESSAGES/setup.po @@ -19,13 +19,14 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../src/setup.md:5 715f40c8e3f544e4805ae2b456b9d699 +#: 29bb5c68be6042e5aa4a370e9c4024b3 msgid "This page has moved" msgstr "" #: ../../src/setup.md:9 c9641546c55a44eab9ae40ec272d5df8 +#: 8bcf31398c34491da1a1590422a72cbe msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. The information on this page has been migrated to the " -"[FAQ](/faq.md) section of the new user guide." +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." msgstr "" - diff --git a/locales/es/LC_MESSAGES/sphinx.po b/locales/es/LC_MESSAGES/sphinx.po index 1c2687a9..27d21259 100644 --- a/locales/es/LC_MESSAGES/sphinx.po +++ b/locales/es/LC_MESSAGES/sphinx.po @@ -19,10 +19,11 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../src/_templates/sidebar-nav-bs.html:1 ada5c93414a84374b3eaea93dc11ae74 +#: b896fd5e11fe4674a7f46ad489476692 msgid "Main navigation" msgstr "" #: ../../src/_templates/sidebar-nav-bs.html:3 a3cc1c498bad434ebadd4a2e92dbf5f0 +#: acede4e78f7e4aefa0ad9425928cbb42 msgid "Section Navigation" msgstr "" - diff --git a/locales/es/LC_MESSAGES/tutorials.po b/locales/es/LC_MESSAGES/tutorials.po index 9aee982a..0c412e90 100644 --- a/locales/es/LC_MESSAGES/tutorials.po +++ b/locales/es/LC_MESSAGES/tutorials.po @@ -19,40 +19,46 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../src/tutorials.md:1 cba829ebca95427ca72b0c259e199cc1 +#: d32522e2993f4b48a789f46537fa5ebf msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 413874a8cfb84860b7bce0ee5f4e6022 +#: 63a51dccb29045fd8f78d5e396c6e050 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to " -"the list." +"this page` link in the menu if you would like to add another tutorial to the " +"list." msgstr "" #: ../../src/tutorials.md:7 5242c591a9814c9793856f432d06adc1 +#: cb5f8748a5544be2835467ab07eb7a1c msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 4a3e41ee134d491eafc9a7b07776b926 +#: 685d0cb2faa04703bcef408ecc2b92f4 msgid "" -"[Introduction to Workflows with Common Workflow Language: For " -"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" -"tutorial/)" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 207a4a90ec2f406b8541f687540a71a5 +#: 20f45705145d45fc8420c4119b06a49f msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 ead7b80dc37647289f83036eef8ca959 +#: 2bccd19d542d4458a1ba8616236f1840 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 95a0dd8e5c354219a3eb3140565aa853 +#: c491c73e4c00476980438ffc79c6e4d3 msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 82e0cb6989494cef91c464d45cc64728 +#: b8485449206542e097584eca7363c8ce msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" - diff --git a/locales/pt/LC_MESSAGES/LICENSE.po b/locales/pt/LC_MESSAGES/LICENSE.po new file mode 100644 index 00000000..c3591ece --- /dev/null +++ b/locales/pt/LC_MESSAGES/LICENSE.po @@ -0,0 +1,102 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../LICENSE.md:2 +#: 3d749a78eb3e47c991d603c2cabd1b91 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 +#: 4689ade8475a4c8a9d5e325f072c1392 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: ef8ec0f072d947fbba997c4b2191abc2 +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 696f3824ca814c9eb314abae51be8202 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 72ebe92edf58434e9d7a4fc6bddf8880 +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 9b403f96d4194ffaab3f309d7d12f360 +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: 10b1befd0f834d79880c8aeb70b595d4 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 9017d0b760bb4370926d511b97a604c6 +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." +msgstr "" + +#: ../../LICENSE.md:22 +#: 1faadcaead6748dfb34886e5819af9b9 +msgid "Under the following terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 7a49ed3a728349c9b486f3d0b1dbf577 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 57da6294edce46eab00e7d15e6f6d4fa +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 8fc8a30cd63c4a0a9d8ba1b913687029 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: fe59e74a4d024831a6d5cbcfd3e4ee38 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: 3ea41d5a14ad46729cabb387a33814b0 +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 23751e2552ff450c83e3dd255da56dac +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 13fb5eb48a8a434e95dbbb717ccaef8a +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../LICENSE.md:57 +#: e262fbd0e7de4f148f31afe39d1cb9e9 +msgid "Trademark" +msgstr "" diff --git a/locales/pt/LC_MESSAGES/episodes.po b/locales/pt/LC_MESSAGES/episodes.po new file mode 100644 index 00000000..94101eb0 --- /dev/null +++ b/locales/pt/LC_MESSAGES/episodes.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/episodes.md:5 +#: 0cbb5e7334a647c3bcae7333ec3ced90 +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: fabb221482cb4ac0a98bbe10943ed025 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" diff --git a/locales/pt/LC_MESSAGES/faq.po b/locales/pt/LC_MESSAGES/faq.po new file mode 100644 index 00000000..ce416d3d --- /dev/null +++ b/locales/pt/LC_MESSAGES/faq.po @@ -0,0 +1,292 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/faq.md:1 +#: 5daa5afac36f46dd8329e5629056384c +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 40c8efda3caf4c6089bda3027c522f37 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: ee854bcb685941cab45ae7f33b0efe48 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: a4cdd5ab6fe341a3ad3e3055556d96c3 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: d1f359d47f124dfab23a75b196cd5884 +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: d83ced40605e411c92c4ae38761d7ffa +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: bc8997df2e6746cebc2068534f30ee82 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 20b6ae57e1cf4410877a60fb3ef87264 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 73c66b809e9a4218b624338ccb88a05e +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 9be72b7d5d604526b125b63148e99320 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: fd96d178901545008a43fa99e3aa6cf3 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: db58a582e66244468f4d31e9213933d1 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 3e70f0da5cd7460b90c1690366f40820 +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: db28dc27c82b4b29a7a9a768550bba9b +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 4474b16fb3fd4cdc85da931159804967 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: 23c9b2e21cec4ee8ade087e6630f62c2 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c01309dcd65c4f1080c396e6a9efb75d +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 0a36801172fd4e24a04b3ba85cf74e29 +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: 433e788ba01141e98ea5a9e73ef71e6f +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: b6de2761ce454992904775a06b7ba326 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: e36c2d53e8ba40f4a602b489a6688e24 +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: a9310166cb514e4e8824bba7fcfcb277 +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: f6144f77152e4284963951abaa30adb2 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 790709dfc2854e4a89fcc4769f84b0f4 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: 438789c8def549d1b4b8a187d5acc48e +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: 23ede7dfd5c84492baee1d5bbb9a91d9 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 37c0474e48164160b23c4094d583d2d3 +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 3b2be0a4a87041b7a5bda20c6df2ffc8 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: 886300d2dcff4861aae503d34b0bee44 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: fe393ecdff25428da6cbcd30171c7811 +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: ebfd4991d917413b858da8b437a55805 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: 2919ff4f51254e69aea40146e2d911f1 +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 61ed4e87457c41eea31f51740557597e +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 1e6624104b024eb092682cd0dd0f6a3c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: b741b8333e104feaa6d1f41fd4476304 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 334673ae870a4dada817857f3a49326e +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: 362f85270df04712b2e2f21c7019e3cb +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: ad6997f24c7c42fe965b5d7bfd1e633e +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99dce9d60b6a4f99bc39899b7c8c10ef +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 6b68fe24cbf64624b49ea56fce2eecad +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: d23326837eb74e7faf1f54e25f8309c4 +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 2e2eabe92670412e95474b25ad9cda4c +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: 81f9308adbee4a3c9e585b8e0f0c4844 +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: a5d3ed6cac28415288e7fc7fbfc6e8a6 +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: 72f9692803304daf9f846e2b90139660 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: a7eb20c817704811b3bcf2f94ec2e51d +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 20fa869849ef4b358a11db46111017de +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: 35032fcd9f23403ca006d62a7d6e7be7 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: f6d6a4e3691446378c8fb01a2d19f8ad +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: 44608fed1048458e999e13b014327e7e +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 96ede8a8f1f34786aabd4004bf2e7acc +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 84634a368e704e8d828678785c784595 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 545c4db9c24f42ee946081254d9ca7a8 +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 1c1e6d583d5646a8a5c9316dcd743d9f +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: cf7d336d444e4f59aa83585b7abb1fe5 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" diff --git a/locales/pt/LC_MESSAGES/index.po b/locales/pt/LC_MESSAGES/index.po new file mode 100644 index 00000000..0a5d7d38 --- /dev/null +++ b/locales/pt/LC_MESSAGES/index.po @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/index.md:1 +#: a58ca61ccefc401588f91699bc98bd32 +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: 6dcf12053f104cb3a8d23ce8d4f90363 +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 1cc90206170d46119c5756f31a9e8799 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: b54801d84a944dadb4e4637551e3f7b9 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 860afd2eda4847e0a0d8834de3af4aa8 +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: d6046316c84b40ffb5478c90b2604911 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: c3c89ac756a74d9688e179b8718c9bf0 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: 0eb795062b484537b090c4d5c361f7f4 +msgid "Table of Contents" +msgstr "" diff --git a/locales/pt/LC_MESSAGES/setup.po b/locales/pt/LC_MESSAGES/setup.po new file mode 100644 index 00000000..06186f03 --- /dev/null +++ b/locales/pt/LC_MESSAGES/setup.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/setup.md:5 +#: 29bb5c68be6042e5aa4a370e9c4024b3 +msgid "This page has moved" +msgstr "" + +#: ../../src/setup.md:9 +#: 8bcf31398c34491da1a1590422a72cbe +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" diff --git a/locales/pt/LC_MESSAGES/sphinx.po b/locales/pt/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..68ce7729 --- /dev/null +++ b/locales/pt/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:27+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: b896fd5e11fe4674a7f46ad489476692 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: acede4e78f7e4aefa0ad9425928cbb42 +msgid "Section Navigation" +msgstr "" diff --git a/locales/pt/LC_MESSAGES/tutorials.po b/locales/pt/LC_MESSAGES/tutorials.po new file mode 100644 index 00000000..f893e551 --- /dev/null +++ b/locales/pt/LC_MESSAGES/tutorials.po @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/tutorials.md:1 +#: d32522e2993f4b48a789f46537fa5ebf +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 63a51dccb29045fd8f78d5e396c6e050 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: cb5f8748a5544be2835467ab07eb7a1c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 685d0cb2faa04703bcef408ecc2b92f4 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 20f45705145d45fc8420c4119b06a49f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 2bccd19d542d4458a1ba8616236f1840 +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: c491c73e4c00476980438ffc79c6e4d3 +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: b8485449206542e097584eca7363c8ce +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" From f067761345c6dc0ef62645648feb424f5c93ac22 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 25 Jan 2023 09:03:16 +0100 Subject: [PATCH 35/49] Translations update from Hosted Weblate (#363) * Added translation using Weblate (Portuguese) * Added translation using Weblate (Portuguese) * Added translation using Weblate (Portuguese) --- locales/pt/LC_MESSAGES/_includes.po | 22 + locales/pt/LC_MESSAGES/introduction.po | 607 +++++++ locales/pt/LC_MESSAGES/topics.po | 2083 ++++++++++++++++++++++++ 3 files changed, 2712 insertions(+) create mode 100644 locales/pt/LC_MESSAGES/_includes.po create mode 100644 locales/pt/LC_MESSAGES/introduction.po create mode 100644 locales/pt/LC_MESSAGES/topics.po diff --git a/locales/pt/LC_MESSAGES/_includes.po b/locales/pt/LC_MESSAGES/_includes.po new file mode 100644 index 00000000..6d6635cc --- /dev/null +++ b/locales/pt/LC_MESSAGES/_includes.po @@ -0,0 +1,22 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_includes/what-is-cwl.md:1 +#: 46f474e1b364495181698bd13ce28a1e +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" diff --git a/locales/pt/LC_MESSAGES/introduction.po b/locales/pt/LC_MESSAGES/introduction.po new file mode 100644 index 00000000..fe9de9a5 --- /dev/null +++ b/locales/pt/LC_MESSAGES/introduction.po @@ -0,0 +1,607 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/basic-concepts.md:1 +#: 92c85569d9e746d8a5b7a5e8f9773545 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: 5e501be2f49044c9897f6e8d65186abb +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: a6f5f188f9af4b608b8401996a558e83 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:2 +#: 2ecb1a3a4c7546ba94e560924cfb09a8 +#: 3c0da8bd74824f8b88223c2a9dcc6ec2 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: 7fb9ad094d844047b0d35dc70c295400 +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 303d1a15612846c1b60a4d651f9d1d4a +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: c84c4bde07034846b043c4f281f8e00c +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: d774877d6e4447b7b83d56ebbaf09e96 +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: e8884f39f08c41bab29c4284077fd860 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: 984ac8cee64e4e41957d8c5a4aff0cfd +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 17381e8872414c49b178d91ace2e3e82 +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: c4cdbf2a42644e0eb4eb74512388e9f7 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 7d994284e320413bb8dbb2a42cd16a4e +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: ce92487ca4e3495ebd0693c502773626 +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 0ce512c3cd744652b5feb2d8dcfdb613 +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: dd7d6a1399b04923b25df70abb1becf5 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: ce4c76b46531416bb4006a9c01f45a23 +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 0256a343321447559471d731c86d3546 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: e1235589f24942babe54adaae4f169af +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 81baaa297562452f80afe68657c8099d +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: 0c8bbd88bd8c4c71b19011812e7487c3 +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 3b64da1f14964cea9e5cbf8376578789 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: bf33807babb64befab3385eca4c92131 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: afdb75d374624f4798f358a3dfe7752e +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: bc28744d5fa644218ef55672d726307f +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 24ffb5bfa767424585b6b6c93169de93 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: bd53afe50cc14f2ca428adddb0e60dc9 +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: 35c98c4b352c4f9bb9572c740894dc57 +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: f7fb57fdf9344a7eb0f334aca8d3e85f +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 0dc6a8f19fda4e9eaa80b8e1bd1fc5be +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: ff1224487c35402d8afee6da3803e19b +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 63c2dd9aaec54df088e82febfd7bc49c +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 18f310d11c9b48b4a447b6662446cd3e +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: a3922283fdce4f99832c816626d5f098 +#: 19245373c2e84793a72462b7d2fa1c34 +#: 7c3ea7150c7d41fead10ddf2a6205ec8 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: cf39d3563e344ad9b31d5268c4069972 +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 97b0113a847044b98f79b5e00941f4c3 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 8cf4edbb4b344ac7b3eae86ed52beff8 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: c1dfc170fdf54c9e846539a5170f204f +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: 778babbcfb2648a1ad7a7ad8f80653a8 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: 23abed59f5d44bfb96e8fa13aa213b83 +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: ee93304de4e447c1bd5626e72b99b6fe +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: a79f07e33fc5437c9fa204111d0290d8 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: 3cf08b553a814478b4b2c6c84ebe354e +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 98751950a97f44fdb16e826fece810fb +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: eac153b881fa47ab8bb08074dad8eed2 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: 806ff7b185d74538a9b0e20c6ad84ffe +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: 1f9573b6cd45479bae2481a251132d53 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: c3995fd5588741148e3b2c91ca011ca9 +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: 8a67b172ce524aa09858acd9d1a62762 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: a567e0f952bc46be8b82d0a357f2c209 +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: 21d3bb850bb14fdcb6d4c4a15c9966b6 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 62cbb29459b24e9fa83c7cd7994bdf12 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: aaa319d4446c41ba82bf925f29f7d9dd +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: c49938a0100a4850b67d067a61304d01 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 91e986d0c1f44d7f9c3b32366160da6a +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 301c5a3baaaf46bb81bdc25b53a31f23 +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: 1664589ced314daebfb163e6424f220f +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 1223fecd61f34ad98ebbb7e45eaf4ac7 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 242c496599d84a64959db275ee1e212e +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 9b749d47f48341cb9ac8cd14098e6c47 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: e8ec351d7b79447bb15f4d4518b8de87 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: 58d5613243914dc8bc4ce88676525783 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 731a6c30786f43d88160f9642cbb05d2 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: ca2088eb9565429dbc1ce0b28b2ef1fb +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 5ac9c6bfb50b48878aff52f1194e53c4 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: b8d0c12ff07f4269bba87cd653803345 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 83780c1b43f744b4ae87a917b26293f5 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 2919320c41e94930a0aa9bc6aacb5a87 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b8e799c075214d539aa0a7c04dbc33c0 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: ccbd51a29ca841efb74c5e0a25d1eb87 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 5f3330c1e15a402781c3325f9d3dc779 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: 314fbc9f866a405b86e7bd704781dea1 +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 9434e3680aa9487fab9ddb782c6ff3d0 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: 2ce0bda38d814b248a2c23ebc26bf462 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 105c3be6f5f34f4388b9999603275bb5 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: bd378c8483a14c93b5fe00d76e5b0a06 +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 5ace5416560247c7a3304c41caa000c6 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: 5d7a175b3c5a4f888daf037672211d61 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: 4e0c0c345527412eaf70e8efe67fab8f +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 6dd8379682824d1397c48ac10db4b894 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 57691f7bd87741d68f4e1a963da91654 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: 13a4d71f127b4bd09c12a37752d27c8b +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: a574ed30000541b2816fbfe66b32c314 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 9bb9c9052ad14c7c9fc0275c8f1b651b +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 5afcf2e79ceb424ea0a570797a712321 +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: cc5b91b8c5b14a40bdd09d3bd45fe9bb +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: d5e36c7827334fc69498459db5137d30 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 39d3eff64d004a0f8257d61f2a90b186 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 19946d0d9a6f42d487537273225b91cd +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: 66048204601a439d8245455c48b08826 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: dcc41d0ce48e42a0ba209ca1fa37220a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: e2ebe32f12b74608b35217cea30cd0e0 +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: 37a4f461b82f4e48948c5eab400b14a5 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 371c6801e92448f9875fff60a509f509 +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: e3fb51cd196542008cb16458fdef7c1f +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: d00cd96d47c6450a8c0955765eff9ac1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: e06fdf0744344d0193b99791b9b94c7d +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: 6e2191fbb8794f83a51897028a2e50f7 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 931b6b49a46d4d5581a05446ac2e9a7d +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: 5cb281f4d0ea4163af0f7203c150345e +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: 4e6c4c2b6bae49a2b2d93bc95538c7b9 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: b37ba76e0dd940559e13543ea241376e +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: 22d7ac26f2ca41b2aa141fd4774b6f5c +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 15033ad0574d46b2951bb2121c80c462 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 2b2fc79461674b9ebdef49750f7fb319 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 8b11c9920b97427aa2d29498664e24bb +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: d11de6ee015f46c991fbc8b48cd1fb60 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: 71adfebd042a4820ac533a2e6e07c0ca +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: 8f199e6778a84ba68d385b42169f6b26 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: 28ec66afdad24dfd871ef1a2686f9976 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: cccb84844ce0453cb77ce3db65ffbc1b +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 0c5a431846f241829975552ef8dd9c32 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 8e383a7ea5b54c56adb9cb0c6ed6c179 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 98473d00529345d4989f0f5d2101da1b +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: d105326cb76b455d907c283a509f038c +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d4d00a573e36474f9c915563d4ea8709 +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: aa8195d109974f9da3b9da97479525cb +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" diff --git a/locales/pt/LC_MESSAGES/topics.po b/locales/pt/LC_MESSAGES/topics.po new file mode 100644 index 00000000..7d6384c1 --- /dev/null +++ b/locales/pt/LC_MESSAGES/topics.po @@ -0,0 +1,2083 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 1a006f1604c0405aaa4b93e41edc5184 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: b61b4d7ed53a436486c1429987a2a21b +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: 1bf9e65f1cc249ee93656a53ddd354ca +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: 3329dc69c32f4b9092b196d79ae5d0c1 +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: a003a3d1de0e4dfe8c777905e55fb9fe +#: e2dc24c683054cd785326de2c3f3f136 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: aca6a0cd24a2411c8cfb1ad392f6d315 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: bcf37e403eb041269e351d7f98a19587 +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: c5f68f8a9f34445ebcbd5783f96cb046 +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: 4eca90c659ba43158db373d36ee681df +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 7474eeb128624dc4b1e980dbd0f04ca4 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 0c520e5add334609a1afddc559abe19a +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 125a69207077425fa54f346abc45342d +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 6ca38a04844c403b836942b2f2f1e1e2 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 1da05be0d97d429a84085459ebae54cf +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: fb1b2a8c54f34d78ac61dd4b5ffd9063 +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: a8b1b5caf9904fc5b9eef8c110474b84 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 42a5a8cb3b284549aabb817b73ce5810 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: eddd878eb0324851997de2a69bcbb43f +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: b05c8ff667174f6798feb811cdd3c41d +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: 9dc16d1a6b0546cead6967f5e9b1526a +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: b8bf85e8523a4553a58face698aa863b +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: 6fb9a1a2ffe14f39b01af8736a9698eb +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 0a935aa93e554c0987af7349f94ccd3a +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: cadb5982a13e4621807ad976cf9b1524 +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: bd7ab2cc6234458181e9b99938eba824 +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 7beb72d7dd5a405f9be8b6fb6a310f10 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: e5942c4d4b4d4e1a8c0e9ed3da80960e +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: 5a5dbc9b9d2242ba8d15ecf39123694b +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: dd3016d33b7d4340a09a7c8e5aec4f0b +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 45d110a660b348f58a1107476df18cee +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: 97a5b141592e4415aa4acef4f6228045 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: 85f624f8879348e8bb368ec2749925bf +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 20a851dae87941c7975173ed9cd1e360 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: bb19e1b689564a11bb9e72d5f82cf3d9 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: b14199173add4585be62c4e8278b49f4 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: 9e883f18843a41d7b10102bc11655839 +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: fe3a1468aa864742b92c6e8f4ff1a38f +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: e9dbf14538404cceb02507962a173ee8 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a650a7dacbb547db97158a8ac2c9d0dc +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 501217b98c424a319e70ef963de506f6 +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: 7143809471454e00880ad8faaf43f141 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: 7ad86e42708a465980a56f735644de9f +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a8f29712337b4d1daf3190cc8973b8f7 +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 534843389795437991fad0b5a702b483 +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2052170aa2624feeb2253477895aa838 +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d5ed098a33ae4c1ab2a30eba483ecc6f +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: 2b55c028602f41babb6e535b425ba5dc +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 47408669ae8b4432a43d763dba12a466 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: b2e5e925971849a09a8d54d9c649a32d +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 9a39f53bdcc94904a90effb507767645 +#: f296149bf19947528b134b01a4d7ce81 +#: 965fa9769dea4ac9b3dd252e0a3bc603 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 79d8ea95f0c34585a3dec4f83453de60 +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 4afab699247b4f619702c4086eb1b6f3 +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 693b91423f004118b806bb8ee7952eaf +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: e4a25f04a6fa4001bb1e58cb775cdd84 +#: c771cbc64607412a9164c28934e9e0f5 +#: bdd5a3eac1e3436496e05a13c4f06073 +#: 1e62b28ef0184081b4d6e53f34b753e1 +#: 33edd6deb38740ed98466b6e023b0393 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: a3a8bcdfadc4484ea5e4c13a25b2da85 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 7800570badf149b3bb1f81d470dbf4be +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 496313f8ec67403ca78ba66130df261e +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: f7cc0d1ac5dd47658093cd0360f90329 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 0d563f15c1cc4484b6b2955bdc70e1a9 +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: 06425b6cdaf244b198fdde312e864190 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: 26c3762a637a4492a6c12588544cb0a7 +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: 221433aa39104642af8afb70ebd08576 +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: 197bf36a5d7741b3a9ac56c19d4a7686 +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: d9249cf936d24ab3b3fc508d17d94745 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: 2ff7ce81cd3a492a8549484ba8d1f135 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 2bb45c56e2fc49e094be2cf742222e67 +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: e2a4a531c6164f15bc711618db058f52 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 90f7960bd24d4481bd05da1d61ef146b +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: a51814548e44467c841ca65b2ac63b2c +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: fa13573d9c174ca1accf20a449e5984f +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: f2912b17e3be47b0b7186efdb4c4010f +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 4d9c95d18c1a4880845e7194a99aed3c +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: c656a020978f465b85b8754346ea5b6d +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: ff4d0b6bc0264650a21adc811b8caf4c +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: 77e00be2c0984465af5bf501b4031f32 +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: 3d7b7238be974c0487f219cb5c030149 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 03a62f421c8241779c0e79f4dbad96cc +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 31a85893835748339b6c84fb98fde14b +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 08d9ecd7d3294c5b9dd4db228a1d8d5b +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: d94d6c69aaa64edd9c75624286713c2e +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: 020019b8aedb494fad022d19b7106f83 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: a6b66e0fc0de442e8f72f0d0c37c7e8c +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: 48b7d9ddac2940c0815e5c855bfca6d9 +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 894b843f9c064d56913e1a8c48093314 +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 2319e845caee41a3bc5888c3f1fc28d1 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 9ea661d749db428eacd2207dc7a01e36 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: 4ff76250f28144a4a9d8807a9d4ed3b4 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: 7f9f2df357a740feb89bfbcc44ff4d61 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: 12633ed841dd447a8753faeb4f9e5096 +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 4db64481d38c4896a85a8f6038a9931c +#: 1b4ff3eeddde4a9a8018235b9d706567 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: 50547062ee404e2ebeae7eeb54b9de4b +#: 88933bc02fa84412944673c3463af1ad +#: 4fde39d8a50e49f09bd28a8598760682 +#: b933cbf847d94c5fb8471918ce8cb4ad +#: 0145c520b85a4bc29302bb654f08f23b +#: a3e322ac8a0d4e2ba9bfbece6b5ae64b +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: d9b166225120432f9a2bf2cc7b6ffdfe +#: 28f8ec2fc5c0436aaba19e9d479aa466 +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: b866a0e5897e44329714f4c55eb20d2e +#: e64b5027878346d79f9ab52b3d3b916e +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: ed38ec582fbb48ff9f9cffa7962ef515 +#: 6cc0788250624fd69fa4e3881191ab7f +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 17eefb5f38534c1b87116c3a061ea1bb +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: ce0572fc81b343e6991c88ca0195149a +#: f8b77ad06ebe43d7b03b2135737902e2 +#: c7953486c99d4c7898c0155a6085dfd5 +#: 46d99b1f7f0747479bd58486cf7941d2 +#: cd0a797b3619404f964ba9efb33756bd +#: 528cd5e0d3994230b719fbfb39b1f13e +#: 324241aae8ff4505ab0467f2a7f27fe2 +#: f4086b1ad2e44c2b9de2636f8bc1eb90 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 764d7cf3fb5444d58dc9e0eb6b8fc649 +#: 0450a4b8de3046998d30ce1f09c10daf +#: fd6bf79cbb694dbb89e8731aed733e6c +#: e6048a64e09d46099132fee40a2e0644 +#: 9512391eb96440bd8e48c3754821e3d0 +#: 3e8669bf4a6741f9aba170864b251dac +#: a02ede726d3f4eec9602f72054c0d963 +#: 4ed593dfc39246789f1e4ecdc742323b +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 304de40206cb43d7b651245586cfa55b +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: 7855471c93bc44aabb1a2b9beb52b56a +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: f0452f324bfa451f9f3264f9a55e0e5d +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 6dc476cf8689465ea3993f49a9eead75 +#: 4dfc0be21065471d91def850bc2528fb +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: 09d69778a89044099b3e5d7cf02471bb +#: e3077bdff0dc4dfdae60eb60f3d66d8b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: b28843f7b57745db9cb3648ef23fda0f +#: 6a745fa266dd42849c95410775b690e0 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: be00ed49197f48ecb7cb244ecc214369 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: 90ad2b27f97b4ca089cf23a073cdf17b +#: 38d062892cb04bc7bbf0b56f263079e1 +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: c2d2756d617743b886c67160c2face21 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: 8681600183d1429cbd1b15639e1a222f +#: 1d49cd7337004fc38f4e8e9aa4270481 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: 24b7f85116cc4d2f904600555aa19b8b +#: c401a68b4f384d3eb13ab3e89a4a7195 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: 0e1f9d22d0714bc5b80e420f63b34cff +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: 5fed95f16aaf42d4b41c569d9546b7f0 +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: b539a931f31d4cfe9d72aa5800115fb2 +#: 48e497c024bc4c38a86dd027aaa4fd2d +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: be638c80121948c99cc9fdb67a5d291e +#: 1fd8fe769ba8497eb8a9520af91ea33e +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: b5f3ad78a233411c97520c1fffdec18f +#: 7854e46c7fd24afd9c1942808521bee1 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 211bd57896494fca9ea8aa2fc142eea2 +#: 28ec0718d3114bfdaae4524c009da944 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: c6a421f7a0214d89958d4c258b58aac8 +#: 07bd0bc74ad74187bdc24c26041467ca +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 3afc146cde2e47d5b52e62fbd1f37426 +#: 2225f5acb44a4ce0ad16be5c4f6cba48 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 9acd61d4d67a4d2c82171a79462fb458 +#: cd7e7fea3b8346268618c31b70581326 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 140e449e46a84e3ca1a604176e583f44 +#: 3d8b717d4568458eb53b0b91695b3de8 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 76f35653e34b433d8e9fedc6d12ce856 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 1a2edf61fda8404689e3c0a7389d7d02 +#: 3bced6d84fa6453195be82dbc6d7ec83 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 0b5aceb6c9d24bd9bfe95cc04fdc61ad +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 3523cc46c6324fca9053d6b1dd8c7495 +#: 21eee2c1cb6b430486446d223dcca0eb +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: b4f126415048402ca388c4c63f34ebe5 +#: fdf588cf8cd34d60bfb6cece3ef859e0 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 1b494245c14e4e22918c43ad9f26cc8d +#: df4d781178f2465b8a421651bdd2f66f +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: a88008a23ede4ea49ffcaccba7029d31 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: a256b51f1e944b7d9659b945d8ab05c9 +#: 23bbd631e73147e3af561eb4a14d2d6c +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: a446842e26e44781ad10cdaad73bc49d +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 3cc10263ab2f4dbfb6ccb12612b89cf1 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 995f6af5fc244293b34f5d840f01ce1c +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: b556a1d134764505aa25003d79a53e88 +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: ad23da5452bd46248606f6799ce93db0 +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: c63036ac68344465af6c7756be00b60b +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 2f7f270b0ac24f2f8df506f5dde72cf7 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: f49272e5e4c1491eb59c79d2dfb88a86 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 8b50c892d36d4d178ec4268c7c13887d +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: 9d22117a6f5a434593d5144bf824999f +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 4fbc454a144a466b9dd7ff74903fc5fb +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 281b129a76a24b0a818092acd1038757 +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 4dda6ca233d54c12b6ddceabae198495 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 59d87fecfd7f4438b68e0bcdecdcfb46 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: 0f7e33673ad349e5ad41a078032e5806 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 77a7141f897048139ef3785b5f870b43 +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: 14ed183bc7e346598921445c0dea11e0 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 9406d05bf0ed4774af50fd66d24aa299 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: f5a9048ef9e047528c291505ef9a2c12 +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: 51e8c5a231eb45fb8c15be49b37a7bff +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 860a6f01ebac45938abd220758fd1109 +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 32155f96d47f4d76998a401aa9e9591f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: a62bbb9251794560ace0e52be3d9ebd3 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: e301af8f675444c69cfb6b578c02fdc7 +#: 3da1dec243994409bd764b133d4fc243 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 82c6efcfb5d5410eb316399b7c4f638e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: 29c3d25c657340a1bab7123a166b78c2 +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: ef8e7bd7e944429da78474d2fc5e0348 +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 08dd50bc6a5942ec8f3b6c201fc4497f +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 78c51215a68f40b280cc21d0e412eacf +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: bb8e2203374a4ae7b833c543ecc563b0 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: f34aa1e4d08944c497602b2a35f38a50 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 2932972efc94447987b02a7707c62656 +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: 968f4e83c511425d8faf4c8d0f18097e +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 2eb89bdbaee04a899a961a7b87f0aef1 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: 3781fc7cd22d48bdb5aa4abc0c93b06f +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: f4af4a85efb243728d2ee783393dce14 +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: dbf8350f003a46b984b7432160e6def5 +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: db2993fe83814747a52f9db0b2fcc81e +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 39fe18bf5d4b4539b2f98e3bf0feea2a +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 58e7b0e7d0a149498e846dd2790c0eee +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: 4b78c5437904492ea3e692372d2fc163 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: f2626686125d4ec29fb2338373b54c93 +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 46327aca33cb49d1ba61149e94884991 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 43f2e7020da94f77bce4e1f852ab11f1 +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 8342aa3f84624325aff8f7f4de788187 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: 2d54f11f99b245e5b2802b984bc024a5 +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: 83a357dc06b343549876035b03b8c5d1 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: 0461538fa12a44c5a9d230a928ae930d +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: 2b2552958f404447b711d09650d22395 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: 82c97e60f8634bd6b4d3e88524722412 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 0ae1393a80e94b899023c29f4af6084b +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 74339f624bba49d6b68e1dfc4724f673 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 3a4473864ec04d2e9a0d550b2051f717 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: 575661b36a2040699956f897bd6cc614 +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 3d18a704f5a94e2889e847c32a78aaab +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: fceca2b53d0646b2ae9f1cf9dbefe2fc +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: cba49054785b4ec2a7acd3aaa2e165d8 +#: 647c0e302af841d7b1789447281d7344 +#: d23de44d5d5b4bc7b32f3726afa97500 +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: dd867685663f4728b9fbe446a9b14a3d +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 67bf2c2cbbc44f6eb870af3a3a852676 +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 94d66455bfd04697814495e116176ffe +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: 39a9d3583f29451d8035158c54266ed6 +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: eba6af5cf8224d198fc04f090362307c +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: b48377cceff342e793e982c9fa2095d3 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: b64ef70d944c461b8ec7219e14e47795 +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 73cd08a2226f4cbe99fcde2d3636d640 +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 3c33bffa2c574ef888b041c1e6735b8e +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: 23bd067b32724dad9daba1e924757d86 +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 1be92fc3d0b44ea089273cfcd47318ef +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: 3d08125883b74f49bba042ed58d34648 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 7636c7e8b6e04d7089ba1cb10c4c475d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: e1c95ce96db043eb86ff9b3ae595017b +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: e6588c4b8fa64959b2dcac52403a6415 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: e7f85cb69a5342889525fbb81b44c86c +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: 71756719e0274300a839b38c8b4ea986 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: 88bf75fce3064eaf823b5d88be0ce053 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: 60374713dea84fff92b89b4ebaa8d7ac +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: 7616d5ea746f47ac972183150b97e8b0 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 0ca022c095334ec4a9fe41cb732e11a1 +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 1c807f8fd1c540ae8802092fbcec7159 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: c51956eb3ece432ea0ed5b676b2f037a +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 45e6ab3a53b94f5b90136d68c1c0e479 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 7e05dc23d6be4428b4a414b3a65c4727 +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 96e7266ef25b429da42337c3582cc201 +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 9cb6959a877f4590bccb977416753410 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 7b54a3cd870d4b038dff685064bbca1a +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 0d661c96ac2d41ee94641a397aa3bdf7 +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 94d39b79923a4a65b1a6ce5c464528c6 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 56801121f70b4cb2ab6207e254ec8bbf +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 42418ff882d44c1b9584fb9f7887f744 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 1118de96d202444d9bb4db74ebe4792d +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: aca51d371db84aa79418c79a18310055 +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: 3473e6d2942e4546a2c1590edeb502f8 +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: c210ad12f61047b68302e67da9b5dae0 +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: 1c15cff5a4614d88a62c8d2df97029fc +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: 4beae917368545688c01a4a929685cae +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 4f4f63b7107e4dc194760802c4581c2a +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: d942035c4c914ccb9de75836af9761c7 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 0e9064cf55fe43588053d37100634538 +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: aa1dcfc618e74a53b3c579380e5e1558 +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: 3ec3f4a2d1c547b18780db17fbff060c +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: 21e598983ce94d22b9d40a77577a6608 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 62f79a2c055b455d9626ca5a18d1bd72 +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 19c2b9b13bcc480aa7474301422faab3 +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 17bb520489a74f64b76ddbe2ffedcb5e +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 9e2b97aa3bfe4eae8524b325bf2ea3f1 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: 028c844ef208450f994b3949210ca996 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 2b758e44e4be4fdf89a5897385db6c59 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 16395173b7ee468f85ee8450493504de +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 51e2e929dadc41a78cea98f779e2e2a3 +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b757d4b151ef46fa96897bf00a0d9ab4 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: 2f2f46a81e8946bf8a9b48a5956c82f8 +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: 75177c797c704385bfa5ce86e03266c9 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: 4d05d16c3cb74eb291da7586fa859b90 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: c115b7ed044346d6a9c4c06306ee82d8 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 8f83261e3e91424b9a3c38280c643f02 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 269af269348e4da5b93cb25dcd10374a +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: c376ab464fec4ee78a33d42dfed5dc1c +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 53d468d14703494699478e6847d82e34 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: 32bd7abe387e4999a0864f6e6a48e435 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 0712e952fe2442daa9ceb0cee79a3ebf +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: ef2b8db0c8d64e41b839b47aae34d0ec +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: f9f45dcc2bcb4fd1a1021d2843137fa3 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 4ffbc016a5344e6e9272793d921e4900 +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7118718b98c5488c9d9a54e5ec84c055 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 20fe8fa105a84171972722158bafbc0d +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 836fa2a818854cf9af13d674f5bb859c +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: 5d56e1ac063d48c2b140a72db9f78540 +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: 0166655553ac4d8fb868138936176986 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: e43fe4a9340b458786c51499c75b5556 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: 0ba13966a1364d4e9992b5cfeb6871d1 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: feb8bce610be4a3a92053f2e2e5aab76 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 0f5fd76c57e7412097b4ebdeb074f2fd +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: b645dd17256543b0a42d231171140c95 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: c8d5743769bd4fee93f77a52ba318883 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: af6cbb89b7a84bf78b7443b6746484fe +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: ad9394b163a94340975a66ea2bba7094 +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: 677bce1f24f449beb2bac5ed8469f624 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 4c0d14a24b354feabf4b6ad4852f9543 +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: d407e5c9aa9043b0b6ab234348467db0 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: f06b60c926204ca88b4355803f1b7b11 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 0a7c19b054d2400abd327736b6829670 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: cd1773f336544b3688bc76c28e9d1f79 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 6b7bbca601f04f7183bc75988bd6db13 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: 069d1dd1f03f4cd79e44f2dcd890b531 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 4924b1a69a5f48b0aa6af943b40ffc68 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: e100d8d8f23c4d6996ac59c5ad68acf0 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: a87dfd0dc0274ff4b34354678f2d49d2 +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 772078ff701a477cae9acb8dda16ef1f +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: d2d67048e93e40c4820b805f1ba28cc9 +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 580477152be041a8ae5c5f546ecbf21d +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: 05f8faea082b4fb9b9c22b8eff7eb356 +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 4c107fb18fb34c2dba7743118c51e8c8 +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: 729ea19aa03b49bdadccc6e6f0d2e7d9 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: e849cda9fb1d4a48b5b1f9a4e44213a1 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: bfc20f529d2d4797b87c63c7b2c05e91 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: 761a900275a044f28ddcebe509a4637a +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 59af21cf1ee848e993563ad47f7bb248 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: d711ce1ccdcf427aba25a2ab3d11165d +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: eaaaa01fe0894f479a42a9c3ce199819 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: 92489f186e3f449295b0dc864ebf17f7 +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 1360c3a2d43b48f3b3e1153bb26b3f30 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 2e993e21a3624910b4282bd088694fec +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: df5b4b041dc944be8580e43012339168 +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: 92ac2766d118428ea148094c022a8b0d +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: e4ddaca03eb449eabbf2d2fce752c367 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 0bc50411a4b748d8864305070d11a304 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 74453227279a46cea3644f3ca7df61b9 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 75ce3269886645eda46a6575fca186eb +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 1e7e5b46017a476a80d57ab7eb614758 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: 1ee41e983ca14a959caa199b1ce12700 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: 070e6a00d09e4675b89afec5d066aec1 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: fd37ebe3aad9473891cc764a47363f8e +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: 85176099018c4ae19bed1261e92e6e92 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 952e9a347f444ef496fa0cdf00160ffd +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 2b5ad46ca3024ce1b37e1c92a820aabf +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: ea17d17cd08b4c40a842598c8521af56 +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 6e5f1266974d4a32995aaa69fbbfd648 +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 20be823f70c348bbaad6bfc8b88201a9 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 02311e5310cb49d19bf2998513f73124 +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: ca6e4a3fe04145a9a21cc43cc53a07bc +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 75452467551a46a2b2b3685f1a4aae0d +#: 93efa8e941a7427f949afc794ed16e75 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: 39beed65cb114bd78c79aa4a5d6f4398 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: dd880d0589fe45dbaf9b7d799402f158 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 671d0bd54bb147518c35f0844a76c61d +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 66de58a51b034f6a8d5dbe742046f817 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 564e68d58e364715aa72183cb16b3d72 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: 558739ceb3fe40de8ea87ff1e7d3fe9d +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: fdc601ee1aa54e1f84cd00eed2e44e52 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: e4f4a76cee96473d9da3bc1c9e35324a +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: d524ed5f1e964688af9d74eef8e46e04 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: c646e4714d78437fb450127b119fbd70 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 8351ddfd726c40159d81c017ef221606 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: 456794c7274f4654b54aae8d4073a2df +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: 6485e8d6814144d1bcbe66bfe4fcbdb9 +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: a2b9e47cc923466f8bd2fbc4b33fc4fa +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 698cc640807247fd8d512c59ce32ee48 +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: dd658e10da624918b7dec1ea18bbf432 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: f6bd95a4fbc44ffdbfec7fcac90f6bb6 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: ac7b02a71d3544848d4fb539b2a4f115 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: 4380dbd066a44102a71c7e42ca7de8d8 +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: da946c9d59f44fb995daa6aadc44031d +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: 7c73bc555f604afd8491c1619d6905eb +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: e79ce424410e4682881fe14326955a14 +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: be8d2b89052e4f9d96ff2bf15526e229 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 967b064ec4284d0aaf374509915497e1 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 02d667b922264f8e8021844df0085578 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: db8734e07541495188d9ee97eaaaeff3 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: 22542da60ac24403827e2e2a14595770 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: d10f35716f9c4b878da0f2b4ff3d44aa +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 1fd555d1f8ca499ead8d5601eb62266a +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: f5fc85accf8c4bb9bc701ba0b4ee2e21 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: e69cb5e87f4b4670abbc1606197d804c +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 15d763c45a2749a8926b1f965db9d97f +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: c2aac63fc0c347d9833d253039000fa3 +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: 06a23beb753c4a97b302943f59128d78 +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 45985434cfe9438cb558075e1fd73809 +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: e92da36d865142289b11d245221ff8d4 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 3ed7a2b9f77b4eadae3bf6e4a98d14b9 +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: fd66c4fb9c2a4beea0ed5ed8874fcd61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 65944dc8b32a46a4beb73dbdebb7b01a +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 6250fe161ab0421b8799040b79ce695a +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: cc40c0f1ade34ab3b400a02b59b7ba01 +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 29f53a5d64fa498bad0dbe94b238fd97 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: 037fccb419bc4e9f839c665ae31e28ee +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: fdd4bec90c484a618ed8e4d1199deff8 +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 11afb584f37947358963f6510935c5d5 +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: a77e0bfb589c40b6a61a9ca559961a7c +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: 3f4aa12588204fe5b33db590a9446283 +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 640c67f3bcd740c59f90c361024acbcc +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: 8c4d30cbbea146a584731d164d4ad9ef +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: 5d0fd4f8b58e4a8e8f46902e64e6556b +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: e98ab273645340f9a1446183a642e79e +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 37a83ed92d9e44689cfd3a31c2785418 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 7cebef0a9e1444149b1dc58d30f6c10e +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 0cd2bd98918b4622bc586d50f1ce1fa4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: 92458de979564d19a634bb8d3bf6f586 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: d4ee6cc8903f4e6992439ca2586246ed +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 62b438c4ed8a409f96974f3d59cc5854 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: f0f288aeae4f4649ba3615437b531e97 +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: f35023cb05504d1db0cbee41c4e5f371 +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: 01564f1d2038489685160f03db92085f +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: ad662dce1e4149728b8e17f74d8f975f +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 4f6a57f34f094418b7c13aa07eef95c7 +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: 373a6c24de9144e69f37418d6ce8857d +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: f804a8493c8e40178772d94bdc45b43e +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: b3c504b8ab1a42788ef4e3339d27b0dc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 2c2681fe72e24a5d8d98f0aa8e8c56a2 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 571e5c13552c4381bb6de53c02fe5f43 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: fd789f444d9a4061b4fc61bac70353bb +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 2cef838551994b078e460c63214517f9 +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: 2a3a8a553d3c455e9288f63b9a02898d +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: b0b8def4623a4018b1ac913a9256c0a2 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 3f0d4346f0104cc08c059eed9ab4b3a9 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 22e0ac963278414d8141ce5ce4031029 +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: 49cad54646d04adc8e5ac9f0f3c8f895 +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: c8776a4511b24f46bbe0a34d52cf3c8b +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 401b053bd08a4286b9059cb6ebf8d679 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: 8d48a277f37f458f88c54f362534d7b5 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: de90253a11f24f29a4a57348b4f60941 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: 1e20968f957441c58cabfbc46c21e8ca +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 4cf2e158afb348d7b3fd6274fe888129 +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 44c5c010c97a40068a6b930949dcd8cf +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: c6277b2a7a934f81a91e406ef317a1fb +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: 8b3ece04170c447e9b5a8f76374c4c23 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: 6b952b7369b447bdb0bf1e9ff8540194 +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: a6024fb7ce664896a6858d5ea3562fb7 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" From eb2c36b7c02b92feedf6f78e762a205461ef5b6e Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Wed, 25 Jan 2023 10:14:57 +0100 Subject: [PATCH 36/49] remove unused trademarks sections --- LICENSE.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/LICENSE.md b/LICENSE.md index 4345a729..75596a51 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -16,9 +16,9 @@ You are free: for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the -license terms. +license terms: + -Under the following terms: * **Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow @@ -53,7 +53,7 @@ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. -## Trademark + [cc-by-human]: https://creativecommons.org/licenses/by/4.0/ From ba5c9e53875937cc243c5ae9ea2c0d75eefba57c Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Wed, 25 Jan 2023 12:54:27 +0100 Subject: [PATCH 37/49] Add troubleshooting docs (#364) --- CONTRIBUTING.md | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7b954969..559a0293 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -125,6 +125,10 @@ source venv/bin/activate # Open in your browser ``` +You can use `udocker` or any other Docker compatible engine to build the +user guide, by setting the following environment variable: +`CWLTOOL_OPTIONS=--udocker`, or `CWLTOOL_OPTIONS=--podman` for Podman, or `CWLTOOL_OPTIONS=--singularity` for Singularity/Apptainer. + > NOTE: When you modify the packages installed with apt or pip, please verify > if the change needs to be applied to either or to both of CI and readthedocs. > ReadTheDocs builds and deploys previews. CI builds and deploys production @@ -185,6 +189,34 @@ If you are having trouble with links to sections or code blocks, it might be due to duplicated sections, or to spaces or other characters. To preview the generated links, use the `myst-anchors` tool. +### Troubleshooting + +General advice for troubleshooting is to increase the verbosity of Sphinx +logs. When using `make`, change your command to the following pattern: +`make SPHINXOPTS="-vvv" html`. Or if you are using `sphinx-build`, then +use the following: `sphinx-build -vvv -b html src build/`. + +It is also worth removing build directories and files such as `_build`, `build`, +and [`~/.cache/salad`](https://github.com/common-workflow-language/user_guide/issues/268#issuecomment-1276068865). +You may want to start afresh with a new Python virtual environment, +installing the dependencies from scratch. + +If running `make html` or `make watch` appears to run fine but [gets stuck +](https://github.com/common-workflow-language/user_guide/issues/268) at some +part of the process (`10%`, `33%`, `57%`, etc.) for longer than 2-5 minutes +you may have to try the following: + +1. Check if the Python dependencies installed in your Python virtual environment + have updates available (you can re-create the virtual environment, use `--upgrade` + for `pip`, or manually verify in PyPI and `pip`). +2. Use `top` or `htop` to find out if there is any `cwltool` command running. Then + try running that command individually to see what is the error message. +3. Upgrade your version of `docker` if you have [an error message]( + https://github.com/docker/compose/issues/8121#issuecomment-806055733) similar to + `docker: Failed to create the container ID file: open /tmp/....cid: no such file or directory.`. +4. Try using `udocker` instead of `docker`, by using `pip` to install it, and setting + `CWLTOOL_OPTIONS` to `--udocker`. + ## Other Resources General discussion of [Common Workflow Language][cwl-site] project From 2d7f5595882ed3d92143241536dbcdcb3947aa2c Mon Sep 17 00:00:00 2001 From: Michael Crusoe Date: Wed, 25 Jan 2023 14:37:58 +0100 Subject: [PATCH 38/49] Translated using Weblate (Spanish) Currently translated at 64.7% (11 of 17 strings) Translated using Weblate (Portuguese) Currently translated at 88.2% (15 of 17 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-license/es/ Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-license/pt/ Translation: Common Workflow Language/CWL User Guide: License --- locales/es/LC_MESSAGES/LICENSE.po | 67 +++++++++++++++++++++++++------ locales/pt/LC_MESSAGES/LICENSE.po | 61 +++++++++++++++++++++++----- 2 files changed, 105 insertions(+), 23 deletions(-) diff --git a/locales/es/LC_MESSAGES/LICENSE.po b/locales/es/LC_MESSAGES/LICENSE.po index 87af7480..719078bf 100644 --- a/locales/es/LC_MESSAGES/LICENSE.po +++ b/locales/es/LC_MESSAGES/LICENSE.po @@ -4,32 +4,38 @@ # Language User Guide package. # FIRST AUTHOR , 2023. # -#, fuzzy msgid "" msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" +"Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" +"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Spanish \n" +"Language: es\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" #: ../../LICENSE.md:2 385524707375429989b7b4fc7e4c7aa5 #: 3d749a78eb3e47c991d603c2cabd1b91 +#, fuzzy msgid "Licenses" -msgstr "" +msgstr "Licencias" #: ../../LICENSE.md:4 7682a147e3f74921948bde67ac684338 #: 4689ade8475a4c8a9d5e325f072c1392 +#, fuzzy msgid "Instructional Material" -msgstr "" +msgstr "Material didáctico" #: ../../LICENSE.md:6 7273f384601c4f18a4cc33c833f05e56 #: ef8ec0f072d947fbba997c4b2191abc2 +#, fuzzy msgid "" "All Common Workflow Language project instructional material and changes to " "the structure are also made available under the [Creative Commons " @@ -37,27 +43,34 @@ msgid "" "of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" "[cc-by-legal]." msgstr "" +"Todo el material instructivo del proyecto Common Workflow Language y los " +"cambios en la estructura también están disponibles bajo la [licencia " +"Creative Commons Attribution][cc-by-human]. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del [texto legal completo de la " +"licencia CC BY 4.0][cc-by-legal]." #: ../../LICENSE.md:12 2cd9327d0e2e43aaa963633db1320b96 #: 696f3824ca814c9eb314abae51be8202 msgid "You are free:" -msgstr "" +msgstr "Usted es libre de:" #: ../../LICENSE.md:14 793123b1e0ba4603a0c54c952ea4a590 #: 72ebe92edf58434e9d7a4fc6bddf8880 msgid "" "to **Share**---copy and redistribute the material in any medium or format" msgstr "" +"**Compartir**---copiar y redistribuir el material en cualquier medio o " +"formato" #: ../../LICENSE.md:15 151178e4c9a9444fb65dbf926edad28d #: 9b403f96d4194ffaab3f309d7d12f360 msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" +msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" #: ../../LICENSE.md:17 e44aed84ff0d48b3aea3946b3a7c85fc #: 10b1befd0f834d79880c8aeb70b595d4 msgid "for any purpose, even commercially." -msgstr "" +msgstr "para cualquier propósito, incluso comercialmente." #: ../../LICENSE.md:19 d8bb44ca55b642d6bb4a88eaa8292204 #: 9017d0b760bb4370926d511b97a604c6 @@ -65,11 +78,13 @@ msgid "" "The licensor cannot revoke these freedoms as long as you follow the license " "terms." msgstr "" +"La licenciante no puede revocar estas libertades en tanto usted siga los " +"términos de la licencia." #: ../../LICENSE.md:22 6859f286e52c417096b072c923b9f235 #: 1faadcaead6748dfb34886e5819af9b9 msgid "Under the following terms:" -msgstr "" +msgstr "Bajo los siguientes términos:" #: ../../LICENSE.md:24 ee4ea8e1fd044924b34b2d96ca158257 #: 7a49ed3a728349c9b486f3d0b1dbf577 @@ -81,6 +96,13 @@ msgid "" "made. You may do so in any reasonable manner, but not in any way that " "suggests the licensor endorses you or your use." msgstr "" +"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " +"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " +"Language Project» y, cuando sea práctico, con un enlace a https://www." +"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " +"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " +"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " +"licenciante." #: ../../LICENSE.md:32 7598558aee3244b6b7892b06df94a393 #: 57da6294edce46eab00e7d15e6f6d4fa @@ -89,6 +111,9 @@ msgid "" "technological measures that legally restrict others from doing anything the " "license permits. With the understanding that:" msgstr "" +"**No hay restricciones adicionales**---No puede aplicar términos legales ni " +"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " +"permitido por la licencia. Con el entendimiento de que:" #: ../../LICENSE.md:36 a83123e7ae79486c80107d176ea951c7 #: 8fc8a30cd63c4a0a9d8ba1b913687029 @@ -97,6 +122,9 @@ msgid "" "the public domain or where your use is permitted by an applicable exception " "or limitation." msgstr "" +"No tiene que cumplir con la licencia para elementos del materiale en el " +"dominio público o cuando su uso esté permitido por una excepción o " +"limitación aplicable." #: ../../LICENSE.md:39 0cc05e8ed5274019998b1dfd6ab76824 #: fe59e74a4d024831a6d5cbcfd3e4ee38 @@ -105,22 +133,32 @@ msgid "" "necessary for your intended use. For example, other rights such as " "publicity, privacy, or moral rights may limit how you use the material." msgstr "" +"No se dan garantías. La licencia podría no darle todos los permisos que " +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " +"publicidad, privacidad, o derechos morales pueden limitar la forma en que " +"utilice el material." #: ../../LICENSE.md:44 d70e680300524c8583f1e7fd361ad2ba #: 3ea41d5a14ad46729cabb387a33814b0 msgid "Software" -msgstr "" +msgstr "Software" #: ../../LICENSE.md:46 d17e76d478354904b679b4f5ebde418d #: 23751e2552ff450c83e3dd255da56dac +#, fuzzy msgid "" "Except where otherwise noted, the example programs and other software " "provided by Common Workflow Language project are made available under the " "[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" +"Excepto cuando se indique lo contrario, los programas de ejemplo y otro " +"software proporcionado por el proyecto Common Workflow Language están " +"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " +"la [OSI][Osi]." #: ../../LICENSE.md:51 015fba86005946eebc5959cc3b0493d0 #: 13fb5eb48a8a434e95dbbb717ccaef8a +#, fuzzy msgid "" "Unless required by applicable law or agreed to in writing, software " "distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " @@ -128,6 +166,11 @@ msgid "" "License for the specific language governing permissions and limitations " "under the License." msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." #: ../../LICENSE.md:57 524088befae04f5485dc731d505c769b #: e262fbd0e7de4f148f31afe39d1cb9e9 diff --git a/locales/pt/LC_MESSAGES/LICENSE.po b/locales/pt/LC_MESSAGES/LICENSE.po index c3591ece..885e610a 100644 --- a/locales/pt/LC_MESSAGES/LICENSE.po +++ b/locales/pt/LC_MESSAGES/LICENSE.po @@ -8,95 +8,134 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" +"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Portuguese \n" "Language: pt\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" #: ../../LICENSE.md:2 #: 3d749a78eb3e47c991d603c2cabd1b91 msgid "Licenses" -msgstr "" +msgstr "Licenças" #: ../../LICENSE.md:4 #: 4689ade8475a4c8a9d5e325f072c1392 msgid "Instructional Material" -msgstr "" +msgstr "Material instrucional" #: ../../LICENSE.md:6 #: ef8ec0f072d947fbba997c4b2191abc2 +#, fuzzy msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." msgstr "" +"Todo o material instrucional do projeto Common Workflow Language e " +"alterações na estrutura também são disponibilizados sob a [licença Creative " +"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o [texto legal completo da licença CC " +"BY 4.0][cc-by-legal]." #: ../../LICENSE.md:12 #: 696f3824ca814c9eb314abae51be8202 msgid "You are free:" -msgstr "" +msgstr "Você tem o direito de:" #: ../../LICENSE.md:14 #: 72ebe92edf58434e9d7a4fc6bddf8880 msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " +"formato" #: ../../LICENSE.md:15 #: 9b403f96d4194ffaab3f309d7d12f360 msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" +msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" #: ../../LICENSE.md:17 #: 10b1befd0f834d79880c8aeb70b595d4 msgid "for any purpose, even commercially." -msgstr "" +msgstr "para qualquer fim, mesmo que comercial." #: ../../LICENSE.md:19 #: 9017d0b760bb4370926d511b97a604c6 msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." msgstr "" +"O licenciante não pode revogar estes direitos desde que você respeite os " +"termos da licença." #: ../../LICENSE.md:22 #: 1faadcaead6748dfb34886e5819af9b9 msgid "Under the following terms:" -msgstr "" +msgstr "De acordo com os termos seguintes:" #: ../../LICENSE.md:24 #: 7a49ed3a728349c9b486f3d0b1dbf577 msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" +"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " +"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " +"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " +"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " +"uso." #: ../../LICENSE.md:32 #: 57da6294edce46eab00e7d15e6f6d4fa msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" +"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " +"algo que a licença permita. Com o entendimento de que:" #: ../../LICENSE.md:36 #: 8fc8a30cd63c4a0a9d8ba1b913687029 msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" +"Não tem de cumprir com os termos da licença relativamente a elementos do " +"material que estejam no domínio público ou cuja utilização seja permitida " +"por uma exceção ou limitação que seja aplicável." #: ../../LICENSE.md:39 #: fe59e74a4d024831a6d5cbcfd3e4ee38 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" +"Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " +"autorizações necessárias para o uso pretendido. Por exemplo, outros " +"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " +"podem limitar o uso do material." #: ../../LICENSE.md:44 #: 3ea41d5a14ad46729cabb387a33814b0 msgid "Software" -msgstr "" +msgstr "Software" #: ../../LICENSE.md:46 #: 23751e2552ff450c83e3dd255da56dac msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" +"Salvo indicação em contrário, os programas de exemplo e outro software " +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" +"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." #: ../../LICENSE.md:51 #: 13fb5eb48a8a434e95dbbb717ccaef8a msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." #: ../../LICENSE.md:57 #: e262fbd0e7de4f148f31afe39d1cb9e9 +#, fuzzy msgid "Trademark" -msgstr "" +msgstr "Marca registrada" From 055f34d9884ace18a47fb6a2d4be60bc000a62df Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 25 Jan 2023 12:54:27 +0100 Subject: [PATCH 39/49] Switch to a single gettext --- locales/LICENSE.pot | 102 - locales/_includes.pot | 22 - locales/episodes.pot | 27 - locales/es/LC_MESSAGES/LICENSE.po | 135 - locales/es/LC_MESSAGES/_includes.po | 28 - locales/es/LC_MESSAGES/episodes.po | 32 - locales/es/LC_MESSAGES/faq.po | 358 --- locales/es/LC_MESSAGES/index.po | 57 - locales/es/LC_MESSAGES/introduction.po | 746 ----- locales/es/LC_MESSAGES/setup.po | 32 - locales/es/LC_MESSAGES/sphinx.po | 9 +- locales/es/LC_MESSAGES/topics.po | 2577 ---------------- locales/es/LC_MESSAGES/tutorials.po | 64 - locales/es/LC_MESSAGES/user_guide.po | 3827 ++++++++++++++++++++++++ locales/faq.pot | 292 -- locales/index.pot | 57 - locales/introduction.pot | 607 ---- locales/pt/LC_MESSAGES/LICENSE.po | 102 - locales/pt/LC_MESSAGES/_includes.po | 22 - locales/pt/LC_MESSAGES/episodes.po | 27 - locales/pt/LC_MESSAGES/faq.po | 292 -- locales/pt/LC_MESSAGES/index.po | 57 - locales/pt/LC_MESSAGES/introduction.po | 607 ---- locales/pt/LC_MESSAGES/setup.po | 27 - locales/pt/LC_MESSAGES/sphinx.po | 25 +- locales/pt/LC_MESSAGES/topics.po | 2083 ------------- locales/pt/LC_MESSAGES/tutorials.po | 57 - locales/pt/LC_MESSAGES/user_guide.po | 3820 +++++++++++++++++++++++ locales/setup.pot | 27 - locales/sphinx.pot | 6 +- locales/tutorials.pot | 57 - locales/{topics.pot => user_guide.pot} | 1931 +++++++++--- src/conf.py | 2 +- 33 files changed, 9153 insertions(+), 8961 deletions(-) delete mode 100644 locales/LICENSE.pot delete mode 100644 locales/_includes.pot delete mode 100644 locales/episodes.pot delete mode 100644 locales/es/LC_MESSAGES/LICENSE.po delete mode 100644 locales/es/LC_MESSAGES/_includes.po delete mode 100644 locales/es/LC_MESSAGES/episodes.po delete mode 100644 locales/es/LC_MESSAGES/faq.po delete mode 100644 locales/es/LC_MESSAGES/index.po delete mode 100644 locales/es/LC_MESSAGES/introduction.po delete mode 100644 locales/es/LC_MESSAGES/setup.po delete mode 100644 locales/es/LC_MESSAGES/topics.po delete mode 100644 locales/es/LC_MESSAGES/tutorials.po create mode 100644 locales/es/LC_MESSAGES/user_guide.po delete mode 100644 locales/faq.pot delete mode 100644 locales/index.pot delete mode 100644 locales/introduction.pot delete mode 100644 locales/pt/LC_MESSAGES/LICENSE.po delete mode 100644 locales/pt/LC_MESSAGES/_includes.po delete mode 100644 locales/pt/LC_MESSAGES/episodes.po delete mode 100644 locales/pt/LC_MESSAGES/faq.po delete mode 100644 locales/pt/LC_MESSAGES/index.po delete mode 100644 locales/pt/LC_MESSAGES/introduction.po delete mode 100644 locales/pt/LC_MESSAGES/setup.po delete mode 100644 locales/pt/LC_MESSAGES/topics.po delete mode 100644 locales/pt/LC_MESSAGES/tutorials.po create mode 100644 locales/pt/LC_MESSAGES/user_guide.po delete mode 100644 locales/setup.pot delete mode 100644 locales/tutorials.pot rename locales/{topics.pot => user_guide.pot} (57%) diff --git a/locales/LICENSE.pot b/locales/LICENSE.pot deleted file mode 100644 index 67ae058a..00000000 --- a/locales/LICENSE.pot +++ /dev/null @@ -1,102 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../LICENSE.md:2 -#: 087fa59ef53947e683e1b0d1097cfa14 -msgid "Licenses" -msgstr "" - -#: ../../LICENSE.md:4 -#: e134424e12c14d46a8cfa417dbb39dbf -msgid "Instructional Material" -msgstr "" - -#: ../../LICENSE.md:6 -#: 44fc3047733e40408793ef3438e4a21c -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." -msgstr "" - -#: ../../LICENSE.md:12 -#: b2a65a97826d48aa859843a1dbe646a0 -msgid "You are free:" -msgstr "" - -#: ../../LICENSE.md:14 -#: 922b2a5bc70b49e299d0662622aca1b2 -msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "" - -#: ../../LICENSE.md:15 -#: 51700e62261a4a20a887c6c5ef4d3f46 -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" - -#: ../../LICENSE.md:17 -#: f84b26c1e38e46d79fa6b5cdcc7c6434 -msgid "for any purpose, even commercially." -msgstr "" - -#: ../../LICENSE.md:19 -#: 435cf52ad40643139c4eaec84b263132 -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." -msgstr "" - -#: ../../LICENSE.md:22 -#: 4eeaef6ed7304ea8ad815fb8b35f374c -msgid "Under the following terms:" -msgstr "" - -#: ../../LICENSE.md:24 -#: 9295c98517134bc0b8b08e088ad630fb -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." -msgstr "" - -#: ../../LICENSE.md:32 -#: c07512980b6a4433944edf2e80a88c6c -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" -msgstr "" - -#: ../../LICENSE.md:36 -#: 6a4d80c1331c470facd6ccc060a0cd94 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." -msgstr "" - -#: ../../LICENSE.md:39 -#: d00d862c37ef4371bc40ad101c433199 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." -msgstr "" - -#: ../../LICENSE.md:44 -#: 93ba22a55b954a86af163557e05c52a4 -msgid "Software" -msgstr "" - -#: ../../LICENSE.md:46 -#: 367e01c9a6ad426a83bf5f5374e6a8ab -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" - -#: ../../LICENSE.md:51 -#: 565193677802418693fdbc123b34dd2b -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." -msgstr "" - -#: ../../LICENSE.md:57 -#: a4a99fc7709a49c29482f6e992d9e2bc -msgid "Trademark" -msgstr "" diff --git a/locales/_includes.pot b/locales/_includes.pot deleted file mode 100644 index 41cc9fb0..00000000 --- a/locales/_includes.pot +++ /dev/null @@ -1,22 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/_includes/what-is-cwl.md:1 -#: 46f474e1b364495181698bd13ce28a1e -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" diff --git a/locales/episodes.pot b/locales/episodes.pot deleted file mode 100644 index ecff4e32..00000000 --- a/locales/episodes.pot +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/episodes.md:5 -#: 5b500989fc13480681ecb39954c13fd7 -msgid "This page has moved" -msgstr "" - -#: ../../src/episodes.md:9 -#: ff7a3cc03e2048278bcb9af2429b8dee -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." -msgstr "" diff --git a/locales/es/LC_MESSAGES/LICENSE.po b/locales/es/LC_MESSAGES/LICENSE.po deleted file mode 100644 index 87af7480..00000000 --- a/locales/es/LC_MESSAGES/LICENSE.po +++ /dev/null @@ -1,135 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../LICENSE.md:2 385524707375429989b7b4fc7e4c7aa5 -#: 3d749a78eb3e47c991d603c2cabd1b91 -msgid "Licenses" -msgstr "" - -#: ../../LICENSE.md:4 7682a147e3f74921948bde67ac684338 -#: 4689ade8475a4c8a9d5e325f072c1392 -msgid "Instructional Material" -msgstr "" - -#: ../../LICENSE.md:6 7273f384601c4f18a4cc33c833f05e56 -#: ef8ec0f072d947fbba997c4b2191abc2 -msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable summary " -"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" -"[cc-by-legal]." -msgstr "" - -#: ../../LICENSE.md:12 2cd9327d0e2e43aaa963633db1320b96 -#: 696f3824ca814c9eb314abae51be8202 -msgid "You are free:" -msgstr "" - -#: ../../LICENSE.md:14 793123b1e0ba4603a0c54c952ea4a590 -#: 72ebe92edf58434e9d7a4fc6bddf8880 -msgid "" -"to **Share**---copy and redistribute the material in any medium or format" -msgstr "" - -#: ../../LICENSE.md:15 151178e4c9a9444fb65dbf926edad28d -#: 9b403f96d4194ffaab3f309d7d12f360 -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" - -#: ../../LICENSE.md:17 e44aed84ff0d48b3aea3946b3a7c85fc -#: 10b1befd0f834d79880c8aeb70b595d4 -msgid "for any purpose, even commercially." -msgstr "" - -#: ../../LICENSE.md:19 d8bb44ca55b642d6bb4a88eaa8292204 -#: 9017d0b760bb4370926d511b97a604c6 -msgid "" -"The licensor cannot revoke these freedoms as long as you follow the license " -"terms." -msgstr "" - -#: ../../LICENSE.md:22 6859f286e52c417096b072c923b9f235 -#: 1faadcaead6748dfb34886e5819af9b9 -msgid "Under the following terms:" -msgstr "" - -#: ../../LICENSE.md:24 ee4ea8e1fd044924b34b2d96ca158257 -#: 7a49ed3a728349c9b486f3d0b1dbf577 -msgid "" -"**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a [link to the license][cc-by-human], and indicate if changes were " -"made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." -msgstr "" - -#: ../../LICENSE.md:32 7598558aee3244b6b7892b06df94a393 -#: 57da6294edce46eab00e7d15e6f6d4fa -msgid "" -"**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" -msgstr "" - -#: ../../LICENSE.md:36 a83123e7ae79486c80107d176ea951c7 -#: 8fc8a30cd63c4a0a9d8ba1b913687029 -msgid "" -"You do not have to comply with the license for elements of the material in " -"the public domain or where your use is permitted by an applicable exception " -"or limitation." -msgstr "" - -#: ../../LICENSE.md:39 0cc05e8ed5274019998b1dfd6ab76824 -#: fe59e74a4d024831a6d5cbcfd3e4ee38 -msgid "" -"No warranties are given. The license may not give you all of the permissions " -"necessary for your intended use. For example, other rights such as " -"publicity, privacy, or moral rights may limit how you use the material." -msgstr "" - -#: ../../LICENSE.md:44 d70e680300524c8583f1e7fd361ad2ba -#: 3ea41d5a14ad46729cabb387a33814b0 -msgid "Software" -msgstr "" - -#: ../../LICENSE.md:46 d17e76d478354904b679b4f5ebde418d -#: 23751e2552ff450c83e3dd255da56dac -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" - -#: ../../LICENSE.md:51 015fba86005946eebc5959cc3b0493d0 -#: 13fb5eb48a8a434e95dbbb717ccaef8a -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." -msgstr "" - -#: ../../LICENSE.md:57 524088befae04f5485dc731d505c769b -#: e262fbd0e7de4f148f31afe39d1cb9e9 -msgid "Trademark" -msgstr "" diff --git a/locales/es/LC_MESSAGES/_includes.po b/locales/es/LC_MESSAGES/_includes.po deleted file mode 100644 index ed23c04f..00000000 --- a/locales/es/LC_MESSAGES/_includes.po +++ /dev/null @@ -1,28 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/_includes/what-is-cwl.md:1 66189f9a18df470791d7e6ab690b3475 -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - diff --git a/locales/es/LC_MESSAGES/episodes.po b/locales/es/LC_MESSAGES/episodes.po deleted file mode 100644 index 897540f7..00000000 --- a/locales/es/LC_MESSAGES/episodes.po +++ /dev/null @@ -1,32 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/episodes.md:5 49382fe02e4f4aae96ce4d1b666d649a -#: 0cbb5e7334a647c3bcae7333ec3ced90 -msgid "This page has moved" -msgstr "" - -#: ../../src/episodes.md:9 ebd3b75bc9a347029e9e164e94b43374 -#: fabb221482cb4ac0a98bbe10943ed025 -msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. Please use the new [Table of Contents](index.md#table-of-" -"contents) to browse the User Guide." -msgstr "" diff --git a/locales/es/LC_MESSAGES/faq.po b/locales/es/LC_MESSAGES/faq.po deleted file mode 100644 index 4b38c453..00000000 --- a/locales/es/LC_MESSAGES/faq.po +++ /dev/null @@ -1,358 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/faq.md:1 e53c79b325b749a691434bf2f7825a5a -#: 5daa5afac36f46dd8329e5629056384c -msgid "FAQ" -msgstr "" - -#: ../../src/faq.md:11 d95bfefa6344474d9820a266922831f8 -#: 40c8efda3caf4c6089bda3027c522f37 -msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" - -#: ../../src/faq.md:41 991a77ca372d4324843ed340ffbfbae7 -#: ee854bcb685941cab45ae7f33b0efe48 -msgid "Rename an Input File" -msgstr "" - -#: ../../src/faq.md:43 4654eac499464be4845a59bc281ec242 -#: a4cdd5ab6fe341a3ad3e3055556d96c3 -msgid "" -"This example demonstrates how to change the name of an input file as part of " -"a tool description. This could be useful when you are taking files produced " -"from another step in a workflow, and don't want to work with the default " -"names that these files were given when they were created." -msgstr "" - -#: ../../src/faq.md:59 4fcb9907771940d8857fab5b8211d337 -#: d1f359d47f124dfab23a75b196cd5884 -msgid "Rename an Output File" -msgstr "" - -#: ../../src/faq.md:61 9f3ed67bcb13459d9e7196e9d82cb58f -#: d83ced40605e411c92c4ae38761d7ffa -msgid "" -"This example demonstrates how to change the name of an output file from the " -"default name given to it by a tool:" -msgstr "" - -#: ../../src/faq.md:82 af6d80606de6412a8fe63ee379702eac -#: bc8997df2e6746cebc2068534f30ee82 -msgid "Referencing a Local Script" -msgstr "" - -#: ../../src/faq.md:84 fc7c21e08e8e45adb8f1265af494160e -#: 20b6ae57e1cf4410877a60fb3ef87264 -msgid "There are two ways to reference a local script:" -msgstr "" - -#: ../../src/faq.md:86 e37343ad3edd412f981397b995e6c841 -#: 73c66b809e9a4218b624338ccb88a05e -msgid "" -"The first method involves adding the folder containing your scripts to the " -"`PATH` environment variable. This allows you to run the shell script " -"directly without using `sh` or `bash` commands." -msgstr "" - -#: ../../src/faq.md:89 2b7e94e816fa46f4a221b5ce6b2214b2 -#: 9be72b7d5d604526b125b63148e99320 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" - -#: ../../src/faq.md:95 0fd0fd13672d48cda0f3ef7f2b0701da -#: fd96d178901545008a43fa99e3aa6cf3 -msgid "" -"After that, make the script executable with the command `chmod +x scriptname." -"sh`" -msgstr "" - -#: ../../src/faq.md:97 a21be18c313d430a8986760ee3725198 -#: db58a582e66244468f4d31e9213933d1 -msgid "" -"Finally, modify your `PATH` to add the directory where your script is " -"located. (It is good practice to use `$HOME/bin` for storing your own " -"scripts)." -msgstr "" - -#: ../../src/faq.md:104 404295b5792747c8a87306181d078cbc -#: 3e70f0da5cd7460b90c1690366f40820 -msgid "" -"Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" - -#: ../../src/faq.md:113 92582f3845b446d08ca9cbc4ad76a0a7 -#: db28dc27c82b4b29a7a9a768550bba9b -msgid "" -"When you wish to share your work later, you can place your script in a " -"software container in the Docker format." -msgstr "" - -#: ../../src/faq.md:115 2d62b6e5d7944818acd0f43b7d37ce67 -#: 4474b16fb3fd4cdc85da931159804967 -msgid "" -"The second method involves including an input of `type: File` in the script " -"itself:" -msgstr "" - -#: ../../src/faq.md:135 c72fa80f79594d479cb99dc6bfcb207d -#: 23c9b2e21cec4ee8ade087e6630f62c2 -msgid "In CWL, everything must be directly stated." -msgstr "" - -#: ../../src/faq.md:138 5f2b7881a7c64cf29b05b4d78158e176 -#: c01309dcd65c4f1080c396e6a9efb75d -msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" - -#: ../../src/faq.md:140 eb11641ac17e496384a60e4aacc5209b -#: 0a36801172fd4e24a04b3ba85cf74e29 -msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their input " -"binding makes use of `self`. Below is an example workaround for this, " -"pending a more sophisticated fix." -msgstr "" - -#: ../../src/faq.md:165 c0aee2cf9ee046128002b09a8aa397d8 -#: 433e788ba01141e98ea5a9e73ef71e6f -msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" - -#: ../../src/faq.md:167 34a04d6d09e94fd796a5ee13c6b9856a -#: b6de2761ce454992904775a06b7ba326 -msgid "" -"Below is an example showing how to specify different strings to be added to " -"a command line, based on the value given to a Boolean parameter." -msgstr "" - -#: ../../src/faq.md:188 b1ee951a6e6e4f4c8e88de4dc93bd616 -#: e36c2d53e8ba40f4a602b489a6688e24 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" - -#: ../../src/faq.md:190 1664807c6b264fc3b58e9f2c40a9543c -#: a9310166cb514e4e8824bba7fcfcb277 -msgid "" -"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" -"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/faq.md:194 a7ab83c7f31e4e8d83fbfba1abadef2b -#: f6144f77152e4284963951abaa30adb2 -msgid "merge_nested" -msgstr "" - -#: ../../src/faq.md:196 908451dc6990489e88edc1012899c440 -#: 790709dfc2854e4a89fcc4769f84b0f4 -msgid "" -"The input must be an array consisting of exactly one entry for each input " -"link. If \"merge_nested\" is specified with a single link, the value from " -"the link must be wrapped in a single-item list." -msgstr "" - -#: ../../src/faq.md:199 30947198b46d4151a5d92076c30659c0 -#: 438789c8def549d1b4b8a187d5acc48e -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" - -#: ../../src/faq.md:201 0b320fb2e40442608137ed9d6f2a74cd -#: 23ede7dfd5c84492baee1d5bbb9a91d9 -msgid "" -"Or in other words: if the destination is of type `File[]` (an array of " -"`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " -"add `linkMerge: merge_nested` under the appropriate `in` entry of the " -"destination step." -msgstr "" - -#: ../../src/faq.md:229 a143590b23384ed79fc37b17a0abd46e -#: 37c0474e48164160b23c4094d583d2d3 -msgid "Optional Inputs 💯" -msgstr "" - -#: ../../src/faq.md:231 6b36effcb80040c79396a1df241f635e -#: 3b2be0a4a87041b7a5bda20c6df2ffc8 -msgid "" -"To make an input parameter optional, add a question mark to the type " -"declaration." -msgstr "" - -#: ../../src/faq.md:247 2873af63ee324fab948d16a9e14db5a7 -#: 886300d2dcff4861aae503d34b0bee44 -msgid "" -msgstr "" - -#: ../../src/faq.md:248 a11f170a082a4df2b4a0c068dd0573ed -#: fe393ecdff25428da6cbcd30171c7811 -msgid "Enum Inputs ⚜️" -msgstr "" - -#: ../../src/faq.md:250 bd2ccba5ac7e486c9af1d906ad96b07a -#: ebfd4991d917413b858da8b437a55805 -msgid "" -"For command line flags that require a specific input as the argument an enum " -"type can be declared in CWL. **Specifying null here is known as long form " -"style. It does the same thing as the question mark on the other inputs.**" -msgstr "" - -#: ../../src/faq.md:267 3f1d8cf3390c43f8b78ce33fc020f1a0 -#: 2919ff4f51254e69aea40146e2d911f1 -msgid "" -msgstr "" - -#: ../../src/faq.md:268 89626d59c2164bb99d0b123def33f701 -#: 61ed4e87457c41eea31f51740557597e -msgid "Record Inputs 📀" -msgstr "" - -#: ../../src/faq.md:270 028c6179803b4dc8a718669312804101 -#: 1e6624104b024eb092682cd0dd0f6a3c -msgid "" -"For commandline flags that are either **mutually exclusive** or " -"**dependent** a special record type can be defined. You can also specify " -"null here to create optional inputs." -msgstr "" - -#: ../../src/faq.md:322 23d9d603d4d44880aea5ebfd86e02d8d -#: b741b8333e104feaa6d1f41fd4476304 -msgid "Setting Mutually Exclusive Parameters" -msgstr "" - -#: ../../src/faq.md:324 06ae9317c6af481bbf4fd70236ca10a9 -#: 334673ae870a4dada817857f3a49326e -msgid "" -"To properly set fields in a record input type, you need to pass a dictionary " -"to the input to properly set the parameters. This is done by using inline " -"JavaScript and returning the dictionary with the key of the field you want " -"to set. The source field is set to indicate the input from the workflow to " -"be used as the value." -msgstr "" - -#: ../../src/faq.md:342 0c6c0af33a274a8cb64ae3111c014338 -#: 362f85270df04712b2e2f21c7019e3cb -msgid "Setting Booleans" -msgstr "" - -#: ../../src/faq.md:344 1139a2f4e58046f9aac4c64b7d5a2e4d -#: ad6997f24c7c42fe965b5d7bfd1e633e -msgid "These can be set by using the default field" -msgstr "" - -#: ../../src/faq.md:349 ca97418a37bb4ae99bce1b44eebefbad -#: 99dce9d60b6a4f99bc39899b7c8c10ef -msgid "Concatenating Strings in Inputs" -msgstr "" - -#: ../../src/faq.md:351 7a5d2d6c6474492fa65ffd8a5048c733 -#: 6b68fe24cbf64624b49ea56fce2eecad -msgid "The valueFrom field must be used instead of default." -msgstr "" - -#: ../../src/faq.md:359 2549c8887b204ddabe4221978dce7e57 -#: d23326837eb74e7faf1f54e25f8309c4 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" - -#: ../../src/faq.md:361 d15ae28e932446b48bfc1dbdc34d8eab -#: 2e2eabe92670412e95474b25ad9cda4c -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" - -#: ../../src/faq.md:363 925a0bb31c5f428b93232e42d96bddeb -#: 81f9308adbee4a3c9e585b8e0f0c4844 -msgid "" -"For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" - -#: ../../src/faq.md:371 591dd97f12ca4b8ca263b17abe674fd6 -#: a5d3ed6cac28415288e7fc7fbfc6e8a6 -msgid "" -"If you can not avoid these dangerous characters, then pass `--relax-path-" -"checks` to `cwltool`." -msgstr "" - -#: ../../src/faq.md:373 3ccdf1a970c14cbe8e1d269dc4ae77b3 -#: 72f9692803304daf9f846e2b90139660 -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" - -#: ../../src/faq.md:375 4cefff22947f4d9eb2f66d1b6bca2a8f -#: a7eb20c817704811b3bcf2f94ec2e51d -msgid "If `cwltool --validate` returns valid" -msgstr "" - -#: ../../src/faq.md:384 bfcbe4003ccb4e59baeed0b631871970 -#: 20fa869849ef4b358a11db46111017de -msgid "But executing it causes an error like:" -msgstr "" - -#: ../../src/faq.md:396 d729277d8bc0488eadddf507ba63202f -#: 35032fcd9f23403ca006d62a7d6e7be7 -msgid "The file is here" -msgstr "" - -#: ../../src/faq.md:410 ca99353cf8f94d11add95ba36408ee46 -#: f6d6a4e3691446378c8fb01a2d19f8ad -msgid "Problem caused by `-` (hyphen character)." -msgstr "" - -#: ../../src/faq.md:423 deb9ae92120d4e30aebd6e4d0374a0a2 -#: 44608fed1048458e999e13b014327e7e -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" - -#: ../../src/faq.md:436 7f4054de28a243c89bd3aca1e2764b93 -#: 96ede8a8f1f34786aabd4004bf2e7acc -msgid "" -"If it is not possible to change the input identifier, then you can use an " -"alternative CWL Parameter Reference syntax:" -msgstr "" - -#: ../../src/faq.md:442 29658fd7b5724addb5074891942f79fe -#: 84634a368e704e8d828678785c784595 -msgid "Use CWL and cwltool with Singularity" -msgstr "" - -#: ../../src/faq.md:445 2dd0d8092e5640e3a930478497b78efd -#: 545c4db9c24f42ee946081254d9ca7a8 -msgid "" -"The CWL standards are built around (optional) Docker format containers. The " -"reference runner and several other CWL implementations support running those " -"Docker format containers using the Singularity engine. Directly specifying a " -"Singularity format container is not part of the CWL standards." -msgstr "" - -#: ../../src/faq.md:450 0d385ebff8c14cbfa418fa45c9b42e51 -#: 1c1e6d583d5646a8a5c9316dcd743d9f -msgid "Debug JavaScript Expressions" -msgstr "" - -#: ../../src/faq.md:452 67d82ee82a184ed3921da6fd1928e83e -#: cf7d336d444e4f59aa83585b7abb1fe5 -msgid "" -"You can use the --js-console option of cwltool, or " -"you can try creating a JavaScript or TypeScript project for your code, and " -"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" -"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" diff --git a/locales/es/LC_MESSAGES/index.po b/locales/es/LC_MESSAGES/index.po deleted file mode 100644 index b87c1d09..00000000 --- a/locales/es/LC_MESSAGES/index.po +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: es\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/index.md:1 -#: a58ca61ccefc401588f91699bc98bd32 -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../src/index.md:3 -#: 6dcf12053f104cb3a8d23ce8d4f90363 -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../src/index.md:7 -#: 1cc90206170d46119c5756f31a9e8799 -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../src/index.md:9 -#: b54801d84a944dadb4e4637551e3f7b9 -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." -msgstr "" - -#: ../../src/index.md:16 -#: 860afd2eda4847e0a0d8834de3af4aa8 -msgid "Navigating the User Guide" -msgstr "" - -#: ../../src/index.md:18 -#: d6046316c84b40ffb5478c90b2604911 -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." -msgstr "" - -#: ../../src/index.md:23 -#: c3c89ac756a74d9688e179b8718c9bf0 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." -msgstr "" - -#: ../../src/index.md:28 -#: 0eb795062b484537b090c4d5c361f7f4 -msgid "Table of Contents" -msgstr "" diff --git a/locales/es/LC_MESSAGES/introduction.po b/locales/es/LC_MESSAGES/introduction.po deleted file mode 100644 index 3452a5bc..00000000 --- a/locales/es/LC_MESSAGES/introduction.po +++ /dev/null @@ -1,746 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/introduction/basic-concepts.md:1 7d238c155d6a40df8c8471ebb448a41e -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 4af76ab7bd674e6ab73765ddcc81d5bf -msgid "" -"This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are " -"expected to be familiar with workflow managers, YAML, and comfortable " -"with following instructions for the command-line. The other sections of " -"the user guide cover the same concepts, but in more detail. If you are " -"already familiar with CWL or you are looking for more advanced content, " -"you may want to skip this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 4fafbbbfec734215872f455f1c7e62e9 -msgid "The CWL Specification" -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:2 7250962d9fcc4338a7c9e64e0c2b3868 -#: f8759274ac67447ab61551060918d9bc -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:21 106e3e4dd19b42beaa90908e17529869 -msgid "" -"The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered " -"in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 eb85aefcc6824c028479e299f3477c5a -msgid "" -"The specification version can have up to three numbers separated by `.`s " -"(dots). The first number is the major release, used for backward-" -"incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes " -"that are backward-compatible. The last number is used for bug fixes, like" -" typos and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 59a0083e4e594253b5eb0a6d2756f271 -msgid "" -"The model used for the specification version is called Semantic " -"Versioning. See the end of this section to [learn more](#learn-more) " -"about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 19dbee8336704859b5bd9f232879e81e -msgid "Implementations" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:39 947d98768fef4c3cb5b87208303b5712 -msgid "" -"An implementation of the CWL specification is any software written " -"following what is defined in a version of the specification document. " -"However, implementations may not implement every aspect of the " -"specification. CWL implementations are licensed under both Open Source " -"and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 de6edc23dc9b4759b2aaa0954050b6be -msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud" -" and high performance computing environments where tasks are scheduled in" -" parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 ccee7288b79745d9a6a4bb32e9249594 -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: 10b787163c2e418291616a7bc1caf0bd -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: 0176badcaff14e79ba00f1f26c40f42d -msgid "" -"A process is a computing unit that takes inputs and produces outputs. The" -" behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification" -" {{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: 36e1e02745a44b4ab7f80f593eb3c408 -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: c3e19102cf7d44c795dbd57897e4ad8a -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: 288483391ca742e18ed19cd89666c4a1 -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: 5f5df951ffd6414eb054ca3af83a1abe -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 430425889a4c4f0a9f774d1b2e67debb -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: 9e42047299834ec6b41edf6c1b6d6513 -msgid "" -"A command-line tool is a wrapper for a command-line utility like `echo`, " -"`ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: f6d4657261e042fd8bd9782047d19ea9 -msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be " -"used to simplify workflows and command-line tools, moving common parts of" -" a workflow execution into reusable JavaScript code that takes inputs and" -" produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: fb8fa26ade2e4555bc5904a680d4de23 -msgid "" -"Operation is an abstract process that also takes inputs, produces " -"outputs, and can be used in a workflow. But it is a special operation not" -" so commonly used. It is discussed in the [Operations " -"section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 1eb86d0cb6c74685829e7f978b177212 -msgid "" -"The workflow is a process that contains steps. Steps can be other " -"workflows (nested workflows), command-line tools, or expression tools. " -"The inputs of a workflow can be passed to any of its steps, while the " -"outputs produced by its steps can be used in the final output of the " -"workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: dda24aff00964493ae997f36dff74c04 -msgid "" -"The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through " -"*requirements*. There are many requirements defined in the CWL " -"specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: e696bf67d6d04416b3f9c43f12376a10 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: b9746c3e3e554c2684be3917a31c7d10 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 8605fc09a1a04ab7ad271ac2bea9a17b -msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input " -"directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: a1fb5f8dd8964b6fb8990f7e877f8e3f -msgid "" -"Some CWL runners may provide requirements that are not in the " -"specification. For example, GPU requirements are supported in `cwltool` " -"through the `cwltool:CUDARequirement` requirement, but it is not part of " -"the {{ cwl_version }} specification and may not be supported by other CWL" -" runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: 8fe3e01579524ef2badf284092ce00de -msgid "" -"Hints are similar to requirements, but while requirements list features " -"that are required, hints list optional features. Requirements are " -"explained in detail in the [Requirements](../topics/requirements-and-" -"hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: c0ca689a49334564baf49359b582c491 -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: fa9a58da83a04493bee1d1e6c1cba8e1 -msgid "" -"The FAIR principles have laid a foundation for sharing and publishing " -"digital assets, and in particular, data. The FAIR principles emphasize " -"machine accessibility and that all digital assets should be Findable, " -"Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created." -" It is thus important that workflows support the creation of FAIR data " -"and adhere to the FAIR principles. — [FAIR Computational " -"Workflows](https://workflows.community/groups/fair/), Workflows Community" -" Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: 93e390de3c1445e5afa0a8bc8ee99480 -msgid "" -"CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\"," -" CWL tasks are isolated, and you must be explicit about your inputs and " -"outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: 4b5b1dfad3aa4fee9a41463d5feeb8ea -msgid "" -"The benefit of explicitness and isolation are flexibility, portability, " -"and scalability; tools and workflows described with CWL can transparently" -" leverage technologies such as Docker and be used with CWL " -"implementations from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: 6c0621375a704ed0a79d4ae65538bb31 -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 357ae9a25a644caab49ddb3c9ead1028 -#: 646006005df94092ac1134bc194d5fe7 e495fae55ee1480c88438ec4dcc1fc5c -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:180 -#: ab4a78d72dfa43b180615e565080d07a -msgid "Semantic Versioning - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:181 -#: ba8d7155363b4ed59912fc426b207ffc -msgid "" -"The CWL Specification page in the CWL website: " -"" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:182 -#: 37fc683fd3564bd698e3a8843ed7e401 -msgid "" -"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:183 -#: e6af1cb1c3484a1db8fa8577dd5684c6 -msgid "" -"The list of Implementations in the CWL website: " -"" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:184 -#: fe7682c04d344a71a2d1de3586f83f38 -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:185 -#: caf02d5ff6c04255a2144ff453884b0b -msgid "" -"CWL Operations are covered in the [Operations](../topics/operations.md) " -"section of this user guide." -msgstr "" - -#: ../../src/introduction/index.md:1 a22112574264441eb4b775ce72f7ee62 -msgid "Introduction" -msgstr "" - -#: ../../src/introduction/index.md:3 fe9e792085024abb95180662bf0657a9 -msgid "" -"This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that" -" are useful to know before reading the rest of the user guide." -msgstr "" - -#: ../../src/introduction/prerequisites.md:1 23849325192045f5aa48c9f3d9a2080a -msgid "Prerequisites" -msgstr "" - -#: ../../src/introduction/prerequisites.md:6 c7c0e1cd18d54dcca7062d7d053dcc35 -msgid "" -"The software and configurations listed in this section are prerequisites " -"for following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements " -"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" -"compatible runner or workflow system, but the results and interface may " -"look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 5d7a4a2cccbb47bbaa9ba2ca2de1eff2 -msgid "CWL Implementations" -msgstr "" - -#: ../../src/introduction/prerequisites.md:14 a0ebb398fd1944858fde855a37938446 -msgid "" -"There are many implementations of the CWL standards. Some are complete " -"CWL runners, while others could be plug-ins or extensions to workflow " -"engines. We have a better explanation in the [Implementations](basic-" -"concepts.md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 83d90d246db24c07a73bcd73a3c6bfb6 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 c2fd09dd72af46ca8e3284d0c1c7dffb -msgid "" -"We recommend using an up-to-date operating system. You can choose any of " -"the following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 00694f21c8bd435f9de10785d2a829dc -msgid "Linux" -msgstr "" - -#: ../../src/introduction/prerequisites.md:25 3cd6a5a0a9754a678ec4eb5a9569a2ab -msgid "macOS" -msgstr "" - -#: ../../src/introduction/prerequisites.md:26 2b0d2a5dc85c4216840c2ce406e10413 -msgid "Windows" -msgstr "" - -#: ../../src/introduction/prerequisites.md:29 0f8ab0f07c9f4e92b6907685a21e0d09 -msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem" -" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " -"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" -"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " -"details on installing WSL2. Your operating system also needs internet " -"access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:35 eb1b97c2f64c43c78cf620f0b3197707 -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:41 b0fff1b3d67e4e01b7140def8004924a -msgid "" -"The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL " -"community. It is also the CWL reference runner, which means it must " -"support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 dfad9ccfdc5949adb5785e57a3f0a345 -msgid "" -"`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create " -"and activate a Python virtual environment using the `venv` module, and " -"install `cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 229d3b94015c46f89a7fcf3035a06e38 -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:62 bede33df513b4ff0bf31a1c4a1b76304 -msgid "" -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` " -"and `conda`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:65 f20e6ae025fc48cf82b490aa1e45d978 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:67 10c729f31bd94b2580a494a07e8c8c06 -msgid "`true.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:73 55571e0099af459bb38ef2cbb5ce3720 -msgid "" -"The `cwltool` command has an option to validate CWL tool and workflow " -"descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the " -"CWL standards. However, these actions will be performed without running " -"the document. To validate CWL workflows (or even a standalone command " -"line tool description like the above) pass the `--validate` option to the" -" `cwltool` command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:79 436d10464d0540da9227bff0e7721928 -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:84 db76c196cff7476c9f0059410071109e -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:86 5c34965d08704905af72df2d02f399ea -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 c4b1c6f7a6214a2a8cda037dfd1ce5e7 -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../src/introduction/prerequisites.md:93 22b70a1995e24ae1a5e688b08d69be78 -msgid "" -"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be " -"invoked independently, and is not reliant on a particular CWL runner " -"program name. Users can invoke `cwl-runner` instead of invoking a CWL " -"runner like `cwltool` directly. The `cwl-runner` is installed by a system" -" administrator or user to point to the preferred CWL implementation. This" -" is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:101 2b078afe85c9496ebe7c4fd5fa849506 -msgid "" -"The CWL community publishes a Python package with the name `cwlref-" -"runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:104 edb107bbbef94363a531344862b0646b -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:111 c92da002f02148e485fccabfb80f78c6 -msgid "" -"Now you can validate and run your workflow with the `cwl-runner` " -"executable, which will invoke `cwltool`. You should have the same results" -" and output as in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:115 5ff5383fffc646cf860b9e6adffe0d4a -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:120 3fb6539b1da24c6d8cab103ebaa728e9 -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:125 56f8f92a8e4e46de9def7d33926a9354 -msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For" -" that, the first thing you need to do is copy `true.cwl` workflow into a " -"new file: `true_shebang.cwl`, and include a special first line, a " -"*shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:129 f024c312097941cc838f6e4684709e2d -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 27eb4624fa6a4fbca5c842bc69e277ff -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:137 a086a591e5034a768d6ed9f95ccffb41 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:144 dacb4f334ee64afa9da1418b806fbb8a -msgid "" -"And finally, you can execute it directly in the command-line. On " -"execution, the program specified in the shebang (`cwl-runner`) will be " -"used to execute the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 64cb2e80ed554f75aa64bc856c011e74 -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 7c008d7286b242c4989809773075e369 -msgid "" -"The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute " -"the script using the executable specified after the shebang. It is " -"considered a good practice to use `/usr/bin/env ` rather than" -" using a hard-coded location, since `/usr/bin/env ` looks for" -" the `` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 3d0c3d9473b64745aaadd1c97f86e6bd -msgid "Text Editor" -msgstr "" - -#: ../../src/introduction/prerequisites.md:163 f87429becda74bdab6e9e8956da16786 -msgid "" -"You can use any text editor with CWL, but for syntax highlighting we " -"recommend an editor with YAML support. Popular editors are Visual Studio " -"Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:167 40faebbbe3974365adbf4190ac9571af -msgid "" -"There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting" -" and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:171 24ce76cffa4c4dc3b1471c932ce34d28 -msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " -"" -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 1a14a5c5c15941ff8f957be9b7e346fd -msgid "" -"cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:174 6fccaea992b74740b91aa4dea1e9b6f6 -msgid "" -"The CWL community also maintains a list of editors and viewers: " -"" -msgstr "" - -#: ../../src/introduction/prerequisites.md:177 ff2d02dada844e349ce39147eaec02a0 -msgid "Docker" -msgstr "" - -#: ../../src/introduction/prerequisites.md:181 756d50a22d9944989e83fd49691b7dc1 -msgid "" -"`cwltool` uses Docker to run tools, workflows, and workflow steps that " -"specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: " -"." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 208ae40269d64a95922c3b6b88fa7af0 -msgid "" -"You do not need to know how to write and build Docker containers. In the " -"rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models " -"with and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:191 676cbeed9ecf468587f88adf03f088f2 -msgid "" -"`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for " -"pulling images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:198 97048cb2351f4408946828ff46cd513e -msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the " -"next section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:199 28810c389a8f480d8af7af37580fba6e -msgid "The Python `venv` module: " -msgstr "" - -#: ../../src/introduction/quick-start.md:1 6eba770f0a494294ada23cdfe563ada6 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 bc84e8e2bd7b4e2eadf8e09b64f8b11e -msgid "" -"This section will show you a brief overview of what CWL is, and where you" -" can learn more about it. No previous knowledge of CWL is required, but " -"you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 244007c12d0e4c11b5bc5a50fbb7b263 -msgid "“Hello World”" -msgstr "" - -#: ../../src/introduction/quick-start.md:12 1b7f68f5a3214f4da4f1887d14ced464 -msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " -"The example below shows a simple CWL “Hello World” workflow annotated " -"with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 aab574ceba8348b7a62c1c645c7ae300 -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 e3e88da22e65425292b19d8159e6bcdc -msgid "" -"The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the" -" same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 fbdbaead418f4246b4216acce9c6a51f -msgid "" -"In CWL, there is a distinction between a command-line tool and a " -"workflow. But for the sake of simplicity, we are using the term " -"“workflow” here. You will learn more about this in the [basic concepts" -"](basic-concepts.md) section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 008fc4481f1c4c7bb215fa3b6096048f -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 31d3ab3f31c44729989ee72a756c7242 -msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the " -"CWL *Reference Runner* for the specification, and it is compliant with " -"the latest version of the specification: {{ cwl_version }}. You can " -"install `cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 069fa8bae74d4c24b680c4199d714277 -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../src/introduction/quick-start.md:47 62cacbc189d0440ebe4a8dde4878450c -msgid "" -"If installing the cwltool using the pip command doesn't work for you, the" -" [prerequisites](prerequisites.md) section contains other ways to install" -" `cwltool` and a more detailed list of software and libraries used for " -"following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 f208e50c0089409aa7463c915be80092 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../src/introduction/quick-start.md:53 6c551e9af341475496b7b6b104330183 -msgid "" -"The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the " -"`hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 da2c9a63648342aab3f3b8a34660a4bc -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:62 1217d999216f47aa8f1903e2417fc57a -msgid "" -"Or you can override the default value of the input parameter `message`, " -"similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 3559a76a1fc64f3eb61a503bf7c77757 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 21386999503341408b798efa9fc4f262 -msgid "" -"Another way of passing values to your workflow input parameters is via an" -" *Inputs Object*. This is a file containing the input fields with their " -"corresponding values. The Inputs Objects file can be written in JSON or " -"YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 215e425a5ae64cd0ac5e8d34d7f47b58 -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../src/introduction/quick-start.md:80 963c003c4a334dbe874edc0ab38ea92f -msgid "" -"You can use this Inputs Object file now to execute the “Hello World” " -"workflow:" -msgstr "" - -#: ../../src/introduction/quick-start.md:82 83921375eed44fc695cbc172d9317032 -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:88 9795092d234e4fa5a2bdfc4c9c02460f -msgid "" -"We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but " -"it is not a requirement. You can choose any name for your workflows and " -"Inputs Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:96 8846a5ff35b64859b8ec7b16be9f8f6b -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../src/introduction/quick-start.md:97 785c9e2330b045b39bf02f77ab6513f6 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../src/introduction/quick-start.md:98 b6d05398bca648b8ac25755fbaab91c0 -msgid "" -"The [`common-workflow-language` organization](https://github.com/common-" -"workflow-language) at GitHub." -msgstr "" - -#: ../../src/introduction/quick-start.md:99 2ccf7e847e0b476493ae514381ca3612 -msgid "" -"[Common Workflow Language at " -"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../src/introduction/quick-start.md:100 d7168eb1f7384733be6316fe72f486eb -msgid "" -"[YAML.org](http://yaml.org/) and [YAML at " -"Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../src/introduction/quick-start.md:101 14bbd3ce1f2a488ca919d4f26c8f1e5a -msgid "" -"The {{'[CWL Specification " -"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " -"cwl_version_text) }}." -msgstr "" - -#: ../../src/introduction/quick-start.md:102 86f1fc65d2d14a41ac282eb63fd9de86 -msgid "" -"[Workflow management system at " -"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" - diff --git a/locales/es/LC_MESSAGES/setup.po b/locales/es/LC_MESSAGES/setup.po deleted file mode 100644 index 6b6fd9db..00000000 --- a/locales/es/LC_MESSAGES/setup.po +++ /dev/null @@ -1,32 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/setup.md:5 715f40c8e3f544e4805ae2b456b9d699 -#: 29bb5c68be6042e5aa4a370e9c4024b3 -msgid "This page has moved" -msgstr "" - -#: ../../src/setup.md:9 c9641546c55a44eab9ae40ec272d5df8 -#: 8bcf31398c34491da1a1590422a72cbe -msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. The information on this page has been migrated to the [FAQ](/faq." -"md) section of the new user guide." -msgstr "" diff --git a/locales/es/LC_MESSAGES/sphinx.po b/locales/es/LC_MESSAGES/sphinx.po index 27d21259..38526232 100644 --- a/locales/es/LC_MESSAGES/sphinx.po +++ b/locales/es/LC_MESSAGES/sphinx.po @@ -9,7 +9,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -18,12 +18,11 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" "Generated-By: Babel 2.10.3\n" -#: ../../src/_templates/sidebar-nav-bs.html:1 ada5c93414a84374b3eaea93dc11ae74 -#: b896fd5e11fe4674a7f46ad489476692 +#: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" msgstr "" -#: ../../src/_templates/sidebar-nav-bs.html:3 a3cc1c498bad434ebadd4a2e92dbf5f0 -#: acede4e78f7e4aefa0ad9425928cbb42 +#: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" msgstr "" + diff --git a/locales/es/LC_MESSAGES/topics.po b/locales/es/LC_MESSAGES/topics.po deleted file mode 100644 index 80ee8dd9..00000000 --- a/locales/es/LC_MESSAGES/topics.po +++ /dev/null @@ -1,2577 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/topics/additional-arguments-and-parameters.md:1 -#: be1d17fdb27345ffb7fe0cbe92002434 -msgid "Additional Arguments and Parameters" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:3 -#: 82ff1f5ebb0647e886d131f7a8c4f5c3 -msgid "" -"Sometimes tools require additional command line options that don't " -"correspond exactly to input parameters." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 4dbbc91d876746b59f53d3ba49df43f8 -msgid "" -"In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files " -"in the same directory as the source file. However, CWL input files (and " -"the directories in which they appear) may be read-only, so we need to " -"instruct \"javac\" to write the class file to the designated output " -"directory instead." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 82f4844017ec4f609c8f0f5bf9812f75 -msgid "`arguments.cwl`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 afb24d50c0a94693ab9ef9271068e58d -#: ca7a2bce1de34dd2ad8f77095854037b -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 23f9dcf2c7344a40aa2d512f1349135a -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 3d26cfb6a1204ba89ac812bc4fe3df4f -msgid "" -"And now invoke `cwltool` providing the tool description and the input " -"object on the command line:" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 317f82f2a0d54af29baaf5e3fca1558e -msgid "" -"Here we use the `arguments` field to add an additional argument to the " -"command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:43 -#: c5f85db684c842a5a2d55afb8ea44e94 -msgid "" -"This example references a runtime parameter. Runtime parameters provide " -"information about the hardware or software environment when the tool is " -"actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include " -"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " -"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " -"Environment][runtime] section of the CWL specification for details." -msgstr "" - -#: ../../src/topics/best-practices.md:1 92154668e72240e48268a3dc593f65c5 -msgid "Best Practices" -msgstr "" - -#: ../../src/topics/best-practices.md:3 df0c80b10cde412c901b9bfa235b4521 -msgid "" -"The following are a set of recommended good practices to keep in mind " -"when writing a Common Workflow Language description for a tool or " -"workflow. These guidelines are presented for consideration on a scale of " -"usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 93e66f6c1c9643a3944ad3c7651464a1 -msgid "" -"No `type: string` parameters for names of input or reference " -"files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../src/topics/best-practices.md:11 7b54e111b9a2485d912b9c1dde0e6816 -msgid "" -"A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that" -" the usual rules of software licensing apply to this document. For " -"example, if the workflow is shared publicly, licensing terms must be " -"clear so that a future user understands under what conditions they can " -"run the workflow, modify it and/or combine it with other workflows. For " -"this reason, please consider including a license field in the document. " -"The authors of this guide urge you to choose a pre-existing license " -"rather than trying to write your own (see the link below to learn more " -"about choosing a license), and our recommended practice is to choose a " -"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" -"license]." -msgstr "" - -#: ../../src/topics/best-practices.md:20 c58100a01b034441b247e761df1f6a12 -msgid "" -"If possible, the license should be specified with its corresponding [SPDX" -" identifier][spdx]. Construct the metadata field for the license by " -"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " -"`SPDX-ID` is taken from the list of identifiers linked above. See the " -"example snippet below for guidance. For non-standard licenses without an " -"SPDX identifier, provide a URL to the license." -msgstr "" - -#: ../../src/topics/best-practices.md:26 53c3357a75df4704a96848aebc093327 -msgid "" -"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" -"Programmer][sci-license]\"" -msgstr "" - -#: ../../src/topics/best-practices.md:28 a9ae73ef4d3447038d1180032b41255c -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../src/topics/best-practices.md:37 a2a654e113d64f37bb3bfcb8828301ce -msgid "" -"For more examples of providing metadata within CWL descriptions, see " -"[the Metadata and Authorship section of this User Guide](../topics" -"/metadata-and-authorship.md)." -msgstr "" - -#: ../../src/topics/best-practices.md:40 66ad30cdce23481d90042b63c3bf8d16 -msgid "" -"Include [attribution information][license-example] for the author(s) of " -"the CWL tool or workflow description. Use unambiguous identifiers like " -"[ORCID][orcid]." -msgstr "" - -#: ../../src/topics/best-practices.md:44 f3c0be3d1a3249288a8cd3053bc1cdcf -msgid "" -"In tool descriptions, list dependencies using short name(s) under " -"`SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:47 07ad1cf2508d4cb780a6e703c07d5a5b -msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in " -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../src/topics/best-practices.md:50 f0931e33e50a495aabd1c58daca72c3e -msgid "" -"All `input` and `output` identifiers should reflect their conceptual " -"identity. Use informative names like `unaligned_sequences`, " -"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " -"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../src/topics/best-practices.md:55 3da4c1e61c53469e8e313553130a5b28 -msgid "" -"In tool descriptions, include a list of version(s) of the tool that are " -"known to work with this description under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:58 8d3930c2039347beb1383b0dab7ea1d5 -msgid "" -"`format` should be specified for all input and output `File`s. " -"Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " -"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" -"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " -"types). For non-bioinformatics tools, use or build an appropriate " -"ontology/controlled vocabulary in the same way. Please edit this page to " -"let us know about it." -msgstr "" - -#: ../../src/topics/best-practices.md:66 275a541a634345d2b88a7e982d3a84cb -msgid "" -"Mark all input and output `File`s that are read from or written to in a " -"streaming compatible way (only once, no random-access), as `streamable: " -"true`." -msgstr "" - -#: ../../src/topics/best-practices.md:69 23e3e58d1b5245919d1be053b0c53ddc -msgid "" -"Each `CommandLineTool` description should focus on a single operation " -"only, even if the (sub)command is capable of more. Don't overcomplicate " -"your tool descriptions with options that you don't need or use." -msgstr "" - -#: ../../src/topics/best-practices.md:73 0a7b19343ab34220a615f9d5735f62f3 -msgid "" -"Custom types should be defined with one external YAML per type definition" -" for re-use." -msgstr "" - -#: ../../src/topics/best-practices.md:76 fbb538cc258a445a938333315248a4f8 -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../src/topics/best-practices.md:78 dee070dbc0c54210a3b276dcd1e3b151 -msgid "" -"If useful, include a top-level `doc` as well. This should provide a " -"longer, more detailed description than was provided in the top-level " -"`label` (see above)." -msgstr "" - -#: ../../src/topics/best-practices.md:82 0d5c1c5e50de42809afdf4bcddeb86e0 -msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list" -" of valid values." -msgstr "" - -#: ../../src/topics/best-practices.md:85 63a5664bb6f043529e753fa27faa9104 -msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. " -"One common example: manipulating `File` names and paths? Consider whether" -" one of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc., could be used instead." -msgstr "" - -#: ../../src/topics/best-practices.md:90 e3832fa90bc540dd9c92dc606c8a3d1f -msgid "" -"Give the tool description to a colleague (preferably at a different " -"institution) to test and provide feedback." -msgstr "" - -#: ../../src/topics/best-practices.md:93 8a2e36ed7ae0486b9a569b8a7c336fe9 -msgid "" -"Complex workflows with individual components which can be abstracted " -"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" -" their workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../src/topics/best-practices.md:97 00dd50adbb734f0ab7e08d005cf30487 -msgid "" -"Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics" -" software\"][containers] (also useful to other disciplines)." -msgstr "" - -#: ../../src/topics/command-line-tool.md:1 eb2ea54b83304757ba4b835d4ae45642 -msgid "Command Line Tool" -msgstr "" - -#: ../../src/topics/command-line-tool.md:3 ad6f136a690e4c4d9320cbff4b1a3469 -msgid "" -"A command-line tool is a type of Process object that can be run by itself" -" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " -"`tar`, etc. The command-line tool is defined in the `baseCommand` " -"attribute of the command-line tool CWL document." -msgstr "" - -#: ../../src/topics/command-line-tool.md:8 3018247f156c470ca7b9c7801a6f59bd -msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The " -"following example contains a minimal example of a CWL command-line tool " -"for the `echo` Linux command, using inputs and outputs." -msgstr "" - -#: ../../src/topics/command-line-tool.md:19 7c07c9401a3d424089828def1d272842 -msgid "CWL command-line tool." -msgstr "" - -#: ../../src/topics/command-line-tool.md:50 d5300fa60ee942cc961594a504b0d08d -msgid "`echo.cwl`" -msgstr "" - -#: ../../src/topics/command-line-tool.md:57 f56c8f69d71f4f4da40fbb007008500e -msgid "" -"The example above uses a simplified form to define inputs and outputs. " -"You will learn more about in the [Inputs](../topics/inputs.md) and in the" -" [Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../src/topics/command-line-tool.md:68 4621ef6fe81a4048944814aff22f508f -msgid "Network Access" -msgstr "" - -#: ../../src/topics/command-line-tool.md:69 1d3f1abb81ff4186843df880dc732ee2 -msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network " -"access. If a command-line tool is written manually in CWL v1.1+, there is" -" a need to specify when network access is required." -msgstr "" - -#: ../../src/topics/command-line-tool.md:83 93f0719b3b2c4c5297bf925801c93b45 -msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " -"Network Access automatically." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:1 -#: 46b4df81014846aea9e0fe7c5caade0d -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:3 -#: 722ed10f0fed4ff59852fa09c45a92f1 -msgid "" -"Sometimes you need to create a file on the fly from input parameters, " -"such as tools that expect to read their input configuration from a file " -"rather than the command line parameters, or need a small wrapper shell " -"script." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:7 -#: 20b151c8c270433ab74288011f2ad47d -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:9 -#: 0625cac27fdc4127b50bd7f195117189 -msgid "`createfile.cwl`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:15 -#: 2035501f61434c339a5abdf693696c84 -msgid "" -"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the " -"value at the input `message`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:20 -#: f6e00a5502ef4bb386ee5f88b0085527 -msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later" -" during command line tool invocation. That means that any genuine need " -"for the character `$` must be **escaped** with `\\`. For instance, " -"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " -"be evaluated by the shell script instead of the CWL engine." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:27 -#: 4fbbc941c4f7412b936446fbf9115363 -msgid "" -"To test the above CWL tool, use this job to provide the input value " -"`message`:" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 9f546d2c6a454542a860ead319642479 e6c179499aee4824a5c02babbf26a869 -#: eb2052144d844cdaa0e9e4b3bc487628 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:35 -#: d9ea213b07e64d04b53cdb32a3650322 -msgid "" -"Before we run this, let us look at each step in a little more detail. The" -" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " -"command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:40 -#: fcc7a6d59f8a4e13bf821d488fa17db7 -msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " -"YAML array, we need a `-` on the first line of each element of the array," -" in this case we have just one element. `entryname:` can have any value, " -"but it must match what was specified in the `baseCommand`. The final part" -" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " -"means that you are using a multiline string (without it, we would need to" -" write the whole script on one line)." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:51 -#: f7c967a182734c8ca47f873a0cb28093 -msgid "" -"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " -"formatting." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:54 -#: ../../src/topics/environment-variables.md:18 -#: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 20f1807303474b5c8c18cede5df322a3 2c41b94f3196446ea483c630af9eea67 -#: 5735865bd655415a9a136f441eebafaf 7364d5ebf81e4949b3212b06788e2381 -#: f1195863b1b345f9a718776763466533 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - -#: ../../src/topics/custom-types.md:1 d2e58b004bfb4c6cae7c69658de21321 -msgid "Custom Types" -msgstr "" - -#: ../../src/topics/custom-types.md:3 484ff45699964c2996a0cdfea0fdb329 -msgid "" -"Sometimes you may want to write your own custom types for use and reuse " -"in CWL descriptions. Use of such custom types can reduce redundancy " -"between multiple descriptions that all use the same type, and also allow " -"for additional customisation/configuration of a tool/analysis without the" -" need to fiddle with the CWL description directly." -msgstr "" - -#: ../../src/topics/custom-types.md:9 c30f12911bb649c6b71e7ad73edd0b4c -msgid "" -"The example below is a CWL description of the [biom convert format][biom]" -" tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:12 c8ecf2ef21fa4b8ba562625355ba8a65 -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../src/topics/custom-types.md:18 3f328356740644a582ca21d5fa60b2f6 -msgid "`custom-types.yml`" -msgstr "" - -#: ../../src/topics/custom-types.md:24 b9569867a46745268f37ff47c18079fb -msgid "" -"___Note:___ To follow the example below, you need to [download the " -"example input file](https://github.com/common-workflow-" -"language/user_guide/blob/main/src/_includes/cwl/custom-" -"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " -"`wget`:" -msgstr "" - -#: ../../src/topics/custom-types.md:30 636449effdeb481da9ada5d283db2ab9 -msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to " -"be used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../src/topics/custom-types.md:46 d6d41dc3bbd746bab0a5905a8611a356 -msgid "" -"The reference to a custom type is a combination of the name of the file " -"in which the object is defined (`biom-convert-table.yaml`) and the name " -"of the object within that file (`table_type`) that defines the custom " -"type. In this case the `symbols` array from the imported `biom-convert-" -"table.yaml` file define the allowable table options. For example, in " -"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" -" to create an OTU table in hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:53 e742d68f3a994b9595bae07ee2099831 -msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../src/topics/custom-types.md:55 f338008e7fb646038a7dcec456d9dce6 -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../src/topics/custom-types.md:61 e69fcaf1f01049d6824058969e87e0f0 -msgid "" -"In order for the custom type to be used in the CWL description, it must " -"be imported. Imports are described in " -"`requirements:SchemaDefRequirement`, as below in the example `custom-" -"types.cwl` description:" -msgstr "" - -#: ../../src/topics/custom-types.md:76 31abe821b66643d098ecdb4e207ed064 -msgid "" -"Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number " -"of cores required for the tool to run successfully, as well as details of" -" the version of the software that the description was written for and " -"other useful metadata. These features are discussed further in other " -"chapters of this user guide." -msgstr "" - -#: ../../src/topics/environment-variables.md:1 b2a8bdbc4e4347389dc9e2c34e7c71ca -msgid "Environment Variables" -msgstr "" - -#: ../../src/topics/environment-variables.md:3 8de1ffb0a81547f7a616d5ea912998c3 -msgid "" -"Tools run in a restricted environment and do not inherit most environment" -" variables from the parent process. You can set environment variables " -"for the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../src/topics/environment-variables.md:7 9596b81e881549fba7910947a202ba5e -msgid "`env.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:1 8473228fc0104b4c940a967294276542 -msgid "Expression Tool" -msgstr "" - -#: ../../src/topics/expression-tool.md:3 75f469063959433a8ed459c2b09cd61f -msgid "" -"An expression tool is a type of Process that can be run by itself or as a" -" Workflow step. It executes a pure JavaScript expression. It is meant to " -"be used as a way to isolate complex JavaScript expressions that need to " -"operate on input data and produce some result as output." -msgstr "" - -#: ../../src/topics/expression-tool.md:8 6676f841711d43f682e18d954438fc65 -msgid "" -"Similar to the command-line tool it requires `inputs` and `outputs`. But " -"instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" - -#: ../../src/topics/expression-tool.md:17 d6d043d8ce9a41c59ad0d3239f8f306e -msgid "CWL expression tool." -msgstr "" - -#: ../../src/topics/expression-tool.md:48 f3378c740b854b9695ea6ccfb0ab434a -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:67 c9d5c0dd3eeb4617891f90d1a081a3e7 -msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains" -" a JavaScript call in `.toUpperCase()`. This means to tools using the " -"expression tool that JavaScript is a requirement." -msgstr "" - -#: ../../src/topics/expressions.md:1 08240053421545288788e84dec6d6614 -msgid "Expressions" -msgstr "" - -#: ../../src/topics/expressions.md:3 cf3ebc8d28d2443ca0e67b5974a963ab -msgid "" -"If you need to manipulate input parameters, include the requirement " -"`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by " -"the CWL runner." -msgstr "" - -#: ../../src/topics/expressions.md:9 767a6dc8370b4f9aad42e07a657e3e1f -msgid "" -"JavaScript expressions should only be used when absolutely necessary. " -"When manipulating file names, extensions, paths etc, consider whether one" -" of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " -"practices](best-practices.md)." -msgstr "" - -#: ../../src/topics/expressions.md:16 f38d9e8192614ba689d17c1cc48ac848 -msgid "`expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:22 ce88970e57f2427a905e1bc66c20ffe8 -msgid "" -"As this tool does not require any `inputs` we can run it with an (almost)" -" empty job file:" -msgstr "" - -#: ../../src/topics/expressions.md:25 e7238751e3604a34a15fff753136eada -msgid "`empty.yml`" -msgstr "" - -#: ../../src/topics/expressions.md:31 ff81d45c3f124c738871b40e5b717d7b -msgid "" -"`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object" -" is represented simply by a set of empty brackets." -msgstr "" - -#: ../../src/topics/expressions.md:35 f92515a70adc4366bc46e2eacf49e47b -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../src/topics/expressions.md:37 dcefffb5ecdc4ec3bcc216c21df896ec -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:47 bdb0a61e53cf4521bc0f16593eaa5fdd -msgid "" -"Note that requirements can be provided with the map syntax, as in the " -"example above:" -msgstr "" - -#: ../../src/topics/expressions.md:54 80c3b1fb37aa40038f0bc98905604c47 -msgid "" -"Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" -" describe the additional command line arguments." -msgstr "" - -#: ../../src/topics/expressions.md:62 22a6a66f05c94b988789edfc7acb7951 -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../src/topics/expressions.md:64 f09db29f329141e6b3dc3bf348e62b92 -msgid "" -"Just like [parameter references](parameter-references.md), you can use " -"JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../src/topics/expressions.md:66 ae0f7e0009944da58df73fbc70600fc4 -msgid "" -"From " -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 3c17c559cfbb4fbcabd0dd57afd0f710 -#: b2c2a86928eb40a18e72586ca43ac3f3 -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 -#: ../../src/topics/expressions.md:89 -#: ../../src/topics/parameter-references.md:65 -#: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 0042cbd326484bc985f48f469bedff14 -#: 447dcc99dc59453ca560d6c54bf8d7bb 996a1497269345569208c861d8bcba6b -#: ab62eac4484146cb83f26c5bc74a92e7 ac9c83c8605d47818cd2eceaa107e44a -#: ee13a1bcafb0428abc6f97816476b8a5 -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2054a8bc6ed643129482f73bd0b53823 -#: 4bcda5432fe74135ae0d31b4eb0d5d7b -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 4e5551d884b74e5caa0cad273883fa11 -#: c37ea64ad4f54949b17e442698e25a49 -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 28453a745d8f468b94157409007415de -#: 7b476f5cb3f64cafadbd962d465eacee -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/expressions.md:72 12c9aeec38514f7193d41be7d2b81976 -msgid "" -"From " -"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 -#: ../../src/topics/parameter-references.md:70 -#: ../../src/topics/parameter-references.md:75 -#: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 280eea3ba89e4d84a5a8bbb14c74e36c -#: 447f71c801564eefa5b04659c834ea23 69f163066cc04c30a34d7b97ac7a4bc2 -#: 6a5d8d98b190442f9aadc2c074227835 89fba2d03ddd4cdc943e9175bd0ece33 -#: 9a9fa9f67e434ddeb38b339d004aec53 c533a40746e44835a82b1cc6461576b4 -#: cca5748633ab4899beddd115e0178db6 -msgid "`format`" -msgstr "" - -#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 -#: ../../src/topics/parameter-references.md:71 -#: ../../src/topics/parameter-references.md:76 -#: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 05182018082a474384e29c2ff90cb060 -#: 30217d1193e142729205e28e4cde49d7 308e0245ba0b48fc8f665d12ce5fa0c0 -#: 64bef9a598ed4adab4b517bb8f23fb25 7f7bbf1a07684e54b97ca1950c34930b -#: c3ae98ea21e244e3a76d06b87aa8bfae d4f067c6c06c4059b133c18affdac280 -#: dae8990502254aa99cc1ba44bd42bc89 -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/expressions.md:75 88c61f4dc48f457b828143b1f0e86168 -msgid "" -"From " -"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:77 2473f34317664da3888f6696f1bce0e7 -msgid "" -"From " -"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:80 ced207b70446434bbe64d228a34c825d -msgid "" -"From " -"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 9b6ddcbbd00c4f5fa4088674586b8b60 -#: d02b26eba3b44df5bcc65436f66248f9 -msgid "`glob`" -msgstr "" - -#: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 38ebe3bb55484f61be01dbd31274b05c -#: c6018e429f30454cb30a33a92c39bda6 -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 a13cf40c0af743dea7589c4186465d1f -#: f51dc811ec154fd6a0b60d637ae42f06 -msgid "From `Workflow`" -msgstr "" - -#: ../../src/topics/expressions.md:84 a115dab301e34a958a9acea03c2b76a8 -msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 1540eea771934469b6b092c7eba2c223 -#: 6876d25a0d324dcabc7ae2e6202378a1 -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/expressions.md:88 927df10417db4669916e08b9e4e37641 -msgid "" -"From " -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 75ec03ffd3e64fabab680a2fcc66e0a4 -#: fa2635bff88c49b38401e2c87035d023 -msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 cbe310d7612e4f68b4832692cc0d145e -#: fa897f1a899141fc9e6be1b6af9c01ce -msgid "`expression`" -msgstr "" - -#: ../../src/topics/expressions.md:92 ba5b5e8410df4acab9ad6459df2ff061 -msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:95 935d707d1e31415e806b2bbcb851e322 -msgid "" -"From " -"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 89f051a47b99491b9ce17ded769ad1a3 -#: 9d59f22a9e734f8982b89830b4e7e6fc -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 182e1b73426e4367bf8fe430a415a9c6 -#: 5b5d3f05e6c647a38af612c10b2b8b71 -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 3fa480e44ffe473abb3af953f2d000f9 -#: 6375ee37a7fd4fa19be33c6f0ae75196 -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 b6d5c6ff972a4607873daa53817a6860 -#: d0a0be70585842d8b17a8ddc7fabfc3e -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 0d558c8e126f427ca9862d7dae8a2cb7 -#: 293d592f29e34a5aa4f7420368d2f24b -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 43f37d9ec9b5429ab811039d1e8211d0 -#: b3a9149a14d346fbbc844d4de2cb3acb -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5dbe9152fa2b4554a4ceae0b5163a7f8 -#: e137a1254667427f816aa6b5219e7f26 -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:103 -#: ../../src/topics/parameter-references.md:100 -#: 7af83d9455a944c180349d9f3123901c e8219f72a0854febb800511e2897cea1 -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:104 f3f205c655eb4a2fb8c34407ee02fe76 -msgid "" -"From " -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:105 -#: ../../src/topics/parameter-references.md:102 -#: 0f3325af2b674d07aba8d1b254b7bb67 92c818fc42b64e94b8a3bae737df6ac6 -msgid "`listing`" -msgstr "" - -#: ../../src/topics/expressions.md:106 a8bc743f7dc648889ce51d8a787597dd -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/expressions.md:107 -#: ../../src/topics/parameter-references.md:104 -#: 04b9cd485e1342d0870c341321089d15 a07dc02fe7bd416994f9755934e6a524 -msgid "`entry`" -msgstr "" - -#: ../../src/topics/expressions.md:108 -#: ../../src/topics/parameter-references.md:105 -#: 69d9c547532644408b14655f50175684 df87b2c504dc4ae8865a0f4c94a84dff -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/expressions.md:109 -#: ../../src/topics/parameter-references.md:106 -#: d248acde95024c94b3921e290276a2d1 f77892ff017d48fa833343150cdad6ca -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/expressions.md:110 c0909df1820f40d599151a7b45db2f04 -msgid "" -"From " -"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/expressions.md:111 -#: ../../src/topics/parameter-references.md:108 -#: 2d62117b8b824035916716cc818348d4 9f0237a087b5445eb0a8fe474d3e3869 -msgid "`envValue`" -msgstr "" - -#: ../../src/topics/expressions.md:116 bdbae4965a344e778ed0e80a8e23845d -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../src/topics/expressions.md:118 1af8bb96001e43d9b649044d9631f360 -msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" -" attribute that allows users to load external JavaScript files, or to " -"provide inline JavaScript code." -msgstr "" - -#: ../../src/topics/expressions.md:122 303ce6bcd17d4a219d2c3f4079e9b332 -msgid "" -"Entries added to the `expressionLib` attribute are parsed with the " -"JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts" -" of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:128 d4e0acefb25d458982b37167431c8364 -msgid "" -"The CWL standards (versions 1.0 through 1.2) " -"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" -" that the only version of JavaScript valid in CWL expressions is " -"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " -"that any code that you include or write in your CWL Document must be " -"compliant with ECMAScript 5.1." -msgstr "" - -#: ../../src/topics/expressions.md:135 b43add5b2d72451db8eee00a03b347a2 -msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a " -"JavaScript function inline in `expressionLib`. That function can then be " -"used in other parts of the CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:139 0908315609f1413392b2ed9b5769a62b -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:146 d8aac17a8a9c4c209695ce760fc4cffb -msgid "" -"Running this CWL workflow will invoke the JavaScript function and result " -"in the `echo` command printing the input message with capital initial " -"letters:" -msgstr "" - -#: ../../src/topics/expressions.md:149 2deae9db0d394245bf21ba3e469fb64f -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:155 6849411091ab422f8ebffc27e68c3286 -msgid "" -"Let's move the `capitalizeWords` function to an external file, `custom-" -"functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:158 a74d3576acbc4694bbf75d371c57c4b0 -msgid "`custom-functions.js`" -msgstr "" - -#: ../../src/topics/expressions.md:164 330e32b4188141c083465fd77ac0d962 -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:171 61fae30939644f2e830107bb6815659a -msgid "" -"The `custom-functions.js` file is included in the CWL document with the " -"`$include: custom-functions.js` statement. That makes the functions and " -"variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:175 8e057a368eae43f892cdfcf1492fefae -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:181 108a176667a74331a9c634537c6073be -msgid "" -"Finally, note that you can have both inline and external JavaScript code " -"in your CWL document. In this final example we have added another entry " -"to the `expressionLib` attribute with the new function " -"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" -" the external file `custom-functions.js`." -msgstr "" - -#: ../../src/topics/expressions.md:186 dc1a23ba61fe417aab857a2cf3b87d09 -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:193 683b69656c23424d9a171f72cc1ee355 -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:200 a2d926603ed24b13a77a64606b72f7db -msgid "" -"The `$include` statement can be used to include a file from the local " -"disk or from a remote location. It works with both relative and absolute " -"paths. Read the [text about " -"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " -"the CWL specification to learn more about it." -msgstr "" - -#: ../../src/topics/file-formats.md:1 f00b6549fb2b40c7a0930fa2d70f78e9 -msgid "File Formats" -msgstr "" - -#: ../../src/topics/file-formats.md:3 02364803949047ddbad575b3f7ed27a3 -msgid "" -"Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This " -"helps document for others how to use your tool while allowing you to do " -"some simple type-checking when creating parameter files." -msgstr "" - -#: ../../src/topics/file-formats.md:8 8f25e0b9d6564f089bc07050eecd2cbe -msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM" -" in our example), reference a local ontology for your institution, or do " -"not add a file format initially for quick development before sharing your" -" tool with others. You can browse existing [IANA file format " -"listings][IANA] and [EDAM file format listings][EDAM] on their websites." -msgstr "" - -#: ../../src/topics/file-formats.md:14 051d96f1784a44478c888a692a43020e -msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` " -"section of the document in greater detail, so don't worry about these for" -" now." -msgstr "" - -#: ../../src/topics/file-formats.md:17 c0b16138c24243f7882de4ea02ef14e4 -msgid "" -"Note that for added value `cwltool` can do some basic reasoning based on " -"file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../src/topics/file-formats.md:20 05c4a830b7084575bfd35263d9226104 -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../src/topics/file-formats.md:26 -#: ../../src/topics/metadata-and-authorship.md:22 -#: 1af1e2ed821a435088471aa1d28c039c 441a574563f246118f24fc1ab8324b2e -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/file-formats.md:32 241dfed53c39469d9e340a2494f97572 -msgid "Sample Parameter Files" -msgstr "" - -#: ../../src/topics/file-formats.md:34 c377cf86598d4ca4bf5311a47978e302 -msgid "" -"Below is an example of a parameter file for the example above. We " -"encourage checking in working examples of parameter files for your tool. " -"This allows others to quickly work with your tool, starting from a " -"\"known good\" parameterization." -msgstr "" - -#: ../../src/topics/file-formats.md:39 53ff3c58049a4096ae894c4b0214d5cb -msgid "`sample.yml`" -msgstr "" - -#: ../../src/topics/file-formats.md:45 6c6c380437634412900e3f8dff4558f6 -msgid "" -"___Note:___ To follow the example below, you need to download the example" -" input file, *file-formats.bam*. The file is available from " -" and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/index.md:1 4ca0f8c05d9e451387a1eda0e6a04dad -msgid "Topics" -msgstr "" - -#: ../../src/topics/inputs.md:1 339cc31ba40c4d2cba0ff21d668701b6 -msgid "Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:3 802f62184fd545eabc2afb78d90930c1 -msgid "Essential Input Parameters" -msgstr "" - -#: ../../src/topics/inputs.md:5 9b641ae58d834dcc8a79fc547ead64a0 -msgid "" -"The `inputs` of a tool is a list of input parameters that control how to " -"run the tool. Each parameter has an `id` for the name of parameter, and " -"`type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/inputs.md:9 8886c014968d4e32b0ce1cc44a9068a0 -msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*," -" and *null*; complex types are *array* and *record*; in addition there " -"are special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../src/topics/inputs.md:13 f40f938f5ac140cea72a4146a3329579 -msgid "" -"The following example demonstrates some input parameters with different " -"types and appearing on the command line in different ways." -msgstr "" - -#: ../../src/topics/inputs.md:16 415298524e35434ea19a25c31e9ae649 -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../src/topics/inputs.md:18 e8b631d0d4e64779aa7333b8e756fcbe -msgid "`inp.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:24 c5f3fddee0734d2da9207d64e268463f -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../src/topics/inputs.md:26 fed45d1ab5574bd889af14787ac2cd20 -msgid "`inp-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:33 1654a2e9bca0443c8fb46f7191beb81a -msgid "" -"You can use `cwltool` to create a template input object. That saves you " -"from having to type all the input parameters in a input object file:" -msgstr "" - -#: ../../src/topics/inputs.md:40 b22b453eb5d0497e88243bcfc4d3cb1b -msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template " -"inp.cwl > inp-job.yml`, and then modify the default values with your " -"desired input values." -msgstr "" - -#: ../../src/topics/inputs.md:44 c136e4badbf3429b8c9c9efbc91d7f65 -msgid "" -"Notice that \"example_file\", as a `File` type, must be provided as an " -"object with the fields `class: File` and `path`." -msgstr "" - -#: ../../src/topics/inputs.md:47 31ddeb567d744c21bbfa76e8cdf95e6d -msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" -" command line." -msgstr "" - -#: ../../src/topics/inputs.md:53 b19099fa3f3a4b5491e094f1ababc4a2 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " -"following boxed text describes these two commands and the expected output" -" from the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:64 685e49311ba547f697fc90073168041b -msgid "" -"The CWL reference runner (cwltool) and other runners create temporary " -"directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not " -"explicitly specified" -msgstr "" - -#: ../../src/topics/inputs.md:70 d31fc4e804a34097ab506fa3aa469b1d -msgid "" -"The field `inputBinding` is optional and indicates whether and how the " -"input parameter should appear on the tool's command line. If " -"`inputBinding` is missing, the parameter does not appear on the command " -"line. Let's look at each example in detail." -msgstr "" - -#: ../../src/topics/inputs.md:83 26ca8366924a442d9a3fb26f7223b028 -msgid "" -"Boolean types are treated as a flag. If the input parameter " -"\"example_flag\" is \"true\", then `prefix` will be added to the command " -"line. If false, no flag is added." -msgstr "" - -#: ../../src/topics/inputs.md:95 e9ba36f7d5ff4776aad272c9a0a7a81b -msgid "" -"String types appear on the command line as literal values. The `prefix` " -"is optional, if provided, it appears as a separate argument on the " -"command line before the parameter . In the example above, this is " -"rendered as `--example-string hello`." -msgstr "" - -#: ../../src/topics/inputs.md:109 bde0dfcb13ea4ac8bab41a8c3fa024ec -msgid "" -"Integer (and floating point) types appear on the command line with " -"decimal text representation. When the option `separate` is false (the " -"default value is true), the prefix and value are combined into a single " -"argument. In the example above, this is rendered as `-i42`." -msgstr "" - -#: ../../src/topics/inputs.md:124 0a38fa331eaa41ad9d61c869e5b73574 -msgid "" -"File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the " -"parameter is optional. In the example above, this is rendered as " -"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " -"parameter were not provided in the input, nothing would appear on the " -"command line." -msgstr "" - -#: ../../src/topics/inputs.md:131 afe9f6fca7314610b25aa519d145f1c8 -msgid "" -"Input files are read-only. If you wish to update an input file, you must" -" [first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../src/topics/inputs.md:134 e976913dca354fd1b027ceba53e279fd -msgid "" -"The value of `position` is used to determine where parameter should " -"appear on the command line. Positions are relative to one another, not " -"absolute. As a result, positions do not have to be sequential, three " -"parameters with positions 1, 3, 5 will result in the same command line as" -" 1, 2, 3. More than one parameter can have the same position (ties are " -"broken using the parameter name), and the position field itself is " -"optional. The default position is 0." -msgstr "" - -#: ../../src/topics/inputs.md:142 3f5437225c06473ca6d99f256b735771 -msgid "" -"The `baseCommand` field will always appear in the final command line " -"before the parameters." -msgstr "" - -#: ../../src/topics/inputs.md:146 e0a6c25648394dc4a06c1a1ab11656d1 -msgid "Array Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:148 895ca55530674398af4f3ab0a2ff8295 -msgid "" -"It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to " -"provide `type` field with `type: array` and `items` defining the valid " -"data types that may appear in the array. Alternatively, brackets `[]` may" -" be added after the type name to indicate that input parameter is array " -"of that type." -msgstr "" - -#: ../../src/topics/inputs.md:154 2c9f27b7c4534f5087194653288fc473 -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:160 2f54898bb89b4f24abcbb9e032b14fac -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 07e7e4b0f9d047aba2b860033e9c939c -#: 12a54ad82e994ce485e2996d4e804373 5fb5d18d006242c2ad4cd143c6e6b5c4 -msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:178 36d386d92a7a47099dff930b89063d26 -msgid "" -"The `inputBinding` can appear either on the outer array parameter " -"definition or the inner array element definition, and these produce " -"different behavior when constructing the command line, as shown above. In" -" addition, the `itemSeparator` field, if provided, specifies that array " -"values should be concatenated into a single argument separated by the " -"item separator string." -msgstr "" - -#: ../../src/topics/inputs.md:185 eb22abf9766e441f835aaad0d12fe198 -msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` " -"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " -"lines, where array values that are not defined with an associated key are" -" marked by a leading `-`. This will be demonstrated in the next lesson " -"and is discussed in more detail in the [YAML Guide](yaml-" -"guide.md#arrays). You can specify arrays of arrays, arrays of records, " -"and other complex types." -msgstr "" - -#: ../../src/topics/inputs.md:191 dad1426793764a71ab0a71c8f6872da4 -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:193 22c9fdaebc8c4e0f9e1e8b72ef87003a -msgid "" -"Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be " -"provided together (they are exclusive). You can use records and type " -"unions to group parameters together to describe these two conditions." -msgstr "" - -#: ../../src/topics/inputs.md:198 c1e21b305da34c6b8960ebe5ca0d60bc -msgid "`record.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:204 5f3e64b47249408c9a1e006d27826a48 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:215 76984af8223c45688a49ca7082b24cc3 -msgid "" -"In the first example, you can't provide `itemA` without also providing " -"`itemB`." -msgstr "" - -#: ../../src/topics/inputs.md:217 ff1dff0c91ac4324acc01188f2ef2bab -msgid "`record-job2.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:233 951aff2f38bc43c8bd1086a9e62243fe -msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the " -"first matching item (`itemC`) is added to the command line and remaining " -"item (`itemD`) is ignored." -msgstr "" - -#: ../../src/topics/inputs.md:236 ac93b8f5dd1646b8bbb7f5edc86ad2c7 -msgid "`record-job3.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:252 baa943e150554186ace37f310442a8a0 -msgid "" -"In the third example, only `itemD` is provided, so it appears on the " -"command line." -msgstr "" - -#: ../../src/topics/inputs.md:255 53f7e15ad5dc472faf409f30d902d4ce -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../src/topics/inputs.md:257 1c455770202547a0bc3c62c063a0b3ed -msgid "" -"If you use exclusive input parameters combined with expressions, you need" -" to be aware that the `inputs` JavaScript object will contain one of the " -"exclusive input values. This means that you might need to use an **or** " -"boolean operator to check which values are present." -msgstr "" - -#: ../../src/topics/inputs.md:262 918873fedf60421f9e3713f82ac0c207 -msgid "" -"Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from" -" an enum." -msgstr "" - -#: ../../src/topics/inputs.md:265 4999688d5c954eb48fc42524e7a33176 -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:271 294545640c6148dc8043027d4e4ea7d4 -msgid "" -"Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you " -"provide a valid value, such as “fasta” (one of the values of the enum), " -"your command should execute successfully:" -msgstr "" - -#: ../../src/topics/inputs.md:280 258d3d9ec6bb410eb012f89b44bf4072 -msgid "" -"However, if you do not provide any input value, then `file_format` will " -"be evaluated to a `null` value, which does not match the expected type " -"for the output field (a `string`), resulting in failure when running your" -" workflow." -msgstr "" - -#: ../../src/topics/inputs.md:289 6470c55fcf5e45b09534705df1fb4e7b -msgid "" -"To correct it, you must remember to use an or operator in your JavaScript" -" expression when using exclusive parameters, or any parameter that allows" -" `null`. For example, the expression could be changed to " -"`$(inputs.file_format || 'auto')`, to have a default value if none was " -"provided in the command line or job input file." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:1 -#: 0bf3128f26ef41f7b31418f506dc83d4 -msgid "Metadata and Authorship" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:3 -#: ef7ddf8716214cfbb8a411a13967198a -msgid "" -"Implementation extensions not required for correct execution (for " -"example, fields related to GUI presentation) and metadata about the tool " -"or workflow itself (for example, authorship for use in citations) may be " -"provided as additional fields on any object. Such extensions fields (e.g." -" `format: edam:format_2572`) can use a namespace prefix listed in the " -"`$namespaces` section of the document (e.g. edam: " -"http://edamontology.org/) as described in the [Schema Salad specification" -"][schema-salad]. Once you add the namespace prefix, you can access it " -"anywhere in the document as shown below. Otherwise, one must use full " -"URLs: `format: http://edamontology.org/format_2572`." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:13 -#: 913df947afb7420097be3f15caede947 -msgid "" -"For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to " -"cite your tool." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:16 -#: 4c773c6b1db9460ba58d5d276781d6e7 -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:28 -#: c593b5d1f7e1469da7e97ca737632bc2 -msgid "Extended Example" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:30 -#: 28f6bc9a1465450ead788703b8329902 -msgid "" -"For those that are highly motivated, it is also possible to annotate your" -" tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints" -" at hardware requirements in order to use the tool, and a few more " -"metadata fields." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:35 -#: 84b37f20f8cb4136b274ecef284039fa -msgid "`metadata_example3.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:1 391ca127d3594bf0bd12a3ed29a85fc7 -msgid "Operations" -msgstr "" - -#: ../../src/topics/operations.md:3 e58e02c974ca451ca7e52d4a7e14ad99 -msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-" -"line tool, or an expression tool. It is a step of a workflow that " -"specifies inputs and outputs, but it does not provide enough information " -"to be executed." -msgstr "" - -#: ../../src/topics/operations.md:7 b725956dd0ff4906b54a002afacafd09 -msgid "" -"You can create operations to visualize a workflow during development, " -"before you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../src/topics/operations.md:10 42e684d404aa4715a538bc209e84b469 -msgid "`operations.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:16 3bc2f8d60cce460788cff24274fee913 -msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like" -" a command line tool or an expression. You can also plot it with the CWL " -"Viewer or `cwltool`:" -msgstr "" - -#: ../../src/topics/operations.md:24 910029acb5864b919b452e62a365c789 -msgid "" -"The output of the command above can be rendered with a Graphviz renderer." -" The following image is rendered with the Sphinx Graphviz directive (this" -" user guide is built with Sphinx):" -msgstr "" - -#: ../../src/topics/operations.md:55 edcbb0fc660840f29309e24a1f934d25 -msgid "" -"If you try running it with `cwltool`, the command will fail since " -"`cwltool` does not have enough information to know how to execute it:" -msgstr "" - -#: ../../src/topics/operations.md:58 14bf9940996647ac91ea2de9e95dbe13 -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../src/topics/operations.md:66 71459c6b3efa47a1856c8f22f1b529da -msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A" -" CWL runner could, for instance, use abstract operations with ID's that " -"correspond to steps executed by a different workflow engine." -msgstr "" - -#: ../../src/topics/outputs.md:1 77937377da354c46afb8c7d4988cf964 -msgid "Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:3 7dbd814741e4452e95af2bddbbd41c73 -msgid "Returning Output Files" -msgstr "" - -#: ../../src/topics/outputs.md:5 10965b18de5841eda0658840d0e726c4 -msgid "" -"The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name" -" of parameter, and `type` describing what types of values are valid for " -"that parameter." -msgstr "" - -#: ../../src/topics/outputs.md:10 d1ebab8483744101b29a095067495897 -msgid "" -"When a tool runs under CWL, the starting working directory is the " -"designated output directory. The underlying tool or script must record " -"its results in the form of files created in the output directory. The " -"output parameters returned by the CWL tool are either the output files " -"themselves, or come from examining the content of those files." -msgstr "" - -#: ../../src/topics/outputs.md:16 030b920fe9ee445f9f996aef68087129 -msgid "" -"The following example demonstrates how to return a file that has been " -"extracted from a tar file." -msgstr "" - -#: ../../src/topics/outputs.md:19 81f1b2d425f244728504cab01a06dfeb -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../src/topics/outputs.md:21 d23514327fbd476d87e9a3308cac38e4 -msgid "" -"In previous examples, the `baseCommand` was just a string, with any " -"arguments passed as CWL inputs. Instead of a single string we can use an " -"_array of strings_. The first element is the command to run, and any " -"subsequent elements are mandatory command line arguments" -msgstr "" - -#: ../../src/topics/outputs.md:26 ebae564b85824cd1818837689b134af5 -msgid "`tar.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:32 94a88afd7acc4576b8cc22780991d629 -msgid "`tar-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:38 a4dc894fe82e4b779771b512424ce70c -msgid "Next, create a tar file for the example." -msgstr "" - -#: ../../src/topics/outputs.md:45 dfd9feebfc7049498f807dfeb91e70e3 -msgid "" -"And now invoke `cwltool` with the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:51 343cba8708a14ff9bd281fdff790bf39 -msgid "" -"The field `outputBinding` describes how to set the value of each output " -"parameter." -msgstr "" - -#: ../../src/topics/outputs.md:62 485a5a4cba354640a53832e4c7460fcb -msgid "" -"The `glob` field consists of the name of a file in the output directory. " -"If you don't know name of the file in advance, you can use a wildcard " -"pattern like `glob: '*.txt'`." -msgstr "" - -#: ../../src/topics/outputs.md:65 bafc8ef1a46b4f97af05a146a8903e2f -msgid "Capturing Standard Output" -msgstr "" - -#: ../../src/topics/outputs.md:67 3fafdc8d21344bceb8262e8534e34afe -msgid "" -"To capture a tool's standard output stream, add the `stdout` field with " -"the name of the file where the output stream should go. Then add `type: " -"stdout` on the corresponding output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:71 14fff0b709774a4cbb9213dc97ae9d42 -msgid "`stdout.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:89 ae07eb32467f40189765939c2fb4f6ae -msgid "Array Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:91 98aa9d49f5b14429b5fb9e38ab9c594d -msgid "" -"You can also capture multiple output files into an array of files using " -"`glob`." -msgstr "" - -#: ../../src/topics/outputs.md:93 ddb1cc7a7f6f44cd96748c88753b5bdf -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:99 af69c5bbfac241809fd6e882dc1cafdd -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:112 7910b5ce6997467096db8d432cfb2088 -msgid "" -"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " -"expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions" -" to mark entries in arrays, as demonstrated in several of the upcoming " -"sections." -msgstr "" - -#: ../../src/topics/parameter-references.md:1 11452076e78d4ccd9773b301d831d350 -msgid "Parameter References" -msgstr "" - -#: ../../src/topics/parameter-references.md:3 f8227a94ae9544a189886f90e9a3433c -msgid "" -"In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file " -"we were interested in was called \"hello.txt\", and this was written into" -" the `.cwl` file. This is not the best way to do this, as the " -"\"hello.txt\" filename may vary or be dependent on the input file(s) " -"used. To avoid this we can specify the name of the file we want in the " -"job parameters file (`.yml`). In this example, you will see how to " -"reference the value of input parameters dynamically from other fields, " -"which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 38a045a2b8614cbba3a02d4f27b50127 -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../src/topics/parameter-references.md:19 13529a4cc80a4070b85bf29829c762b1 -msgid "`tar-param-job.yml`" -msgstr "" - -#: ../../src/topics/parameter-references.md:25 da5a588a3155445098b7ad81b78f1fa4 -msgid "" -"Create your input files and invoke `cwltool` with the tool description " -"and the input object on the command line:" -msgstr "" - -#: ../../src/topics/parameter-references.md:36 9e91e38ca0e4473384498c6e28b1f116 -msgid "" -"Certain fields permit parameter references which are enclosed in " -"`$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../src/topics/parameter-references.md:47 a0e0270144df4b6aa3bf0ad261938b17 -msgid "" -"References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " -"`$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../src/topics/parameter-references.md:51 a4a0147041724445b7ab3459cbc786b0 -msgid "" -"The value of the \"inputs\" variable is the input object provided when " -"the CWL tool was invoked." -msgstr "" - -#: ../../src/topics/parameter-references.md:54 ea5153744a3d41dc883c4bb7df4e16de -msgid "" -"Note that because `File` parameters are objects, to get the path to an " -"input file you must reference the path field on a file object; to " -"reference the path to the tar file in the above example you would write " -"`$(inputs.tarfile.path)`." -msgstr "" - -#: ../../src/topics/parameter-references.md:59 84270504a1c445d2917825b8e854a80d -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../src/topics/parameter-references.md:61 9616d24145e74d17ac76cbe80ee4972a -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../src/topics/parameter-references.md:63 fe869638aa4a4cd3a43bc071ed66cb37 -msgid "" -"From " -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:69 1e3f77c12d1c48a7b2df7cdccfe92d41 -msgid "" -"From " -"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:72 2b86b2eb9a2e4310923aa3e3c16fac1a -msgid "" -"From " -"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:74 6ad56ee119684a83b42821f3b366cc73 -msgid "" -"From " -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:77 11b45dd3f4a644b2b6175fb9bf4219ad -msgid "" -"From " -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:81 c5446e59a6bd4a3cbfc0ed2cd21783f4 -msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:85 3fefaf0fbde94a85be6db02643d0a5ec -msgid "" -"From " -"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/parameter-references.md:89 3911b95f4a72415f968ed640f445bd00 -msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:92 841837a2edca4aff8231a0b955def3a4 -msgid "" -"From " -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:101 -#: 665c8d7b622441cda2c1f6b20da5d664 -msgid "" -"From " -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:103 -#: cb71700c69694a53a62a43ef11a62595 -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/parameter-references.md:107 -#: 6be0e1471d164c5099c0ccc2824cf038 -msgid "" -"From " -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/requirements-and-hints.md:5 -#: 5984d3f30ab14197bcc03ce556bad3ab -msgid "Requirements and Hints" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:1 -#: 5357d8f77e504324a2904e7dc327e46a -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:3 -#: 1bbff970e33144148c394d7f18ebfd96 -msgid "" -"Often, tool descriptions will be written for a specific version of a " -"software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may " -"also help to avoid confusion about which version of a tool the " -"description was written for." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:13 -#: 0774b6bc9c8f4ab0acf943ed07f4b0d4 -msgid "" -"In this example, the software requirement being described is InterProScan" -" version 5.21-60." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:25 -#: 5cadc31694ee45d99ffa369983971756 -msgid "" -"Depending on your CWL runner, these hints may be used to check that the " -"required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the " -"[dependency resolvers configuration][dependencies]." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:29 -#: a8a0b7191ce9404292df0699b96c51d6 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the " -"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" -" looked up in the [SciCrunch][scicrunch] registry, which provides a " -"portal for finding, tracking, and referring to scientific resources " -"consistently. If you want to specify a tool as a `SoftwareRequirement`, " -"search for the tool on SciCrunch and use the RRID that it has been " -"assigned in the registry. (Follow this [Adding a Resource Tutorial" -"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " -"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " -"field of your requirement description. Other good choices, in order of " -"preference, are to include the DOI for the main tool citation and the URL" -" to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 86c81fb6d34b4b36ac8778c79cbc0306 -msgid "Staging Input Files" -msgstr "" - -#: ../../src/topics/staging-input-files.md:3 4bd8293be25d401a868df24fabfc6538 -msgid "" -"Normally, input files are located in a read-only directory separate from " -"the output directory. This causes problems if the underlying tool " -"expects to write its output files alongside the input file in the same " -"directory. You use `InitialWorkDirRequirement` to stage input files into" -" the output directory. In this example, we use a JavaScript expression to" -" extract the base name of the input file from its leading directory path." -msgstr "" - -#: ../../src/topics/staging-input-files.md:9 05c39f514e234bd88895716c99eabcda -msgid "`linkfile.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:1 83fa50745b7e486db93f4d7883a778cc -msgid "Troubleshooting" -msgstr "" - -#: ../../src/topics/troubleshooting.md:3 d8d67e5238d049479e9c1a1c4b9b62c3 -msgid "" -"In this section you will find ways to troubleshoot when you have problems" -" executing CWL. We focus on `cwltool` here but some of these techniques " -"may apply to other CWL Runners." -msgstr "" - -#: ../../src/topics/troubleshooting.md:6 60e89aea0d634296a9753910a55a4493 -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:8 7ff74ba8fd9443cc9e1cdda32e38ca7c -msgid "" -"You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor " -"output files, but created while your workflow is running). By default, " -"these files are created in a temporary directory but writing them to a " -"separate directory makes accessing them easier." -msgstr "" - -#: ../../src/topics/troubleshooting.md:14 1c8afaa3ef0c41b2a1ebc57d329d6ed4 -msgid "" -"In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " -"World\" | rev`, which would print the message \"Hello World\" reversed, " -"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," -" where instead of executing the `rev` command it tries to execute `revv`," -" which fails." -msgstr "" - -#: ../../src/topics/troubleshooting.md:20 b540a4f7a25148098a369350e22c247a -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:27 1cda8c6f9ed6421bafb39554bdc9b5f7 -msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " -"value (`cwltool` will create the directory for you if it does not exist " -"already):" -msgstr "" - -#: ../../src/topics/troubleshooting.md:35 93b8b99518474d709a90f5442c0d2b65 -msgid "" -"The workflow is in the `permanentFail` status due to `step_b` failing to " -"execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. " -"You can inspect the intermediate files created:" -msgstr "" - -#: ../../src/topics/troubleshooting.md:44 059deec3f12448b8a673e1d957595d7d -msgid "" -"Each workflow step has received a unique ID (the long value that looks " -"like a hash). The `${HASH}.status` files display the status of each step " -"executed by the workflow. And the `step_a` output file `stdout.txt` is " -"visible in the output of the command above." -msgstr "" - -#: ../../src/topics/troubleshooting.md:48 9c40b03256274b43a484b2a1108186c5 -msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" -" in the `step_b`). After fixing the typo, when you execute `cwltool` with" -" the same arguments as the previous time, note that now `cwltool` output " -"contains information about pre-cached outputs for `step_a`, and about a " -"new cache entry for the output of `step_b`. Also note that the status of " -"`step_b` is now of success." -msgstr "" - -#: ../../src/topics/troubleshooting.md:59 45314aa766a5479f9855cbc054ad17b9 -msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had" -" been cached, and there was no change in its execution or output. " -"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for" -" troubleshooting your CWL documents and also as a way to prevent " -"`cwltool` to re-evaluate steps unnecessarily." -msgstr "" - -#: ../../src/topics/using-containers.md:1 8289b75b054040e5bfa71f482554eb4e -msgid "Using Containers" -msgstr "" - -#: ../../src/topics/using-containers.md:3 333b0ee71bde4ce8aacf4ff8946dfbfe -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../src/topics/using-containers.md:5 54ef32fbf91a4edfa0006f62b51bcbb9 -msgid "" -"[Docker][docker] containers simplify software installation by providing a" -" complete known-good runtime for software and its dependencies. However," -" containers are also purposefully isolated from the host system, so in " -"order to run a tool inside a Docker container there is additional work to" -" ensure that input files are available inside the container and output " -"files can be recovered from the container. A CWL runner can perform this" -" work automatically, allowing you to use Docker to simplify your software" -" management while avoiding the complexity of invoking and managing Docker" -" containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 de34c8de4fda441d80abb9990e75b494 -msgid "" -"One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the " -"container." -msgstr "" - -#: ../../src/topics/using-containers.md:18 fbd75c368e6444d89978f010a235709c -msgid "" -"This example runs a simple Node.js script inside a Docker container which" -" will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../src/topics/using-containers.md:21 88ba9fb9da1d493ca8a4e37982ff27dd -msgid "`docker.cwl`" -msgstr "" - -#: ../../src/topics/using-containers.md:27 76dc921551ac44de9f07583d304bde3a -msgid "`docker-job.yml`" -msgstr "" - -#: ../../src/topics/using-containers.md:33 20b169511e734f0fb8b047b06e442146 -msgid "" -"Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that " -"is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 bb3199ee47b746529f088a323a72a434 -msgid "" -"`baseCommand: node` tells CWL that we will be running this command using " -"the Node Js runtime that is meant for Javascript files. We then need to " -"specify some `hints` for how to find the container we want. In this case" -" we list just our requirements for the docker container in " -"`DockerRequirements`. The `dockerPull:` parameter takes the same value " -"that you would pass to a `docker pull` command. That is, the name of the " -"container image (you can even specify the tag, which is good idea for " -"best practices when using containers for reproducible research). In this " -"case we have used a container called `node:slim`." -msgstr "" - -#: ../../src/topics/using-containers.md:52 562109bed3cc4da896d8307f74244552 -msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` " -"providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/using-containers.md:55 417e5bfea2ac485b880ee544984996ea -msgid "`hello.js`" -msgstr "" - -#: ../../src/topics/using-containers.md:69 ecd67cff285a43b5b66777032c7f690c -msgid "" -"Notice the CWL runner has constructed a Docker command line to run the " -"script." -msgstr "" - -#: ../../src/topics/using-containers.md:72 e5b8c1e93fda4043839ef0dc204f2ec1 -msgid "" -"In this example, the path to the script `hello.js` is " -"`/home/me/cwl/user_guide/hello.js` outside the container but " -"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " -"reflected in the invocation of the `node` command." -msgstr "" - -#: ../../src/topics/workflows.md:1 d09c4c6d692548d4b317e5c74445795f -msgid "Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:3 9e3bc00a91f948eeb26624078dce6823 -msgid "" -"A workflow is a CWL processing unit that executes command-line tools, " -"expression tools, or workflows (sub-workflows) as steps. It must have " -"`inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../src/topics/workflows.md:13 177aaf8abaf940d1ac006423998974fa -msgid "CWL workflow." -msgstr "" - -#: ../../src/topics/workflows.md:41 28308117076d4adcaf0f923c3f52d666 -msgid "" -"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier " -"examples." -msgstr "" - -#: ../../src/topics/workflows.md:51 c851029a3fa542b6ac21e00675661ca1 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:81 30cb988a8f814823a5dfb2f6ca3928fc -msgid "" -"A command-line tool or expression tool can also be written directly in " -"the same CWL document as the workflow. For example, we can rewrite the " -"`echo-uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../src/topics/workflows.md:91 a7c8734f60664e619c63b98e5d3399b9 -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:150 f4bb9b7b6ada46a4a1701daaac993798 -msgid "" -"Having separate files helps with modularity and code organization. But it" -" can be helpful writing everything in a single file for development. " -"There are other ways to combine multiple files into a single file (e.g. " -"`cwltool --pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../src/topics/workflows.md:160 f4da934d636f4455a63f5ecbda2cfdea -msgid "" -"For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this" -" user guide in more detail." -msgstr "" - -#: ../../src/topics/workflows.md:165 529d327e58f64544aa02b075976aee32 -msgid "Writing Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:167 a4207261aa314fd98cbfdc368d96c1b6 -msgid "" -"This workflow extracts a java source file from a tar file and then " -"compiles it." -msgstr "" - -#: ../../src/topics/workflows.md:170 7571eba01bc44d0a97d8f283f19a8b49 -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 8e58b0c4e12e4a1183fe7b33e8ee39e6 c8833b0a5dc04e35a48575713bed3f24 -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../src/topics/workflows.md:180 6a0e9118c6ee49fbb9111504dcebe190 -msgid "" -"[![Visualization of 1st-" -"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" -"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 87e0059d86b64212a1cceee185fe264d -msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a" -" run:" -msgstr "" - -#: ../../src/topics/workflows.md:185 77943b217ba34d409ed4a18fd262388f -msgid "`1st-workflow-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:191 aceb3bee46034a94bdb6784a8c1a484c -msgid "" -"Next, create a sample Java file and add it to a tar file to use with the " -"command-line tool." -msgstr "" - -#: ../../src/topics/workflows.md:205 916621f2ca5d47c4935d68d20c5ea616 -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../src/topics/workflows.md:212 4a0ceee7f9ac4e80994ac8a750d77855 -msgid "" -"The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a " -"workflow." -msgstr "" - -#: ../../src/topics/workflows.md:221 3408935eb4f945349e00486a8df27c39 -msgid "" -"The `inputs` section describes the inputs of the workflow. This is a " -"list of input parameters where each parameter consists of an identifier " -"and a data type. These parameters can be used as sources for input to " -"specific workflows steps." -msgstr "" - -#: ../../src/topics/workflows.md:233 c0790bc2b8a34016b2eb3d64f0b8903e -msgid "" -"The `outputs` section describes the outputs of the workflow. This is a " -"list of output parameters where each parameter consists of an identifier " -"and a data type. The `outputSource` connects the output parameter " -"`classfile` of the `compile` step to the workflow output parameter " -"`compiled_class`." -msgstr "" - -#: ../../src/topics/workflows.md:248 5ad0adb359db4652a4b7ebd98369190e -msgid "" -"The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second " -"step compiles the file from the first step using the java compiler. " -"Workflow steps are not necessarily run in the order they are listed, " -"instead the order is determined by the dependencies between steps (using " -"`source`). In addition, workflow steps which do not depend on one " -"another may run in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:256 753f0dc2fa3a45358dfc66e7a86fb65a -msgid "" -"The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input" -" parameters, `tarfile` and `extractfile` and one output parameter " -"`extracted_file`." -msgstr "" - -#: ../../src/topics/workflows.md:261 7eb328b2d93d4ee3b47ec26340bd3e98 -msgid "" -"The ``in`` section of the workflow step connects these two input " -"parameters to the inputs of the workflow, `tarball` and " -"`name_of_file_to_extract` using `source`. This means that when the " -"workflow step is executed, the values assigned to `tarball` and " -"`name_of_file_to_extract` will be used for the parameters `tarfile` and " -"`extractfile` in order to run the tool." -msgstr "" - -#: ../../src/topics/workflows.md:267 9b2cdf146f3d4906931ec9be50a194e8 -msgid "" -"The `out` section of the workflow step lists the output parameters that " -"are expected from the tool." -msgstr "" - -#: ../../src/topics/workflows.md:278 b48d08c1caa241e68a758934f6d934f9 -msgid "" -"The second step `compile` depends on the results from the first step by " -"connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described " -"previously in [Additional Arguments and Parameters](additional-arguments-" -"and-parameters.md)). The output of this step `classfile` is connected to " -"the `outputs` section for the Workflow, described above." -msgstr "" - -#: ../../src/topics/workflows.md:285 cac7f881e9984afcae77afd99b049334 -msgid "Nested Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:287 2a60f236d6194b2daebed0fa094edc30 -msgid "" -"Workflows are ways to combine multiple tools to perform a larger " -"operations. We can also think of a workflow as being a tool itself; a CWL" -" workflow can be used as a step in another CWL workflow, if the workflow " -"engine supports the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../src/topics/workflows.md:297 6cc53ff3acef4bbc87a5124a4f473b52 -msgid "" -"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " -"workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:300 635696160b8d4b2b9607986a761a0fa0 -msgid "`nestedworkflows.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:309 4511d99ea12f4389a18f9fd061e207ce -msgid "" -"This two-step workflow starts with the `create-tar` step which is " -"connected to the `compile` step in orange; `compile` is another workflow," -" diagrammed on the right. In purple we see the fixed string " -"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 dbd710aa7bd049018af5a693a16f93c6 -msgid "" -" \"Visualization" -msgstr "" - -#: ../../src/topics/workflows.md:322 f9f192f956eb47d7a4fa47c80f1b56c0 -msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " -"its CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " -"mapped to become the step's input/outputs." -msgstr "" - -#: ../../src/topics/workflows.md:336 711bc01e2e5c47f293abe478f43c1b92 -msgid "" -"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and " -"`*.java` filename. This is generally best-practice, as it means it can be" -" reused in multiple parent workflows, or even in multiple steps within " -"the same workflow." -msgstr "" - -#: ../../src/topics/workflows.md:341 68509d8627a14073aabfe2071faf5214 -msgid "" -"Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar" -" file at `tarball`, which we will prepare in the `create-tar` step. At " -"this point it is probably a good idea to refactor `1st-workflow.cwl` to " -"have more specific input/output names, as those also appear in its usage " -"as a tool." -msgstr "" - -#: ../../src/topics/workflows.md:347 0744ac6efec34b61a4a7c3d1060bdb42 -msgid "" -"It is also possible to do a less generic approach and avoid external " -"dependencies in the job file. So in this workflow we can generate a hard-" -"coded `Hello.java` file using the previously mentioned " -"`InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../src/topics/workflows.md:366 2f6f5592fb5d44eb8c9998d8d9e9b9f1 -msgid "" -"In this case our step can assume `Hello.java` rather than be " -"parameterized, so we can use hardcoded values `hello.tar` and " -"`Hello.java` in a `baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../src/topics/workflows.md:383 af8995565822455388c9e32b59f7319b -msgid "" -"Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This " -"is generally not best practice, as the tool then can't be reused. The " -"reason for doing it in this case is because the command line is hard-" -"coded with filenames that only make sense within this workflow." -msgstr "" - -#: ../../src/topics/workflows.md:389 a71808fbee3349079bb3a4fd4382662c -msgid "" -"In this example we had to prepare a tar file outside, but only because " -"our inner workflow was designed to take that as an input. A better " -"refactoring of the inner workflow would be to take a list of Java files " -"to compile, which would simplify its usage as a tool step in other " -"workflows." -msgstr "" - -#: ../../src/topics/workflows.md:394 3684b45ee2b146c2a1470712375b8fb0 -msgid "" -"Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL" -" Tool description, care must be taken to improve its usability in " -"multiple workflows." -msgstr "" - -#: ../../src/topics/workflows.md:398 882cda0615624d7e94c1a8708c35733b -msgid "Scattering Steps" -msgstr "" - -#: ../../src/topics/workflows.md:400 3f5af7cf008446f3ad18a7ea5e8aab5b -msgid "" -"Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish " -"to run a tool or workflow multiple times over a list of inputs. The " -"workflow then takes the input(s) as an array and will run the specified " -"step(s) on each element of the array as if it were a single input. This " -"allows you to run the same workflow on multiple inputs without having to " -"generate many different commands or input yaml files." -msgstr "" - -#: ../../src/topics/workflows.md:411 d927b215d2e3400c941e490f1a102c97 -msgid "" -"The most common reason a new user might want to use scatter is to perform" -" the same analysis on different samples. Let's start with a simple " -"workflow that calls our first example (`hello_world.cwl`) and takes an " -"array of strings as input to the workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:415 52466df4530640d8bf65fa8f8dac87b1 -msgid "`scatter-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:421 15488985c612469d80d9c20b00f1569b -msgid "" -"Aside from the `requirements` section including " -"`ScatterFeatureRequirement`, what is going on here?" -msgstr "" - -#: ../../src/topics/workflows.md:429 ccc00c4b29134214ac79fc6815ba15e0 -msgid "" -"First of all, notice that the main workflow level input here requires an " -"array of strings." -msgstr "" - -#: ../../src/topics/workflows.md:441 93cf2c2587394b00828a7f944d201c84 -msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This " -"field tells the runner that we'd like to scatter over this input for this" -" particular step. Note that the input name listed after scatter is the " -"one of the step's input, not a workflow level input." -msgstr "" - -#: ../../src/topics/workflows.md:445 5151bd4448314e7c9aac6d4841539613 -msgid "" -"For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if " -"you expect that the final output of your workflow will now have multiple " -"outputs to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../src/topics/workflows.md:450 9154dd4987ad44e3bcb227324179a854 -msgid "Using the following input file:" -msgstr "" - -#: ../../src/topics/workflows.md:452 636ad7e5c8ec4b8b9f9ea1e70f166695 -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:458 c3f371626c2f49da9092cd5aabc8e075 -msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" -" calls the command `echo` on a message. If we invoke `cwltool scatter-" -"workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:466 5b186b36c71d42d19b8ef294384a0365 -msgid "" -"You can see that the workflow calls echo multiple times on each element " -"of our `message_array`. Ok, so how about if we want to scatter over two " -"steps in a workflow?" -msgstr "" - -#: ../../src/topics/workflows.md:469 67f8b32d49284698ad5248f7960cb95b -msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding " -"the following lines instead of `outputs: []`" -msgstr "" - -#: ../../src/topics/workflows.md:472 e49cbede4a4942e99b6f90e878898362 -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:480 168b8b8983f84a49ab94c09be99753b4 -msgid "" -"And add a second step that uses `wc` to count the characters in each " -"file. See the tool below:" -msgstr "" - -#: ../../src/topics/workflows.md:483 9d2f8b5fc572494e8e1ff54be1ba146e -msgid "`wc-tool.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:489 0448518b8c514ec18fea6b32676528ce -msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under " -"each step:" -msgstr "" - -#: ../../src/topics/workflows.md:491 315b8d60537c4e1b98136ffed099df1e -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:497 fc4d347151574b95907c3db531b3467d -msgid "" -"Here we have placed the scatter field under each step. This is fine for " -"this example since it runs quickly, but if you're running many samples " -"for a more complex workflow, you may wish to consider an alternative. " -"Here we are running scatter on each step independently, but since the " -"second step is not dependent on the first step completing all languages, " -"we aren't using the scatter functionality efficiently. The second step " -"expects an array as input from the first step, so it will wait until " -"everything in step one is finished before doing anything. Pretend that " -"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " -"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " -"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " -"could finish in 4 minutes, it will actually finish in 8 minutes because " -"the first step must wait on `echo Hallo welt!`. You can see how this " -"might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 235259da671547188634a55a5616b32c -msgid "" -"Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can" -" make an entire workflow a single step in another workflow! Convert our " -"two-step workflow to a single step subworkflow:" -msgstr "" - -#: ../../src/topics/workflows.md:513 8621d777883f41dead6ec6de0bb01094 -msgid "`scatter-nested-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:519 87f8702d0b88446ca01018b08b42e5d7 -msgid "" -"Now the scatter acts on a single step, but that step consists of two " -"steps so each step is performed in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:522 c5dacc8526fa4341a13ce9872c1fcba1 -msgid "Conditional Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:524 9dfd2c7d475245d68052fc30d44b90d3 -msgid "" -"This workflow contains a conditional step and is executed based on the " -"input. This allows workflows to skip additional steps based on input " -"parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../src/topics/workflows.md:527 c48070836d1a4e53a9256f4e40716f3c -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:566 88fc7b9654734d838aaf202083a6dcd1 -msgid "" -"The first thing you'll notice is that this workflow is only compatible " -"for version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../src/topics/workflows.md:573 2fc5956dbad1411f86aeefe5b8655b07 -msgid "" -"The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when`" -" is where the condition validation takes place. In this case only when " -"`in1` from the workflow contains a value `< 1` this step will be " -"executed." -msgstr "" - -#: ../../src/topics/workflows.md:587 e8a7a80a070148e4958af6b4d70250a1 -msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" -" will pass the first conditional step and will therefore be executed and " -"is shown in the log by `INFO [step step1] start` whereas the second step " -"is skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../src/topics/workflows.md:607 6c2980f728e44c82bfad95316f405be8 -msgid "" -"When a value of 3 is given the first conditional step will not be " -"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../src/topics/workflows.md:627 8d0fbfb49a3a4aefa3ec7d71e782dbab -msgid "" -"If no conditions are met for example when using `--val 2` the workflow " -"will raise a permanentFail." -msgstr "" - -#: ../../src/topics/yaml-guide.md:1 b847adf4f9b343518c45eec4b5fb881b -msgid "YAML Guide" -msgstr "" - -#: ../../src/topics/yaml-guide.md:6 51d36eca415b4040ae7cd2dea438b829 -msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers " -"and humans. This guide introduces the features of YAML that are relevant " -"when writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../src/topics/yaml-guide.md:13 12816605aedd40e5babe852973366a9d -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../src/topics/yaml-guide.md:16 9a5c688b2c584362b78fe3041832ee6d -msgid "Contents" -msgstr "" - -#: ../../src/topics/yaml-guide.md:18 b9c062f153ae40f8ae59164f6096a0fa -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:19 2bd3b6f3998a461f9b4f5babe423242e -msgid "[Comments](#comments)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:20 6a7a52d67e954928b57731d64f9962d5 -msgid "[Maps](#maps)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:21 c0fe4464296e448d89fba9adae04ab71 -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:22 c5f7a9a163884b18a7dfd3cccbf6bfae -msgid "[JSON Style](#json-style)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:24 5ebef4a028ef4f0dabd3caae4a0b0bfe -msgid "Key-Value Pairs" -msgstr "" - -#: ../../src/topics/yaml-guide.md:26 08f3b7b52d0d48499445fd30cd71640c -msgid "" -"Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the " -"`:` is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have " -"special meaning in the CWL specification and underscored key names " -"otherwise. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:42 888ae81b155f41a6860428e200948950 -msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, " -"`age_years`, and `home` - with their four respective values. Values can " -"be character strings, numeric (integer, floating point, or scientific " -"representation), Boolean (`true` or `false`), or more complex nested " -"types (see below)." -msgstr "" - -#: ../../src/topics/yaml-guide.md:51 4aa3831e2b9f4fb5b4161c198b9f6419 -msgid "" -"Values may be wrapped in quotation marks, but be aware that this may " -"change the way that they are interpreted i.e. `\"1234\"` will be treated " -"as a character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a" -" command: in CWL all parts of `baseCommand` must be strings so, if you " -"want to specify a fixed numeric value to a command, make sure that you " -"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 952c18ae0fb24c3ab42ae3f7b7db0844 -msgid "Comments" -msgstr "" - -#: ../../src/topics/yaml-guide.md:63 bd5835e2b35349679b1e69a50b958ee6 -msgid "" -"You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program " -"interpreting the YAML. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:76 2d36d90d86c3484c9f767e3fcdb29b25 -msgid "" -"If there is anything on the line before the comment, be sure to add at " -"least one space before the `#`!" -msgstr "" - -#: ../../src/topics/yaml-guide.md:79 48ca1f4243e343c2a3da3c9b5596097d -msgid "Maps" -msgstr "" - -#: ../../src/topics/yaml-guide.md:81 5d15caab19694c58a78d566b2897f6cc -msgid "" -"When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, " -"these hierarchical structures are described in YAML by providing " -"additional key-value pairs as the value of any key. These pairs " -"(sometimes referred to as \"children\") are written on new lines under " -"the key to which they belong (the \"parent\"), and should be indented " -"with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 42cb06c103784fb087a44e55f570cc79 -msgid "" -"The YAML above illustrates how to build up complex nested object " -"descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and " -"`inputBinding`, while one of these children, `inputBinding`, contains a " -"further two key-value pairs (`position` and `prefix`). See the " -"[Arrays](#arrays) section below for more information about providing " -"multiple values/key-value pairs for a single key. For comparison with the" -" example YAML above, here is a graphical representation of the `inputs` " -"object it describes." -msgstr "" - -#: ../../src/topics/yaml-guide.md:127 90b1474dba5442a48f9fdd07b07ed9fd -msgid "Arrays" -msgstr "" - -#: ../../src/topics/yaml-guide.md:129 76a1a131ac7648f9aa14ce14b09d17fe -msgid "" -"In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) " -"section above, more than one key-value pair can be mapped to a single " -"key. However, it is also possible to define multiple values for a key " -"without having to provide a unique key for each value. We can achieve " -"this with an _array_, where each value is defined on its own line and " -"preceded by `-`. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:146 f04cae70233848f7bd051fd553a89b9b -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:167 b6b1ad435b13428cb56c22fc135b303f -msgid "JSON Style" -msgstr "" - -#: ../../src/topics/yaml-guide.md:169 4a45ba50729c42ec949780bbcf495ef7 -msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " -"arrays can also be defined in YAML using the native JSON syntax. For " -"example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:177 57fa577b531645ae890c634c6549d680 -msgid "and:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:184 0cef0765d01e4525878389bb5ae8f6c5 -msgid "" -"Native JSON can be useful in indicating where a field is intentionally " -"left empty (such as `[]` for an empty array), as well as where it makes " -"more sense for the values to be located on the same line (For example, " -"when providing option flags and their values in a shell command). " -"However, as the second example above shows, it can severely affect the " -"readability of a YAML file, and should be used sparingly." -msgstr "" - -#: ../../src/topics/yaml-guide.md:194 1730e578bf2f4a7b8836d0a41e059de8 -msgid "Reference" -msgstr "" - -#: ../../src/topics/yaml-guide.md:196 f5e7fb0d74924c9e9b4ca1434f724ff0 -msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" -" us while we wrote this guide, though it also covers features that are " -"not valid in CWL." -msgstr "" - diff --git a/locales/es/LC_MESSAGES/tutorials.po b/locales/es/LC_MESSAGES/tutorials.po deleted file mode 100644 index 0c412e90..00000000 --- a/locales/es/LC_MESSAGES/tutorials.po +++ /dev/null @@ -1,64 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/tutorials.md:1 cba829ebca95427ca72b0c259e199cc1 -#: d32522e2993f4b48a789f46537fa5ebf -msgid "Tutorials" -msgstr "" - -#: ../../src/tutorials.md:5 413874a8cfb84860b7bce0ee5f4e6022 -#: 63a51dccb29045fd8f78d5e396c6e050 -msgid "" -"This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to the " -"list." -msgstr "" - -#: ../../src/tutorials.md:7 5242c591a9814c9793856f432d06adc1 -#: cb5f8748a5544be2835467ab07eb7a1c -msgid "Beginner Tutorials" -msgstr "" - -#: ../../src/tutorials.md:9 4a3e41ee134d491eafc9a7b07776b926 -#: 685d0cb2faa04703bcef408ecc2b92f4 -msgid "" -"[Introduction to Workflows with Common Workflow Language: For Contributors.]" -"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" -msgstr "" - -#: ../../src/tutorials.md:11 207a4a90ec2f406b8541f687540a71a5 -#: 20f45705145d45fc8420c4119b06a49f -msgid "Advanced Tutorials" -msgstr "" - -#: ../../src/tutorials.md:13 ead7b80dc37647289f83036eef8ca959 -#: 2bccd19d542d4458a1ba8616236f1840 -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../src/tutorials.md:15 95a0dd8e5c354219a3eb3140565aa853 -#: c491c73e4c00476980438ffc79c6e4d3 -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../src/tutorials.md:17 82e0cb6989494cef91c464d45cc64728 -#: b8485449206542e097584eca7363c8ce -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..ba080ed4 --- /dev/null +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -0,0 +1,3827 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Spanish \n" +"Language: es\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 4.16-dev\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "Licencias" + +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "Material didáctico" + +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." +msgstr "" +"Todo el material instructivo del proyecto Common Workflow Language y los " +"cambios en la estructura también están disponibles bajo la [licencia " +"Creative Commons Attribution][cc-by-human]. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del [texto legal completo de la " +"licencia CC BY 4.0][cc-by-legal]." + +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "Usted es libre de:" + +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" +"**Compartir**---copiar y redistribuir el material en cualquier medio o " +"formato" + +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" + +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "para cualquier propósito, incluso comercialmente." + +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" +msgstr "" +"La licenciante no puede revocar estas libertades en tanto usted siga los " +"términos de la licencia." + +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" +"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " +"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " +"Language Project» y, cuando sea práctico, con un enlace a https://www." +"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " +"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " +"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " +"licenciante." + +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" +msgstr "" +"**No hay restricciones adicionales**---No puede aplicar términos legales ni " +"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " +"permitido por la licencia. Con el entendimiento de que:" + +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." +msgstr "" +"No tiene que cumplir con la licencia para elementos del materiale en el " +"dominio público o cuando su uso esté permitido por una excepción o " +"limitación aplicable." + +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." +msgstr "" +"No se dan garantías. La licencia podría no darle todos los permisos que " +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " +"publicidad, privacidad, o derechos morales pueden limitar la forma en que " +"utilice el material." + +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "Software" + +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"Excepto cuando se indique lo contrario, los programas de ejemplo y otro " +"software proporcionado por el proyecto Common Workflow Language están " +"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " +"la [OSI][Osi]." + +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." +msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." + +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 +#: eab02dc13915490bb3c9ba744d78b6a7 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +msgid "" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +msgid "" +"The first method involves adding the folder containing your scripts to " +"the `PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +msgid "" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "" + +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +msgid "" +"The second method involves including an input of `type: File` in the " +"script itself:" +msgstr "" + +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +msgid "" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +msgid "" +"Using " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +msgid "" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." +msgstr "" + +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." +msgstr "" + +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +msgid "" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" +msgstr "" + +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +msgid "" +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +msgid "" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "" + +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +msgid "" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +msgid "" +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." +msgstr "" + +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +msgid "" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +msgid "" +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." +msgstr "" + +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +msgid "" +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +msgid "" +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input " +"directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "" +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "" +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows support the creation of FAIR data " +"and adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 +#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "" +"The CWL Specification page in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +msgid "" +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +msgid "" +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +msgid "" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem" +" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " +"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" +"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " +"details on installing WSL2. Your operating system also needs internet " +"access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create " +"and activate a Python virtual environment using the `venv` module, and " +"install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` " +"and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +msgid "" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +msgid "" +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env ` rather than" +" using a hard-coded location, since `/usr/bin/env ` looks for" +" the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +msgid "" +"cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +msgid "" +"The CWL community also maintains a list of editors and viewers: " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: " +"." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models " +"with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for " +"pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +msgid "" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "" +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +msgid "" +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +msgid "" +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +msgid "" +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "" +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +msgid "" +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "" +"For more examples of providing metadata within CWL descriptions, see " +"[the Metadata and Authorship section of this User Guide](../topics" +"/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +msgid "" +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "" +"Each `CommandLineTool` description should focus on a single operation " +"only, even if the (sub)command is capable of more. Don't overcomplicate " +"your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "" +"Custom types should be defined with one external YAML per type definition" +" for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +msgid "" +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +msgid "" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +msgid "" +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +msgid "" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. If a command-line tool is written manually in CWL v1.1+, there is" +" a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " +"Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "" +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f +#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 +#: f924d65fed0c4cb5b0a019b084a8b535 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +msgid "" +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +msgid "" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +msgid "" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +msgid "" +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +msgid "" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number " +"of cores required for the tool to run successfully, as well as details of" +" the version of the software that the description was written for and " +"other useful metadata. These features are discussed further in other " +"chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "" +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains" +" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by " +"the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +msgid "" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 +#: 1acb064f7a4a482aa0174bdc847c6382 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e +#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 +#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +msgid "" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc +#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd +#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 +#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 +#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d +#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f +#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c +#: f760465a49d64d4c8468ad9c4fea62b1 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +msgid "" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +msgid "" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b +#: d555a3d991e344a5a8e1289168d7c6d1 +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c +#: e9fa9430535c424fa3e8be5d460d2ba4 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c +#: b0290d1a477b48119e17cf1fed9d6dff +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 +#: e1cde4aa32c041238ed2596173c6d824 +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf +#: c2a92d3eca7f4ee39cec649170eeea53 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +msgid "" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 +#: 718ceee9973240ec9c100977bbcc8921 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 +#: c07ab08eb75d4528949c56a3d7c12b28 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +msgid "" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +msgid "" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" +" attribute that allows users to load external JavaScript files, or to " +"provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +msgid "" +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +msgid "" +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +msgid "" +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +msgid "" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +msgid "" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*," +" and *null*; complex types are *array* and *record*; in addition there " +"are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "" +"The field `inputBinding` is optional and indicates whether and how the " +"input parameter should appear on the tool's command line. If " +"`inputBinding` is missing, the parameter does not appear on the command " +"line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +msgid "" +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +msgid "" +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +msgid "" +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "" +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +msgid "" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 +#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +msgid "" +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +msgid "" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +msgid "" +"If you use exclusive input parameters combined with expressions, you need" +" to be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as “fasta” (one of the values of the enum), " +"your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +msgid "" +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to a `null` value, which does not match the expected type " +"for the output field (a `string`), resulting in failure when running your" +" workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript" +" expression when using exclusive parameters, or any parameter that allows" +" `null`. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value if none was " +"provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "" +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/) as described in the [Schema Salad specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +msgid "" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like" +" a command line tool or an expression. You can also plot it with the CWL " +"Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx Graphviz directive (this" +" user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +msgid "" +"If you try running it with `cwltool`, the command will fail since " +"`cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +msgid "" +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +msgid "" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +msgid "" +"The `glob` field consists of the name of a file in the output directory. " +"If you don't know name of the file in advance, you can use a wildcard " +"pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +msgid "" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +msgid "" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +msgid "" +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +msgid "" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +msgid "" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +msgid "" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +msgid "" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +msgid "" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +msgid "" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may " +"also help to avoid confusion about which version of a tool the " +"description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a `SoftwareRequirement`, " +"search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "" +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use `InitialWorkDirRequirement` to stage input files into" +" the output directory. In this example, we use a JavaScript expression to" +" extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +msgid "" +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +msgid "" +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +msgid "" +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the " +"container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +msgid "" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that " +"is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +msgid "" +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier " +"examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +msgid "" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "" +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +msgid "" +"This workflow extracts a java source file from a tar file and then " +"compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +msgid "" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a " +"workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +msgid "" +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +msgid "" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +msgid "" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +msgid "" +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +msgid "" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +msgid "" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +msgid "" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +msgid "" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +msgid "" +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +msgid "" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +msgid "" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +msgid "" +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +msgid "" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to " +"the list." +msgstr "" + +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +msgid "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" + diff --git a/locales/faq.pot b/locales/faq.pot deleted file mode 100644 index f4ead324..00000000 --- a/locales/faq.pot +++ /dev/null @@ -1,292 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/faq.md:1 -#: 38d96ecb6f4f4835a94fce7389f64290 -msgid "FAQ" -msgstr "" - -#: ../../src/faq.md:11 -#: cf04e2bcede444ec84829b20873bb458 -msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" - -#: ../../src/faq.md:41 -#: 7f5a8ebf64a6457290031a9878fcadb4 -msgid "Rename an Input File" -msgstr "" - -#: ../../src/faq.md:43 -#: d2da25aa3d4149c6a839e5a9d260d637 -msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." -msgstr "" - -#: ../../src/faq.md:59 -#: bb7a7c1994c44fd984a3d6daee56ca77 -msgid "Rename an Output File" -msgstr "" - -#: ../../src/faq.md:61 -#: ab649294dceb4701b50840614da498e9 -msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" -msgstr "" - -#: ../../src/faq.md:82 -#: 38a2bfda017f48af91062768c29228d6 -msgid "Referencing a Local Script" -msgstr "" - -#: ../../src/faq.md:84 -#: 73d6982c5a414307943c5100df766a29 -msgid "There are two ways to reference a local script:" -msgstr "" - -#: ../../src/faq.md:86 -#: 81acda6459354bf08b4f1454b3b2dcc4 -msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." -msgstr "" - -#: ../../src/faq.md:89 -#: c06ed26bc9d54aa2803014ba69e9ac78 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" - -#: ../../src/faq.md:95 -#: eb25e79af23e4104b38f6265e677c6a8 -msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" -msgstr "" - -#: ../../src/faq.md:97 -#: b618a3759865456f9ceb02a6a16ccba1 -msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." -msgstr "" - -#: ../../src/faq.md:104 -#: 455b1a1f10044b5c98b7fab451f48ed5 -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" - -#: ../../src/faq.md:113 -#: 6b44a7665da14b6aa887224b2fe3c15f -msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." -msgstr "" - -#: ../../src/faq.md:115 -#: a05b7978ef76413588e211bd9bf9250c -msgid "The second method involves including an input of `type: File` in the script itself:" -msgstr "" - -#: ../../src/faq.md:135 -#: 6caf0ac2ccad4e449dfe5578ff75ec0e -msgid "In CWL, everything must be directly stated." -msgstr "" - -#: ../../src/faq.md:138 -#: ffe1586183ab4a3199639b1f9e8062c1 -msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" - -#: ../../src/faq.md:140 -#: a8314e810d564e198e9fad0e32c23117 -msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." -msgstr "" - -#: ../../src/faq.md:165 -#: 77c15e3d59c74848b3b6ad85f213b30c -msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" - -#: ../../src/faq.md:167 -#: f3d50a6a37494ce9883a4d9cd0ce7870 -msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." -msgstr "" - -#: ../../src/faq.md:188 -#: 9d7e8ab5d8864376814d12f10b52c6a4 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" - -#: ../../src/faq.md:190 -#: 93b78d5afe4541eaba53b6ea29150658 -msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/faq.md:194 -#: 8bfb650cce844e31a30a6e1773d92a48 -msgid "merge_nested" -msgstr "" - -#: ../../src/faq.md:196 -#: 0624c44a35e944c2b463146331c9ba4d -msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." -msgstr "" - -#: ../../src/faq.md:199 -#: 1f4df1cd685e4bd5a695e7ace5a9159d -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" - -#: ../../src/faq.md:201 -#: 1f057777e7a9430bbbc2036e53a6e4fb -msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." -msgstr "" - -#: ../../src/faq.md:229 -#: f64dbbcaac5642cebbd7cbd96d85c40d -msgid "Optional Inputs 💯" -msgstr "" - -#: ../../src/faq.md:231 -#: 71f80d93e08342ad8b6db87ec9c837cf -msgid "To make an input parameter optional, add a question mark to the type declaration." -msgstr "" - -#: ../../src/faq.md:247 -#: 7dec6a02cc364c8a9723043a3e8b7d79 -msgid "" -msgstr "" - -#: ../../src/faq.md:248 -#: 8a06fc5a9f80481888418234671702cd -msgid "Enum Inputs ⚜️" -msgstr "" - -#: ../../src/faq.md:250 -#: 2f3dc891f5b64378abc449947a5117cc -msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" -msgstr "" - -#: ../../src/faq.md:267 -#: b5324b01d6614202b0fac7026a450caa -msgid "" -msgstr "" - -#: ../../src/faq.md:268 -#: 1198ce319b4847f8b74a14d2ec5248d5 -msgid "Record Inputs 📀" -msgstr "" - -#: ../../src/faq.md:270 -#: d9e2a621f8ae455092120ebb711d1f99 -msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." -msgstr "" - -#: ../../src/faq.md:322 -#: 2c4153eb18d94ad7bbad6acab1b5b61a -msgid "Setting Mutually Exclusive Parameters" -msgstr "" - -#: ../../src/faq.md:324 -#: 77b90349be254ceb8de2cf58aa410e6d -msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." -msgstr "" - -#: ../../src/faq.md:342 -#: 31e2b62687b84efda4924d7108e23cb3 -msgid "Setting Booleans" -msgstr "" - -#: ../../src/faq.md:344 -#: 8c72738f5aaa4fcd8457a10e799d0e8d -msgid "These can be set by using the default field" -msgstr "" - -#: ../../src/faq.md:349 -#: 3a83df07178945d4822e3520674d6308 -msgid "Concatenating Strings in Inputs" -msgstr "" - -#: ../../src/faq.md:351 -#: 2aca2690fdac4922bfdc9e5a9f2741b8 -msgid "The valueFrom field must be used instead of default." -msgstr "" - -#: ../../src/faq.md:359 -#: 3d072aa6b914445ca8326ffe260b4e35 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" - -#: ../../src/faq.md:361 -#: fb653b6af6a74231904d2d0f850d1116 -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" - -#: ../../src/faq.md:363 -#: d3d261dd88a94fa8ae8bf65c39eef6a1 -msgid "For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" - -#: ../../src/faq.md:371 -#: f7125b78a28c4924bdd3fcb37a184ff6 -msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." -msgstr "" - -#: ../../src/faq.md:373 -#: dc28c1a8e15b4499b4af492ac3cd2c1e -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" - -#: ../../src/faq.md:375 -#: db57566297534dea82c6f66dd9c14b51 -msgid "If `cwltool --validate` returns valid" -msgstr "" - -#: ../../src/faq.md:384 -#: 09a115ecb8d2487da88cd31e1bac337f -msgid "But executing it causes an error like:" -msgstr "" - -#: ../../src/faq.md:396 -#: 4537ae8ebd5c49f3857b2cbe81032d29 -msgid "The file is here" -msgstr "" - -#: ../../src/faq.md:410 -#: d31aa1c1adf343e8b2b71322511bf7f1 -msgid "Problem caused by `-` (hyphen character)." -msgstr "" - -#: ../../src/faq.md:423 -#: 096f725de9ee4c558d72695a84c40cbb -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" - -#: ../../src/faq.md:436 -#: 58316efc7814473383abb738c5c0b5ef -msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" -msgstr "" - -#: ../../src/faq.md:442 -#: 2ac3f24fd4074acb8e96542b350d5771 -msgid "Use CWL and cwltool with Singularity" -msgstr "" - -#: ../../src/faq.md:445 -#: ef3c267c3282458f891a76e5d467ec8e -msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." -msgstr "" - -#: ../../src/faq.md:450 -#: aa97ef90186747f7b9d0aaccf17535d1 -msgid "Debug JavaScript Expressions" -msgstr "" - -#: ../../src/faq.md:452 -#: bb5bc05d377d441abe02a09e3f1d1a03 -msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" diff --git a/locales/index.pot b/locales/index.pot deleted file mode 100644 index 9000da74..00000000 --- a/locales/index.pot +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/index.md:1 -#: 1e479cad716c478689be58d4b4aabd82 -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../src/index.md:3 -#: 0afc69049ce0403695a03e30416fd9f9 -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../src/index.md:7 -#: 852b4bfd1a374deb803accb90c7fea8c -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../src/index.md:9 -#: d702011b81064e65af1fcbd230d9977e -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." -msgstr "" - -#: ../../src/index.md:16 -#: 884f157b64ce4787ab8da8f9e674c233 -msgid "Navigating the User Guide" -msgstr "" - -#: ../../src/index.md:18 -#: fd0133a1a0214ef49b763ba33e282a9e -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." -msgstr "" - -#: ../../src/index.md:23 -#: e699c33ef40045528c31d74b2d797742 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." -msgstr "" - -#: ../../src/index.md:28 -#: 21aacf872e7a444c891c41ca3411ee06 -msgid "Table of Contents" -msgstr "" diff --git a/locales/introduction.pot b/locales/introduction.pot deleted file mode 100644 index 32cc94f9..00000000 --- a/locales/introduction.pot +++ /dev/null @@ -1,607 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/basic-concepts.md:1 -#: 92c85569d9e746d8a5b7a5e8f9773545 -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 -#: 5e501be2f49044c9897f6e8d65186abb -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 -#: a6f5f188f9af4b608b8401996a558e83 -msgid "The CWL Specification" -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:2 -#: 2ecb1a3a4c7546ba94e560924cfb09a8 -#: 3c0da8bd74824f8b88223c2a9dcc6ec2 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:21 -#: 7fb9ad094d844047b0d35dc70c295400 -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 -#: 303d1a15612846c1b60a4d651f9d1d4a -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 -#: c84c4bde07034846b043c4f281f8e00c -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 -#: d774877d6e4447b7b83d56ebbaf09e96 -msgid "Implementations" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:39 -#: e8884f39f08c41bab29c4284077fd860 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 -#: 984ac8cee64e4e41957d8c5a4aff0cfd -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 -#: 17381e8872414c49b178d91ace2e3e82 -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: c4cdbf2a42644e0eb4eb74512388e9f7 -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: 7d994284e320413bb8dbb2a42cd16a4e -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: ce92487ca4e3495ebd0693c502773626 -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: 0ce512c3cd744652b5feb2d8dcfdb613 -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: dd7d6a1399b04923b25df70abb1becf5 -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: ce4c76b46531416bb4006a9c01f45a23 -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 0256a343321447559471d731c86d3546 -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: e1235589f24942babe54adaae4f169af -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: 81baaa297562452f80afe68657c8099d -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: 0c8bbd88bd8c4c71b19011812e7487c3 -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 3b64da1f14964cea9e5cbf8376578789 -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: bf33807babb64befab3385eca4c92131 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: afdb75d374624f4798f358a3dfe7752e -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: bc28744d5fa644218ef55672d726307f -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 24ffb5bfa767424585b6b6c93169de93 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: bd53afe50cc14f2ca428adddb0e60dc9 -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: 35c98c4b352c4f9bb9572c740894dc57 -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: f7fb57fdf9344a7eb0f334aca8d3e85f -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: 0dc6a8f19fda4e9eaa80b8e1bd1fc5be -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: ff1224487c35402d8afee6da3803e19b -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: 63c2dd9aaec54df088e82febfd7bc49c -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: 18f310d11c9b48b4a447b6662446cd3e -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 -#: a3922283fdce4f99832c816626d5f098 -#: 19245373c2e84793a72462b7d2fa1c34 -#: 7c3ea7150c7d41fead10ddf2a6205ec8 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:180 -#: cf39d3563e344ad9b31d5268c4069972 -msgid "Semantic Versioning - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:181 -#: 97b0113a847044b98f79b5e00941f4c3 -msgid "The CWL Specification page in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:182 -#: 8cf4edbb4b344ac7b3eae86ed52beff8 -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:183 -#: c1dfc170fdf54c9e846539a5170f204f -msgid "The list of Implementations in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:184 -#: 778babbcfb2648a1ad7a7ad8f80653a8 -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:185 -#: 23abed59f5d44bfb96e8fa13aa213b83 -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." -msgstr "" - -#: ../../src/introduction/index.md:1 -#: ee93304de4e447c1bd5626e72b99b6fe -msgid "Introduction" -msgstr "" - -#: ../../src/introduction/index.md:3 -#: a79f07e33fc5437c9fa204111d0290d8 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." -msgstr "" - -#: ../../src/introduction/prerequisites.md:1 -#: 3cf08b553a814478b4b2c6c84ebe354e -msgid "Prerequisites" -msgstr "" - -#: ../../src/introduction/prerequisites.md:6 -#: 98751950a97f44fdb16e826fece810fb -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 -#: eac153b881fa47ab8bb08074dad8eed2 -msgid "CWL Implementations" -msgstr "" - -#: ../../src/introduction/prerequisites.md:14 -#: 806ff7b185d74538a9b0e20c6ad84ffe -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 -#: 1f9573b6cd45479bae2481a251132d53 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 -#: c3995fd5588741148e3b2c91ca011ca9 -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 -#: 8a67b172ce524aa09858acd9d1a62762 -msgid "Linux" -msgstr "" - -#: ../../src/introduction/prerequisites.md:25 -#: a567e0f952bc46be8b82d0a357f2c209 -msgid "macOS" -msgstr "" - -#: ../../src/introduction/prerequisites.md:26 -#: 21d3bb850bb14fdcb6d4c4a15c9966b6 -msgid "Windows" -msgstr "" - -#: ../../src/introduction/prerequisites.md:29 -#: 62cbb29459b24e9fa83c7cd7994bdf12 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:35 -#: aaa319d4446c41ba82bf925f29f7d9dd -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:41 -#: c49938a0100a4850b67d067a61304d01 -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 -#: 91e986d0c1f44d7f9c3b32366160da6a -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 -#: 301c5a3baaaf46bb81bdc25b53a31f23 -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:62 -#: 1664589ced314daebfb163e6424f220f -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:65 -#: 1223fecd61f34ad98ebbb7e45eaf4ac7 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:67 -#: 242c496599d84a64959db275ee1e212e -msgid "`true.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:73 -#: 9b749d47f48341cb9ac8cd14098e6c47 -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:79 -#: e8ec351d7b79447bb15f4d4518b8de87 -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:84 -#: 58d5613243914dc8bc4ce88676525783 -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:86 -#: 731a6c30786f43d88160f9642cbb05d2 -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 -#: ca2088eb9565429dbc1ce0b28b2ef1fb -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../src/introduction/prerequisites.md:93 -#: 5ac9c6bfb50b48878aff52f1194e53c4 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:101 -#: b8d0c12ff07f4269bba87cd653803345 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:104 -#: 83780c1b43f744b4ae87a917b26293f5 -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:111 -#: 2919320c41e94930a0aa9bc6aacb5a87 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:115 -#: b8e799c075214d539aa0a7c04dbc33c0 -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:120 -#: ccbd51a29ca841efb74c5e0a25d1eb87 -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:125 -#: 5f3330c1e15a402781c3325f9d3dc779 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:129 -#: 314fbc9f866a405b86e7bd704781dea1 -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 -#: 9434e3680aa9487fab9ddb782c6ff3d0 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:137 -#: 2ce0bda38d814b248a2c23ebc26bf462 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:144 -#: 105c3be6f5f34f4388b9999603275bb5 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 -#: bd378c8483a14c93b5fe00d76e5b0a06 -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 -#: 5ace5416560247c7a3304c41caa000c6 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 -#: 5d7a175b3c5a4f888daf037672211d61 -msgid "Text Editor" -msgstr "" - -#: ../../src/introduction/prerequisites.md:163 -#: 4e0c0c345527412eaf70e8efe67fab8f -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:167 -#: 6dd8379682824d1397c48ac10db4b894 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:171 -#: 57691f7bd87741d68f4e1a963da91654 -msgid "Visual Studio Code with the Benten (CWL) plugin - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 -#: 13a4d71f127b4bd09c12a37752d27c8b -msgid "cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:174 -#: a574ed30000541b2816fbfe66b32c314 -msgid "The CWL community also maintains a list of editors and viewers: " -msgstr "" - -#: ../../src/introduction/prerequisites.md:177 -#: 9bb9c9052ad14c7c9fc0275c8f1b651b -msgid "Docker" -msgstr "" - -#: ../../src/introduction/prerequisites.md:181 -#: 5afcf2e79ceb424ea0a570797a712321 -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 -#: cc5b91b8c5b14a40bdd09d3bd45fe9bb -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:191 -#: d5e36c7827334fc69498459db5137d30 -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:198 -#: 39d3eff64d004a0f8257d61f2a90b186 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:199 -#: 19946d0d9a6f42d487537273225b91cd -msgid "The Python `venv` module: " -msgstr "" - -#: ../../src/introduction/quick-start.md:1 -#: 66048204601a439d8245455c48b08826 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 -#: dcc41d0ce48e42a0ba209ca1fa37220a -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 -#: e2ebe32f12b74608b35217cea30cd0e0 -msgid "“Hello World”" -msgstr "" - -#: ../../src/introduction/quick-start.md:12 -#: 37a4f461b82f4e48948c5eab400b14a5 -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 -#: 371c6801e92448f9875fff60a509f509 -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 -#: e3fb51cd196542008cb16458fdef7c1f -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 -#: d00cd96d47c6450a8c0955765eff9ac1 -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 -#: e06fdf0744344d0193b99791b9b94c7d -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 -#: 6e2191fbb8794f83a51897028a2e50f7 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 -#: 931b6b49a46d4d5581a05446ac2e9a7d -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../src/introduction/quick-start.md:47 -#: 5cb281f4d0ea4163af0f7203c150345e -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 -#: 4e6c4c2b6bae49a2b2d93bc95538c7b9 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../src/introduction/quick-start.md:53 -#: b37ba76e0dd940559e13543ea241376e -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 -#: 22d7ac26f2ca41b2aa141fd4774b6f5c -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:62 -#: 15033ad0574d46b2951bb2121c80c462 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 -#: 2b2fc79461674b9ebdef49750f7fb319 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 -#: 8b11c9920b97427aa2d29498664e24bb -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 -#: d11de6ee015f46c991fbc8b48cd1fb60 -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../src/introduction/quick-start.md:80 -#: 71adfebd042a4820ac533a2e6e07c0ca -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" -msgstr "" - -#: ../../src/introduction/quick-start.md:82 -#: 8f199e6778a84ba68d385b42169f6b26 -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:88 -#: 28ec66afdad24dfd871ef1a2686f9976 -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:96 -#: cccb84844ce0453cb77ce3db65ffbc1b -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../src/introduction/quick-start.md:97 -#: 0c5a431846f241829975552ef8dd9c32 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../src/introduction/quick-start.md:98 -#: 8e383a7ea5b54c56adb9cb0c6ed6c179 -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." -msgstr "" - -#: ../../src/introduction/quick-start.md:99 -#: 98473d00529345d4989f0f5d2101da1b -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../src/introduction/quick-start.md:100 -#: d105326cb76b455d907c283a509f038c -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../src/introduction/quick-start.md:101 -#: d4d00a573e36474f9c915563d4ea8709 -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." -msgstr "" - -#: ../../src/introduction/quick-start.md:102 -#: aa8195d109974f9da3b9da97479525cb -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/LICENSE.po b/locales/pt/LC_MESSAGES/LICENSE.po deleted file mode 100644 index c3591ece..00000000 --- a/locales/pt/LC_MESSAGES/LICENSE.po +++ /dev/null @@ -1,102 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../LICENSE.md:2 -#: 3d749a78eb3e47c991d603c2cabd1b91 -msgid "Licenses" -msgstr "" - -#: ../../LICENSE.md:4 -#: 4689ade8475a4c8a9d5e325f072c1392 -msgid "Instructional Material" -msgstr "" - -#: ../../LICENSE.md:6 -#: ef8ec0f072d947fbba997c4b2191abc2 -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." -msgstr "" - -#: ../../LICENSE.md:12 -#: 696f3824ca814c9eb314abae51be8202 -msgid "You are free:" -msgstr "" - -#: ../../LICENSE.md:14 -#: 72ebe92edf58434e9d7a4fc6bddf8880 -msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "" - -#: ../../LICENSE.md:15 -#: 9b403f96d4194ffaab3f309d7d12f360 -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" - -#: ../../LICENSE.md:17 -#: 10b1befd0f834d79880c8aeb70b595d4 -msgid "for any purpose, even commercially." -msgstr "" - -#: ../../LICENSE.md:19 -#: 9017d0b760bb4370926d511b97a604c6 -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." -msgstr "" - -#: ../../LICENSE.md:22 -#: 1faadcaead6748dfb34886e5819af9b9 -msgid "Under the following terms:" -msgstr "" - -#: ../../LICENSE.md:24 -#: 7a49ed3a728349c9b486f3d0b1dbf577 -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." -msgstr "" - -#: ../../LICENSE.md:32 -#: 57da6294edce46eab00e7d15e6f6d4fa -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" -msgstr "" - -#: ../../LICENSE.md:36 -#: 8fc8a30cd63c4a0a9d8ba1b913687029 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." -msgstr "" - -#: ../../LICENSE.md:39 -#: fe59e74a4d024831a6d5cbcfd3e4ee38 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." -msgstr "" - -#: ../../LICENSE.md:44 -#: 3ea41d5a14ad46729cabb387a33814b0 -msgid "Software" -msgstr "" - -#: ../../LICENSE.md:46 -#: 23751e2552ff450c83e3dd255da56dac -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" - -#: ../../LICENSE.md:51 -#: 13fb5eb48a8a434e95dbbb717ccaef8a -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." -msgstr "" - -#: ../../LICENSE.md:57 -#: e262fbd0e7de4f148f31afe39d1cb9e9 -msgid "Trademark" -msgstr "" diff --git a/locales/pt/LC_MESSAGES/_includes.po b/locales/pt/LC_MESSAGES/_includes.po deleted file mode 100644 index 6d6635cc..00000000 --- a/locales/pt/LC_MESSAGES/_includes.po +++ /dev/null @@ -1,22 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/_includes/what-is-cwl.md:1 -#: 46f474e1b364495181698bd13ce28a1e -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/episodes.po b/locales/pt/LC_MESSAGES/episodes.po deleted file mode 100644 index 94101eb0..00000000 --- a/locales/pt/LC_MESSAGES/episodes.po +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/episodes.md:5 -#: 0cbb5e7334a647c3bcae7333ec3ced90 -msgid "This page has moved" -msgstr "" - -#: ../../src/episodes.md:9 -#: fabb221482cb4ac0a98bbe10943ed025 -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/faq.po b/locales/pt/LC_MESSAGES/faq.po deleted file mode 100644 index ce416d3d..00000000 --- a/locales/pt/LC_MESSAGES/faq.po +++ /dev/null @@ -1,292 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/faq.md:1 -#: 5daa5afac36f46dd8329e5629056384c -msgid "FAQ" -msgstr "" - -#: ../../src/faq.md:11 -#: 40c8efda3caf4c6089bda3027c522f37 -msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" - -#: ../../src/faq.md:41 -#: ee854bcb685941cab45ae7f33b0efe48 -msgid "Rename an Input File" -msgstr "" - -#: ../../src/faq.md:43 -#: a4cdd5ab6fe341a3ad3e3055556d96c3 -msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." -msgstr "" - -#: ../../src/faq.md:59 -#: d1f359d47f124dfab23a75b196cd5884 -msgid "Rename an Output File" -msgstr "" - -#: ../../src/faq.md:61 -#: d83ced40605e411c92c4ae38761d7ffa -msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" -msgstr "" - -#: ../../src/faq.md:82 -#: bc8997df2e6746cebc2068534f30ee82 -msgid "Referencing a Local Script" -msgstr "" - -#: ../../src/faq.md:84 -#: 20b6ae57e1cf4410877a60fb3ef87264 -msgid "There are two ways to reference a local script:" -msgstr "" - -#: ../../src/faq.md:86 -#: 73c66b809e9a4218b624338ccb88a05e -msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." -msgstr "" - -#: ../../src/faq.md:89 -#: 9be72b7d5d604526b125b63148e99320 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" - -#: ../../src/faq.md:95 -#: fd96d178901545008a43fa99e3aa6cf3 -msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" -msgstr "" - -#: ../../src/faq.md:97 -#: db58a582e66244468f4d31e9213933d1 -msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." -msgstr "" - -#: ../../src/faq.md:104 -#: 3e70f0da5cd7460b90c1690366f40820 -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" - -#: ../../src/faq.md:113 -#: db28dc27c82b4b29a7a9a768550bba9b -msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." -msgstr "" - -#: ../../src/faq.md:115 -#: 4474b16fb3fd4cdc85da931159804967 -msgid "The second method involves including an input of `type: File` in the script itself:" -msgstr "" - -#: ../../src/faq.md:135 -#: 23c9b2e21cec4ee8ade087e6630f62c2 -msgid "In CWL, everything must be directly stated." -msgstr "" - -#: ../../src/faq.md:138 -#: c01309dcd65c4f1080c396e6a9efb75d -msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" - -#: ../../src/faq.md:140 -#: 0a36801172fd4e24a04b3ba85cf74e29 -msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." -msgstr "" - -#: ../../src/faq.md:165 -#: 433e788ba01141e98ea5a9e73ef71e6f -msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" - -#: ../../src/faq.md:167 -#: b6de2761ce454992904775a06b7ba326 -msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." -msgstr "" - -#: ../../src/faq.md:188 -#: e36c2d53e8ba40f4a602b489a6688e24 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" - -#: ../../src/faq.md:190 -#: a9310166cb514e4e8824bba7fcfcb277 -msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/faq.md:194 -#: f6144f77152e4284963951abaa30adb2 -msgid "merge_nested" -msgstr "" - -#: ../../src/faq.md:196 -#: 790709dfc2854e4a89fcc4769f84b0f4 -msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." -msgstr "" - -#: ../../src/faq.md:199 -#: 438789c8def549d1b4b8a187d5acc48e -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" - -#: ../../src/faq.md:201 -#: 23ede7dfd5c84492baee1d5bbb9a91d9 -msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." -msgstr "" - -#: ../../src/faq.md:229 -#: 37c0474e48164160b23c4094d583d2d3 -msgid "Optional Inputs 💯" -msgstr "" - -#: ../../src/faq.md:231 -#: 3b2be0a4a87041b7a5bda20c6df2ffc8 -msgid "To make an input parameter optional, add a question mark to the type declaration." -msgstr "" - -#: ../../src/faq.md:247 -#: 886300d2dcff4861aae503d34b0bee44 -msgid "" -msgstr "" - -#: ../../src/faq.md:248 -#: fe393ecdff25428da6cbcd30171c7811 -msgid "Enum Inputs ⚜️" -msgstr "" - -#: ../../src/faq.md:250 -#: ebfd4991d917413b858da8b437a55805 -msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" -msgstr "" - -#: ../../src/faq.md:267 -#: 2919ff4f51254e69aea40146e2d911f1 -msgid "" -msgstr "" - -#: ../../src/faq.md:268 -#: 61ed4e87457c41eea31f51740557597e -msgid "Record Inputs 📀" -msgstr "" - -#: ../../src/faq.md:270 -#: 1e6624104b024eb092682cd0dd0f6a3c -msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." -msgstr "" - -#: ../../src/faq.md:322 -#: b741b8333e104feaa6d1f41fd4476304 -msgid "Setting Mutually Exclusive Parameters" -msgstr "" - -#: ../../src/faq.md:324 -#: 334673ae870a4dada817857f3a49326e -msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." -msgstr "" - -#: ../../src/faq.md:342 -#: 362f85270df04712b2e2f21c7019e3cb -msgid "Setting Booleans" -msgstr "" - -#: ../../src/faq.md:344 -#: ad6997f24c7c42fe965b5d7bfd1e633e -msgid "These can be set by using the default field" -msgstr "" - -#: ../../src/faq.md:349 -#: 99dce9d60b6a4f99bc39899b7c8c10ef -msgid "Concatenating Strings in Inputs" -msgstr "" - -#: ../../src/faq.md:351 -#: 6b68fe24cbf64624b49ea56fce2eecad -msgid "The valueFrom field must be used instead of default." -msgstr "" - -#: ../../src/faq.md:359 -#: d23326837eb74e7faf1f54e25f8309c4 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" - -#: ../../src/faq.md:361 -#: 2e2eabe92670412e95474b25ad9cda4c -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" - -#: ../../src/faq.md:363 -#: 81f9308adbee4a3c9e585b8e0f0c4844 -msgid "For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" - -#: ../../src/faq.md:371 -#: a5d3ed6cac28415288e7fc7fbfc6e8a6 -msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." -msgstr "" - -#: ../../src/faq.md:373 -#: 72f9692803304daf9f846e2b90139660 -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" - -#: ../../src/faq.md:375 -#: a7eb20c817704811b3bcf2f94ec2e51d -msgid "If `cwltool --validate` returns valid" -msgstr "" - -#: ../../src/faq.md:384 -#: 20fa869849ef4b358a11db46111017de -msgid "But executing it causes an error like:" -msgstr "" - -#: ../../src/faq.md:396 -#: 35032fcd9f23403ca006d62a7d6e7be7 -msgid "The file is here" -msgstr "" - -#: ../../src/faq.md:410 -#: f6d6a4e3691446378c8fb01a2d19f8ad -msgid "Problem caused by `-` (hyphen character)." -msgstr "" - -#: ../../src/faq.md:423 -#: 44608fed1048458e999e13b014327e7e -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" - -#: ../../src/faq.md:436 -#: 96ede8a8f1f34786aabd4004bf2e7acc -msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" -msgstr "" - -#: ../../src/faq.md:442 -#: 84634a368e704e8d828678785c784595 -msgid "Use CWL and cwltool with Singularity" -msgstr "" - -#: ../../src/faq.md:445 -#: 545c4db9c24f42ee946081254d9ca7a8 -msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." -msgstr "" - -#: ../../src/faq.md:450 -#: 1c1e6d583d5646a8a5c9316dcd743d9f -msgid "Debug JavaScript Expressions" -msgstr "" - -#: ../../src/faq.md:452 -#: cf7d336d444e4f59aa83585b7abb1fe5 -msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" diff --git a/locales/pt/LC_MESSAGES/index.po b/locales/pt/LC_MESSAGES/index.po deleted file mode 100644 index 0a5d7d38..00000000 --- a/locales/pt/LC_MESSAGES/index.po +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/index.md:1 -#: a58ca61ccefc401588f91699bc98bd32 -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../src/index.md:3 -#: 6dcf12053f104cb3a8d23ce8d4f90363 -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../src/index.md:7 -#: 1cc90206170d46119c5756f31a9e8799 -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../src/index.md:9 -#: b54801d84a944dadb4e4637551e3f7b9 -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." -msgstr "" - -#: ../../src/index.md:16 -#: 860afd2eda4847e0a0d8834de3af4aa8 -msgid "Navigating the User Guide" -msgstr "" - -#: ../../src/index.md:18 -#: d6046316c84b40ffb5478c90b2604911 -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." -msgstr "" - -#: ../../src/index.md:23 -#: c3c89ac756a74d9688e179b8718c9bf0 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." -msgstr "" - -#: ../../src/index.md:28 -#: 0eb795062b484537b090c4d5c361f7f4 -msgid "Table of Contents" -msgstr "" diff --git a/locales/pt/LC_MESSAGES/introduction.po b/locales/pt/LC_MESSAGES/introduction.po deleted file mode 100644 index fe9de9a5..00000000 --- a/locales/pt/LC_MESSAGES/introduction.po +++ /dev/null @@ -1,607 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/basic-concepts.md:1 -#: 92c85569d9e746d8a5b7a5e8f9773545 -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 -#: 5e501be2f49044c9897f6e8d65186abb -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 -#: a6f5f188f9af4b608b8401996a558e83 -msgid "The CWL Specification" -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:2 -#: 2ecb1a3a4c7546ba94e560924cfb09a8 -#: 3c0da8bd74824f8b88223c2a9dcc6ec2 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:21 -#: 7fb9ad094d844047b0d35dc70c295400 -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 -#: 303d1a15612846c1b60a4d651f9d1d4a -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 -#: c84c4bde07034846b043c4f281f8e00c -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 -#: d774877d6e4447b7b83d56ebbaf09e96 -msgid "Implementations" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:39 -#: e8884f39f08c41bab29c4284077fd860 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 -#: 984ac8cee64e4e41957d8c5a4aff0cfd -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 -#: 17381e8872414c49b178d91ace2e3e82 -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: c4cdbf2a42644e0eb4eb74512388e9f7 -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: 7d994284e320413bb8dbb2a42cd16a4e -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: ce92487ca4e3495ebd0693c502773626 -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: 0ce512c3cd744652b5feb2d8dcfdb613 -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: dd7d6a1399b04923b25df70abb1becf5 -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: ce4c76b46531416bb4006a9c01f45a23 -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 0256a343321447559471d731c86d3546 -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: e1235589f24942babe54adaae4f169af -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: 81baaa297562452f80afe68657c8099d -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: 0c8bbd88bd8c4c71b19011812e7487c3 -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 3b64da1f14964cea9e5cbf8376578789 -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: bf33807babb64befab3385eca4c92131 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: afdb75d374624f4798f358a3dfe7752e -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: bc28744d5fa644218ef55672d726307f -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 24ffb5bfa767424585b6b6c93169de93 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: bd53afe50cc14f2ca428adddb0e60dc9 -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: 35c98c4b352c4f9bb9572c740894dc57 -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: f7fb57fdf9344a7eb0f334aca8d3e85f -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: 0dc6a8f19fda4e9eaa80b8e1bd1fc5be -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: ff1224487c35402d8afee6da3803e19b -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: 63c2dd9aaec54df088e82febfd7bc49c -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: 18f310d11c9b48b4a447b6662446cd3e -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 -#: a3922283fdce4f99832c816626d5f098 -#: 19245373c2e84793a72462b7d2fa1c34 -#: 7c3ea7150c7d41fead10ddf2a6205ec8 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:180 -#: cf39d3563e344ad9b31d5268c4069972 -msgid "Semantic Versioning - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:181 -#: 97b0113a847044b98f79b5e00941f4c3 -msgid "The CWL Specification page in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:182 -#: 8cf4edbb4b344ac7b3eae86ed52beff8 -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:183 -#: c1dfc170fdf54c9e846539a5170f204f -msgid "The list of Implementations in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:184 -#: 778babbcfb2648a1ad7a7ad8f80653a8 -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:185 -#: 23abed59f5d44bfb96e8fa13aa213b83 -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." -msgstr "" - -#: ../../src/introduction/index.md:1 -#: ee93304de4e447c1bd5626e72b99b6fe -msgid "Introduction" -msgstr "" - -#: ../../src/introduction/index.md:3 -#: a79f07e33fc5437c9fa204111d0290d8 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." -msgstr "" - -#: ../../src/introduction/prerequisites.md:1 -#: 3cf08b553a814478b4b2c6c84ebe354e -msgid "Prerequisites" -msgstr "" - -#: ../../src/introduction/prerequisites.md:6 -#: 98751950a97f44fdb16e826fece810fb -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 -#: eac153b881fa47ab8bb08074dad8eed2 -msgid "CWL Implementations" -msgstr "" - -#: ../../src/introduction/prerequisites.md:14 -#: 806ff7b185d74538a9b0e20c6ad84ffe -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 -#: 1f9573b6cd45479bae2481a251132d53 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 -#: c3995fd5588741148e3b2c91ca011ca9 -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 -#: 8a67b172ce524aa09858acd9d1a62762 -msgid "Linux" -msgstr "" - -#: ../../src/introduction/prerequisites.md:25 -#: a567e0f952bc46be8b82d0a357f2c209 -msgid "macOS" -msgstr "" - -#: ../../src/introduction/prerequisites.md:26 -#: 21d3bb850bb14fdcb6d4c4a15c9966b6 -msgid "Windows" -msgstr "" - -#: ../../src/introduction/prerequisites.md:29 -#: 62cbb29459b24e9fa83c7cd7994bdf12 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:35 -#: aaa319d4446c41ba82bf925f29f7d9dd -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:41 -#: c49938a0100a4850b67d067a61304d01 -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 -#: 91e986d0c1f44d7f9c3b32366160da6a -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 -#: 301c5a3baaaf46bb81bdc25b53a31f23 -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:62 -#: 1664589ced314daebfb163e6424f220f -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:65 -#: 1223fecd61f34ad98ebbb7e45eaf4ac7 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:67 -#: 242c496599d84a64959db275ee1e212e -msgid "`true.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:73 -#: 9b749d47f48341cb9ac8cd14098e6c47 -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:79 -#: e8ec351d7b79447bb15f4d4518b8de87 -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:84 -#: 58d5613243914dc8bc4ce88676525783 -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:86 -#: 731a6c30786f43d88160f9642cbb05d2 -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 -#: ca2088eb9565429dbc1ce0b28b2ef1fb -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../src/introduction/prerequisites.md:93 -#: 5ac9c6bfb50b48878aff52f1194e53c4 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:101 -#: b8d0c12ff07f4269bba87cd653803345 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:104 -#: 83780c1b43f744b4ae87a917b26293f5 -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:111 -#: 2919320c41e94930a0aa9bc6aacb5a87 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:115 -#: b8e799c075214d539aa0a7c04dbc33c0 -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:120 -#: ccbd51a29ca841efb74c5e0a25d1eb87 -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:125 -#: 5f3330c1e15a402781c3325f9d3dc779 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:129 -#: 314fbc9f866a405b86e7bd704781dea1 -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 -#: 9434e3680aa9487fab9ddb782c6ff3d0 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:137 -#: 2ce0bda38d814b248a2c23ebc26bf462 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:144 -#: 105c3be6f5f34f4388b9999603275bb5 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 -#: bd378c8483a14c93b5fe00d76e5b0a06 -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 -#: 5ace5416560247c7a3304c41caa000c6 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 -#: 5d7a175b3c5a4f888daf037672211d61 -msgid "Text Editor" -msgstr "" - -#: ../../src/introduction/prerequisites.md:163 -#: 4e0c0c345527412eaf70e8efe67fab8f -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:167 -#: 6dd8379682824d1397c48ac10db4b894 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:171 -#: 57691f7bd87741d68f4e1a963da91654 -msgid "Visual Studio Code with the Benten (CWL) plugin - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 -#: 13a4d71f127b4bd09c12a37752d27c8b -msgid "cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:174 -#: a574ed30000541b2816fbfe66b32c314 -msgid "The CWL community also maintains a list of editors and viewers: " -msgstr "" - -#: ../../src/introduction/prerequisites.md:177 -#: 9bb9c9052ad14c7c9fc0275c8f1b651b -msgid "Docker" -msgstr "" - -#: ../../src/introduction/prerequisites.md:181 -#: 5afcf2e79ceb424ea0a570797a712321 -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 -#: cc5b91b8c5b14a40bdd09d3bd45fe9bb -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:191 -#: d5e36c7827334fc69498459db5137d30 -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:198 -#: 39d3eff64d004a0f8257d61f2a90b186 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:199 -#: 19946d0d9a6f42d487537273225b91cd -msgid "The Python `venv` module: " -msgstr "" - -#: ../../src/introduction/quick-start.md:1 -#: 66048204601a439d8245455c48b08826 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 -#: dcc41d0ce48e42a0ba209ca1fa37220a -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 -#: e2ebe32f12b74608b35217cea30cd0e0 -msgid "“Hello World”" -msgstr "" - -#: ../../src/introduction/quick-start.md:12 -#: 37a4f461b82f4e48948c5eab400b14a5 -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 -#: 371c6801e92448f9875fff60a509f509 -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 -#: e3fb51cd196542008cb16458fdef7c1f -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 -#: d00cd96d47c6450a8c0955765eff9ac1 -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 -#: e06fdf0744344d0193b99791b9b94c7d -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 -#: 6e2191fbb8794f83a51897028a2e50f7 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 -#: 931b6b49a46d4d5581a05446ac2e9a7d -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../src/introduction/quick-start.md:47 -#: 5cb281f4d0ea4163af0f7203c150345e -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 -#: 4e6c4c2b6bae49a2b2d93bc95538c7b9 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../src/introduction/quick-start.md:53 -#: b37ba76e0dd940559e13543ea241376e -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 -#: 22d7ac26f2ca41b2aa141fd4774b6f5c -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:62 -#: 15033ad0574d46b2951bb2121c80c462 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 -#: 2b2fc79461674b9ebdef49750f7fb319 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 -#: 8b11c9920b97427aa2d29498664e24bb -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 -#: d11de6ee015f46c991fbc8b48cd1fb60 -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../src/introduction/quick-start.md:80 -#: 71adfebd042a4820ac533a2e6e07c0ca -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" -msgstr "" - -#: ../../src/introduction/quick-start.md:82 -#: 8f199e6778a84ba68d385b42169f6b26 -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:88 -#: 28ec66afdad24dfd871ef1a2686f9976 -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:96 -#: cccb84844ce0453cb77ce3db65ffbc1b -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../src/introduction/quick-start.md:97 -#: 0c5a431846f241829975552ef8dd9c32 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../src/introduction/quick-start.md:98 -#: 8e383a7ea5b54c56adb9cb0c6ed6c179 -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." -msgstr "" - -#: ../../src/introduction/quick-start.md:99 -#: 98473d00529345d4989f0f5d2101da1b -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../src/introduction/quick-start.md:100 -#: d105326cb76b455d907c283a509f038c -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../src/introduction/quick-start.md:101 -#: d4d00a573e36474f9c915563d4ea8709 -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." -msgstr "" - -#: ../../src/introduction/quick-start.md:102 -#: aa8195d109974f9da3b9da97479525cb -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/setup.po b/locales/pt/LC_MESSAGES/setup.po deleted file mode 100644 index 06186f03..00000000 --- a/locales/pt/LC_MESSAGES/setup.po +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/setup.md:5 -#: 29bb5c68be6042e5aa4a370e9c4024b3 -msgid "This page has moved" -msgstr "" - -#: ../../src/setup.md:9 -#: 8bcf31398c34491da1a1590422a72cbe -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/sphinx.po b/locales/pt/LC_MESSAGES/sphinx.po index 68ce7729..38526232 100644 --- a/locales/pt/LC_MESSAGES/sphinx.po +++ b/locales/pt/LC_MESSAGES/sphinx.po @@ -1,27 +1,28 @@ # SOME DESCRIPTIVE TITLE. # Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. # +#, fuzzy msgid "" msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" +"Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:27+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" -#: ../../src/_templates/sidebar-nav-bs.html:1 -#: b896fd5e11fe4674a7f46ad489476692 +#: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" msgstr "" -#: ../../src/_templates/sidebar-nav-bs.html:3 -#: acede4e78f7e4aefa0ad9425928cbb42 +#: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" msgstr "" + diff --git a/locales/pt/LC_MESSAGES/topics.po b/locales/pt/LC_MESSAGES/topics.po deleted file mode 100644 index 7d6384c1..00000000 --- a/locales/pt/LC_MESSAGES/topics.po +++ /dev/null @@ -1,2083 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 1a006f1604c0405aaa4b93e41edc5184 -msgid "Additional Arguments and Parameters" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:3 -#: b61b4d7ed53a436486c1429987a2a21b -msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 1bf9e65f1cc249ee93656a53ddd354ca -msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 3329dc69c32f4b9092b196d79ae5d0c1 -msgid "`arguments.cwl`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 -#: a003a3d1de0e4dfe8c777905e55fb9fe -#: e2dc24c683054cd785326de2c3f3f136 -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:24 -#: aca6a0cd24a2411c8cfb1ad392f6d315 -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:30 -#: bcf37e403eb041269e351d7f98a19587 -msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:36 -#: c5f68f8a9f34445ebcbd5783f96cb046 -msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:43 -#: 4eca90c659ba43158db373d36ee681df -msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." -msgstr "" - -#: ../../src/topics/best-practices.md:1 -#: 7474eeb128624dc4b1e980dbd0f04ca4 -msgid "Best Practices" -msgstr "" - -#: ../../src/topics/best-practices.md:3 -#: 0c520e5add334609a1afddc559abe19a -msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 -#: 125a69207077425fa54f346abc45342d -msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../src/topics/best-practices.md:11 -#: 6ca38a04844c403b836942b2f2f1e1e2 -msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." -msgstr "" - -#: ../../src/topics/best-practices.md:20 -#: 1da05be0d97d429a84085459ebae54cf -msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." -msgstr "" - -#: ../../src/topics/best-practices.md:26 -#: fb1b2a8c54f34d78ac61dd4b5ffd9063 -msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" -msgstr "" - -#: ../../src/topics/best-practices.md:28 -#: a8b1b5caf9904fc5b9eef8c110474b84 -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../src/topics/best-practices.md:37 -#: 42a5a8cb3b284549aabb817b73ce5810 -msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." -msgstr "" - -#: ../../src/topics/best-practices.md:40 -#: eddd878eb0324851997de2a69bcbb43f -msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." -msgstr "" - -#: ../../src/topics/best-practices.md:44 -#: b05c8ff667174f6798feb811cdd3c41d -msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:47 -#: 9dc16d1a6b0546cead6967f5e9b1526a -msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../src/topics/best-practices.md:50 -#: b8bf85e8523a4553a58face698aa863b -msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../src/topics/best-practices.md:55 -#: 6fb9a1a2ffe14f39b01af8736a9698eb -msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:58 -#: 0a935aa93e554c0987af7349f94ccd3a -msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." -msgstr "" - -#: ../../src/topics/best-practices.md:66 -#: cadb5982a13e4621807ad976cf9b1524 -msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." -msgstr "" - -#: ../../src/topics/best-practices.md:69 -#: bd7ab2cc6234458181e9b99938eba824 -msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." -msgstr "" - -#: ../../src/topics/best-practices.md:73 -#: 7beb72d7dd5a405f9be8b6fb6a310f10 -msgid "Custom types should be defined with one external YAML per type definition for re-use." -msgstr "" - -#: ../../src/topics/best-practices.md:76 -#: e5942c4d4b4d4e1a8c0e9ed3da80960e -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../src/topics/best-practices.md:78 -#: 5a5dbc9b9d2242ba8d15ecf39123694b -msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." -msgstr "" - -#: ../../src/topics/best-practices.md:82 -#: dd3016d33b7d4340a09a7c8e5aec4f0b -msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." -msgstr "" - -#: ../../src/topics/best-practices.md:85 -#: 45d110a660b348f58a1107476df18cee -msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." -msgstr "" - -#: ../../src/topics/best-practices.md:90 -#: 97a5b141592e4415aa4acef4f6228045 -msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." -msgstr "" - -#: ../../src/topics/best-practices.md:93 -#: 85f624f8879348e8bb368ec2749925bf -msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../src/topics/best-practices.md:97 -#: 20a851dae87941c7975173ed9cd1e360 -msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." -msgstr "" - -#: ../../src/topics/command-line-tool.md:1 -#: bb19e1b689564a11bb9e72d5f82cf3d9 -msgid "Command Line Tool" -msgstr "" - -#: ../../src/topics/command-line-tool.md:3 -#: b14199173add4585be62c4e8278b49f4 -msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." -msgstr "" - -#: ../../src/topics/command-line-tool.md:8 -#: 9e883f18843a41d7b10102bc11655839 -msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." -msgstr "" - -#: ../../src/topics/command-line-tool.md:19 -#: fe3a1468aa864742b92c6e8f4ff1a38f -msgid "CWL command-line tool." -msgstr "" - -#: ../../src/topics/command-line-tool.md:50 -#: e9dbf14538404cceb02507962a173ee8 -msgid "`echo.cwl`" -msgstr "" - -#: ../../src/topics/command-line-tool.md:57 -#: a650a7dacbb547db97158a8ac2c9d0dc -msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../src/topics/command-line-tool.md:68 -#: 501217b98c424a319e70ef963de506f6 -msgid "Network Access" -msgstr "" - -#: ../../src/topics/command-line-tool.md:69 -#: 7143809471454e00880ad8faaf43f141 -msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." -msgstr "" - -#: ../../src/topics/command-line-tool.md:83 -#: 7ad86e42708a465980a56f735644de9f -msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:1 -#: a8f29712337b4d1daf3190cc8973b8f7 -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:3 -#: 534843389795437991fad0b5a702b483 -msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:7 -#: 2052170aa2624feeb2253477895aa838 -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:9 -#: d5ed098a33ae4c1ab2a30eba483ecc6f -msgid "`createfile.cwl`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:15 -#: 2b55c028602f41babb6e535b425ba5dc -msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:20 -#: 47408669ae8b4432a43d763dba12a466 -msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:27 -#: b2e5e925971849a09a8d54d9c649a32d -msgid "To test the above CWL tool, use this job to provide the input value `message`:" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 -#: ../../src/topics/outputs.md:77 -#: 9a39f53bdcc94904a90effb507767645 -#: f296149bf19947528b134b01a4d7ce81 -#: 965fa9769dea4ac9b3dd252e0a3bc603 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:35 -#: 79d8ea95f0c34585a3dec4f83453de60 -msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:40 -#: 4afab699247b4f619702c4086eb1b6f3 -msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:51 -#: 693b91423f004118b806bb8ee7952eaf -msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:54 -#: ../../src/topics/environment-variables.md:18 -#: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 -#: ../../src/topics/workflows.md:198 -#: e4a25f04a6fa4001bb1e58cb775cdd84 -#: c771cbc64607412a9164c28934e9e0f5 -#: bdd5a3eac1e3436496e05a13c4f06073 -#: 1e62b28ef0184081b4d6e53f34b753e1 -#: 33edd6deb38740ed98466b6e023b0393 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/custom-types.md:1 -#: a3a8bcdfadc4484ea5e4c13a25b2da85 -msgid "Custom Types" -msgstr "" - -#: ../../src/topics/custom-types.md:3 -#: 7800570badf149b3bb1f81d470dbf4be -msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." -msgstr "" - -#: ../../src/topics/custom-types.md:9 -#: 496313f8ec67403ca78ba66130df261e -msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:12 -#: f7cc0d1ac5dd47658093cd0360f90329 -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../src/topics/custom-types.md:18 -#: 0d563f15c1cc4484b6b2955bdc70e1a9 -msgid "`custom-types.yml`" -msgstr "" - -#: ../../src/topics/custom-types.md:24 -#: 06425b6cdaf244b198fdde312e864190 -msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/custom-types.md:30 -#: 26c3762a637a4492a6c12588544cb0a7 -msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../src/topics/custom-types.md:46 -#: 221433aa39104642af8afb70ebd08576 -msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:53 -#: 197bf36a5d7741b3a9ac56c19d4a7686 -msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../src/topics/custom-types.md:55 -#: d9249cf936d24ab3b3fc508d17d94745 -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../src/topics/custom-types.md:61 -#: 2ff7ce81cd3a492a8549484ba8d1f135 -msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" -msgstr "" - -#: ../../src/topics/custom-types.md:76 -#: 2bb45c56e2fc49e094be2cf742222e67 -msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." -msgstr "" - -#: ../../src/topics/environment-variables.md:1 -#: e2a4a531c6164f15bc711618db058f52 -msgid "Environment Variables" -msgstr "" - -#: ../../src/topics/environment-variables.md:3 -#: 90f7960bd24d4481bd05da1d61ef146b -msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../src/topics/environment-variables.md:7 -#: a51814548e44467c841ca65b2ac63b2c -msgid "`env.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:1 -#: fa13573d9c174ca1accf20a449e5984f -msgid "Expression Tool" -msgstr "" - -#: ../../src/topics/expression-tool.md:3 -#: f2912b17e3be47b0b7186efdb4c4010f -msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." -msgstr "" - -#: ../../src/topics/expression-tool.md:8 -#: 4d9c95d18c1a4880845e7194a99aed3c -msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" - -#: ../../src/topics/expression-tool.md:17 -#: c656a020978f465b85b8754346ea5b6d -msgid "CWL expression tool." -msgstr "" - -#: ../../src/topics/expression-tool.md:48 -#: ff4d0b6bc0264650a21adc811b8caf4c -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:67 -#: 77e00be2c0984465af5bf501b4031f32 -msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." -msgstr "" - -#: ../../src/topics/expressions.md:1 -#: 3d7b7238be974c0487f219cb5c030149 -msgid "Expressions" -msgstr "" - -#: ../../src/topics/expressions.md:3 -#: 03a62f421c8241779c0e79f4dbad96cc -msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." -msgstr "" - -#: ../../src/topics/expressions.md:9 -#: 31a85893835748339b6c84fb98fde14b -msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." -msgstr "" - -#: ../../src/topics/expressions.md:16 -#: 08d9ecd7d3294c5b9dd4db228a1d8d5b -msgid "`expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:22 -#: d94d6c69aaa64edd9c75624286713c2e -msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" -msgstr "" - -#: ../../src/topics/expressions.md:25 -#: 020019b8aedb494fad022d19b7106f83 -msgid "`empty.yml`" -msgstr "" - -#: ../../src/topics/expressions.md:31 -#: a6b66e0fc0de442e8f72f0d0c37c7e8c -msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." -msgstr "" - -#: ../../src/topics/expressions.md:35 -#: 48b7d9ddac2940c0815e5c855bfca6d9 -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../src/topics/expressions.md:37 -#: 894b843f9c064d56913e1a8c48093314 -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:47 -#: 2319e845caee41a3bc5888c3f1fc28d1 -msgid "Note that requirements can be provided with the map syntax, as in the example above:" -msgstr "" - -#: ../../src/topics/expressions.md:54 -#: 9ea661d749db428eacd2207dc7a01e36 -msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." -msgstr "" - -#: ../../src/topics/expressions.md:62 -#: 4ff76250f28144a4a9d8807a9d4ed3b4 -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../src/topics/expressions.md:64 -#: 7f9f2df357a740feb89bfbcc44ff4d61 -msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../src/topics/expressions.md:66 -#: 12633ed841dd447a8753faeb4f9e5096 -msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 -#: 4db64481d38c4896a85a8f6038a9931c -#: 1b4ff3eeddde4a9a8018235b9d706567 -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/expressions.md:68 -#: ../../src/topics/expressions.md:76 -#: ../../src/topics/expressions.md:89 -#: ../../src/topics/parameter-references.md:65 -#: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 -#: 50547062ee404e2ebeae7eeb54b9de4b -#: 88933bc02fa84412944673c3463af1ad -#: 4fde39d8a50e49f09bd28a8598760682 -#: b933cbf847d94c5fb8471918ce8cb4ad -#: 0145c520b85a4bc29302bb654f08f23b -#: a3e322ac8a0d4e2ba9bfbece6b5ae64b -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 -#: d9b166225120432f9a2bf2cc7b6ffdfe -#: 28f8ec2fc5c0436aaba19e9d479aa466 -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 -#: b866a0e5897e44329714f4c55eb20d2e -#: e64b5027878346d79f9ab52b3d3b916e -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 -#: ed38ec582fbb48ff9f9cffa7962ef515 -#: 6cc0788250624fd69fa4e3881191ab7f -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/expressions.md:72 -#: 17eefb5f38534c1b87116c3a061ea1bb -msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:73 -#: ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 -#: ../../src/topics/expressions.md:93 -#: ../../src/topics/parameter-references.md:70 -#: ../../src/topics/parameter-references.md:75 -#: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 -#: ce0572fc81b343e6991c88ca0195149a -#: f8b77ad06ebe43d7b03b2135737902e2 -#: c7953486c99d4c7898c0155a6085dfd5 -#: 46d99b1f7f0747479bd58486cf7941d2 -#: cd0a797b3619404f964ba9efb33756bd -#: 528cd5e0d3994230b719fbfb39b1f13e -#: 324241aae8ff4505ab0467f2a7f27fe2 -#: f4086b1ad2e44c2b9de2636f8bc1eb90 -msgid "`format`" -msgstr "" - -#: ../../src/topics/expressions.md:74 -#: ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 -#: ../../src/topics/expressions.md:94 -#: ../../src/topics/parameter-references.md:71 -#: ../../src/topics/parameter-references.md:76 -#: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 -#: 764d7cf3fb5444d58dc9e0eb6b8fc649 -#: 0450a4b8de3046998d30ce1f09c10daf -#: fd6bf79cbb694dbb89e8731aed733e6c -#: e6048a64e09d46099132fee40a2e0644 -#: 9512391eb96440bd8e48c3754821e3d0 -#: 3e8669bf4a6741f9aba170864b251dac -#: a02ede726d3f4eec9602f72054c0d963 -#: 4ed593dfc39246789f1e4ecdc742323b -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/expressions.md:75 -#: 304de40206cb43d7b651245586cfa55b -msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:77 -#: 7855471c93bc44aabb1a2b9beb52b56a -msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:80 -#: f0452f324bfa451f9f3264f9a55e0e5d -msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 -#: 6dc476cf8689465ea3993f49a9eead75 -#: 4dfc0be21065471d91def850bc2528fb -msgid "`glob`" -msgstr "" - -#: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 -#: 09d69778a89044099b3e5d7cf02471bb -#: e3077bdff0dc4dfdae60eb60f3d66d8b -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 -#: b28843f7b57745db9cb3648ef23fda0f -#: 6a745fa266dd42849c95410775b690e0 -msgid "From `Workflow`" -msgstr "" - -#: ../../src/topics/expressions.md:84 -#: be00ed49197f48ecb7cb244ecc214369 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 -#: 90ad2b27f97b4ca089cf23a073cdf17b -#: 38d062892cb04bc7bbf0b56f263079e1 -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/expressions.md:88 -#: c2d2756d617743b886c67160c2face21 -msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 -#: 8681600183d1429cbd1b15639e1a222f -#: 1d49cd7337004fc38f4e8e9aa4270481 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 -#: 24b7f85116cc4d2f904600555aa19b8b -#: c401a68b4f384d3eb13ab3e89a4a7195 -msgid "`expression`" -msgstr "" - -#: ../../src/topics/expressions.md:92 -#: 0e1f9d22d0714bc5b80e420f63b34cff -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:95 -#: 5fed95f16aaf42d4b41c569d9546b7f0 -msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 -#: b539a931f31d4cfe9d72aa5800115fb2 -#: 48e497c024bc4c38a86dd027aaa4fd2d -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 -#: be638c80121948c99cc9fdb67a5d291e -#: 1fd8fe769ba8497eb8a9520af91ea33e -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 -#: b5f3ad78a233411c97520c1fffdec18f -#: 7854e46c7fd24afd9c1942808521bee1 -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 -#: 211bd57896494fca9ea8aa2fc142eea2 -#: 28ec0718d3114bfdaae4524c009da944 -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 -#: c6a421f7a0214d89958d4c258b58aac8 -#: 07bd0bc74ad74187bdc24c26041467ca -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 -#: 3afc146cde2e47d5b52e62fbd1f37426 -#: 2225f5acb44a4ce0ad16be5c4f6cba48 -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 -#: 9acd61d4d67a4d2c82171a79462fb458 -#: cd7e7fea3b8346268618c31b70581326 -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:103 -#: ../../src/topics/parameter-references.md:100 -#: 140e449e46a84e3ca1a604176e583f44 -#: 3d8b717d4568458eb53b0b91695b3de8 -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:104 -#: 76f35653e34b433d8e9fedc6d12ce856 -msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:105 -#: ../../src/topics/parameter-references.md:102 -#: 1a2edf61fda8404689e3c0a7389d7d02 -#: 3bced6d84fa6453195be82dbc6d7ec83 -msgid "`listing`" -msgstr "" - -#: ../../src/topics/expressions.md:106 -#: 0b5aceb6c9d24bd9bfe95cc04fdc61ad -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/expressions.md:107 -#: ../../src/topics/parameter-references.md:104 -#: 3523cc46c6324fca9053d6b1dd8c7495 -#: 21eee2c1cb6b430486446d223dcca0eb -msgid "`entry`" -msgstr "" - -#: ../../src/topics/expressions.md:108 -#: ../../src/topics/parameter-references.md:105 -#: b4f126415048402ca388c4c63f34ebe5 -#: fdf588cf8cd34d60bfb6cece3ef859e0 -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/expressions.md:109 -#: ../../src/topics/parameter-references.md:106 -#: 1b494245c14e4e22918c43ad9f26cc8d -#: df4d781178f2465b8a421651bdd2f66f -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/expressions.md:110 -#: a88008a23ede4ea49ffcaccba7029d31 -msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/expressions.md:111 -#: ../../src/topics/parameter-references.md:108 -#: a256b51f1e944b7d9659b945d8ab05c9 -#: 23bbd631e73147e3af561eb4a14d2d6c -msgid "`envValue`" -msgstr "" - -#: ../../src/topics/expressions.md:116 -#: a446842e26e44781ad10cdaad73bc49d -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../src/topics/expressions.md:118 -#: 3cc10263ab2f4dbfb6ccb12612b89cf1 -msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." -msgstr "" - -#: ../../src/topics/expressions.md:122 -#: 995f6af5fc244293b34f5d840f01ce1c -msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:128 -#: b556a1d134764505aa25003d79a53e88 -msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." -msgstr "" - -#: ../../src/topics/expressions.md:135 -#: ad23da5452bd46248606f6799ce93db0 -msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:139 -#: c63036ac68344465af6c7756be00b60b -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:146 -#: 2f7f270b0ac24f2f8df506f5dde72cf7 -msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" -msgstr "" - -#: ../../src/topics/expressions.md:149 -#: f49272e5e4c1491eb59c79d2dfb88a86 -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:155 -#: 8b50c892d36d4d178ec4268c7c13887d -msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:158 -#: 9d22117a6f5a434593d5144bf824999f -msgid "`custom-functions.js`" -msgstr "" - -#: ../../src/topics/expressions.md:164 -#: 4fbc454a144a466b9dd7ff74903fc5fb -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:171 -#: 281b129a76a24b0a818092acd1038757 -msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:175 -#: 4dda6ca233d54c12b6ddceabae198495 -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:181 -#: 59d87fecfd7f4438b68e0bcdecdcfb46 -msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." -msgstr "" - -#: ../../src/topics/expressions.md:186 -#: 0f7e33673ad349e5ad41a078032e5806 -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:193 -#: 77a7141f897048139ef3785b5f870b43 -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:200 -#: 14ed183bc7e346598921445c0dea11e0 -msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." -msgstr "" - -#: ../../src/topics/file-formats.md:1 -#: 9406d05bf0ed4774af50fd66d24aa299 -msgid "File Formats" -msgstr "" - -#: ../../src/topics/file-formats.md:3 -#: f5a9048ef9e047528c291505ef9a2c12 -msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." -msgstr "" - -#: ../../src/topics/file-formats.md:8 -#: 51e8c5a231eb45fb8c15be49b37a7bff -msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." -msgstr "" - -#: ../../src/topics/file-formats.md:14 -#: 860a6f01ebac45938abd220758fd1109 -msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." -msgstr "" - -#: ../../src/topics/file-formats.md:17 -#: 32155f96d47f4d76998a401aa9e9591f -msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../src/topics/file-formats.md:20 -#: a62bbb9251794560ace0e52be3d9ebd3 -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../src/topics/file-formats.md:26 -#: ../../src/topics/metadata-and-authorship.md:22 -#: e301af8f675444c69cfb6b578c02fdc7 -#: 3da1dec243994409bd764b133d4fc243 -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/file-formats.md:32 -#: 82c6efcfb5d5410eb316399b7c4f638e -msgid "Sample Parameter Files" -msgstr "" - -#: ../../src/topics/file-formats.md:34 -#: 29c3d25c657340a1bab7123a166b78c2 -msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." -msgstr "" - -#: ../../src/topics/file-formats.md:39 -#: ef8e7bd7e944429da78474d2fc5e0348 -msgid "`sample.yml`" -msgstr "" - -#: ../../src/topics/file-formats.md:45 -#: 08dd50bc6a5942ec8f3b6c201fc4497f -msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/index.md:1 -#: 78c51215a68f40b280cc21d0e412eacf -msgid "Topics" -msgstr "" - -#: ../../src/topics/inputs.md:1 -#: bb8e2203374a4ae7b833c543ecc563b0 -msgid "Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:3 -#: f34aa1e4d08944c497602b2a35f38a50 -msgid "Essential Input Parameters" -msgstr "" - -#: ../../src/topics/inputs.md:5 -#: 2932972efc94447987b02a7707c62656 -msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/inputs.md:9 -#: 968f4e83c511425d8faf4c8d0f18097e -msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../src/topics/inputs.md:13 -#: 2eb89bdbaee04a899a961a7b87f0aef1 -msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." -msgstr "" - -#: ../../src/topics/inputs.md:16 -#: 3781fc7cd22d48bdb5aa4abc0c93b06f -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../src/topics/inputs.md:18 -#: f4af4a85efb243728d2ee783393dce14 -msgid "`inp.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:24 -#: dbf8350f003a46b984b7432160e6def5 -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../src/topics/inputs.md:26 -#: db2993fe83814747a52f9db0b2fcc81e -msgid "`inp-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:33 -#: 39fe18bf5d4b4539b2f98e3bf0feea2a -msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" -msgstr "" - -#: ../../src/topics/inputs.md:40 -#: 58e7b0e7d0a149498e846dd2790c0eee -msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." -msgstr "" - -#: ../../src/topics/inputs.md:44 -#: 4b78c5437904492ea3e692372d2fc163 -msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." -msgstr "" - -#: ../../src/topics/inputs.md:47 -#: f2626686125d4ec29fb2338373b54c93 -msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:53 -#: 46327aca33cb49d1ba61149e94884991 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:64 -#: 43f2e7020da94f77bce4e1f852ab11f1 -msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" -msgstr "" - -#: ../../src/topics/inputs.md:70 -#: 8342aa3f84624325aff8f7f4de788187 -msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." -msgstr "" - -#: ../../src/topics/inputs.md:83 -#: 2d54f11f99b245e5b2802b984bc024a5 -msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." -msgstr "" - -#: ../../src/topics/inputs.md:95 -#: 83a357dc06b343549876035b03b8c5d1 -msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." -msgstr "" - -#: ../../src/topics/inputs.md:109 -#: 0461538fa12a44c5a9d230a928ae930d -msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." -msgstr "" - -#: ../../src/topics/inputs.md:124 -#: 2b2552958f404447b711d09650d22395 -msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:131 -#: 82c97e60f8634bd6b4d3e88524722412 -msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../src/topics/inputs.md:134 -#: 0ae1393a80e94b899023c29f4af6084b -msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." -msgstr "" - -#: ../../src/topics/inputs.md:142 -#: 74339f624bba49d6b68e1dfc4724f673 -msgid "The `baseCommand` field will always appear in the final command line before the parameters." -msgstr "" - -#: ../../src/topics/inputs.md:146 -#: 3a4473864ec04d2e9a0d550b2051f717 -msgid "Array Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:148 -#: 575661b36a2040699956f897bd6cc614 -msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." -msgstr "" - -#: ../../src/topics/inputs.md:154 -#: 3d18a704f5a94e2889e847c32a78aaab -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:160 -#: fceca2b53d0646b2ae9f1cf9dbefe2fc -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:166 -#: ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 -#: cba49054785b4ec2a7acd3aaa2e165d8 -#: 647c0e302af841d7b1789447281d7344 -#: d23de44d5d5b4bc7b32f3726afa97500 -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:178 -#: dd867685663f4728b9fbe446a9b14a3d -msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." -msgstr "" - -#: ../../src/topics/inputs.md:185 -#: 67bf2c2cbbc44f6eb870af3a3a852676 -msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." -msgstr "" - -#: ../../src/topics/inputs.md:191 -#: 94d66455bfd04697814495e116176ffe -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:193 -#: 39a9d3583f29451d8035158c54266ed6 -msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." -msgstr "" - -#: ../../src/topics/inputs.md:198 -#: eba6af5cf8224d198fc04f090362307c -msgid "`record.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:204 -#: b48377cceff342e793e982c9fa2095d3 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:215 -#: b64ef70d944c461b8ec7219e14e47795 -msgid "In the first example, you can't provide `itemA` without also providing `itemB`." -msgstr "" - -#: ../../src/topics/inputs.md:217 -#: 73cd08a2226f4cbe99fcde2d3636d640 -msgid "`record-job2.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:233 -#: 3c33bffa2c574ef888b041c1e6735b8e -msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." -msgstr "" - -#: ../../src/topics/inputs.md:236 -#: 23bd067b32724dad9daba1e924757d86 -msgid "`record-job3.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:252 -#: 1be92fc3d0b44ea089273cfcd47318ef -msgid "In the third example, only `itemD` is provided, so it appears on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:255 -#: 3d08125883b74f49bba042ed58d34648 -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../src/topics/inputs.md:257 -#: 7636c7e8b6e04d7089ba1cb10c4c475d -msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." -msgstr "" - -#: ../../src/topics/inputs.md:262 -#: e1c95ce96db043eb86ff9b3ae595017b -msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." -msgstr "" - -#: ../../src/topics/inputs.md:265 -#: e6588c4b8fa64959b2dcac52403a6415 -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:271 -#: e7f85cb69a5342889525fbb81b44c86c -msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" -msgstr "" - -#: ../../src/topics/inputs.md:280 -#: 71756719e0274300a839b38c8b4ea986 -msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." -msgstr "" - -#: ../../src/topics/inputs.md:289 -#: 88bf75fce3064eaf823b5d88be0ce053 -msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:1 -#: 60374713dea84fff92b89b4ebaa8d7ac -msgid "Metadata and Authorship" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:3 -#: 7616d5ea746f47ac972183150b97e8b0 -msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:13 -#: 0ca022c095334ec4a9fe41cb732e11a1 -msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:16 -#: 1c807f8fd1c540ae8802092fbcec7159 -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:28 -#: c51956eb3ece432ea0ed5b676b2f037a -msgid "Extended Example" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:30 -#: 45e6ab3a53b94f5b90136d68c1c0e479 -msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:35 -#: 7e05dc23d6be4428b4a414b3a65c4727 -msgid "`metadata_example3.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:1 -#: 96e7266ef25b429da42337c3582cc201 -msgid "Operations" -msgstr "" - -#: ../../src/topics/operations.md:3 -#: 9cb6959a877f4590bccb977416753410 -msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." -msgstr "" - -#: ../../src/topics/operations.md:7 -#: 7b54a3cd870d4b038dff685064bbca1a -msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../src/topics/operations.md:10 -#: 0d661c96ac2d41ee94641a397aa3bdf7 -msgid "`operations.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:16 -#: 94d39b79923a4a65b1a6ce5c464528c6 -msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" -msgstr "" - -#: ../../src/topics/operations.md:24 -#: 56801121f70b4cb2ab6207e254ec8bbf -msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" -msgstr "" - -#: ../../src/topics/operations.md:55 -#: 42418ff882d44c1b9584fb9f7887f744 -msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" -msgstr "" - -#: ../../src/topics/operations.md:58 -#: 1118de96d202444d9bb4db74ebe4792d -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../src/topics/operations.md:66 -#: aca51d371db84aa79418c79a18310055 -msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." -msgstr "" - -#: ../../src/topics/outputs.md:1 -#: 3473e6d2942e4546a2c1590edeb502f8 -msgid "Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:3 -#: c210ad12f61047b68302e67da9b5dae0 -msgid "Returning Output Files" -msgstr "" - -#: ../../src/topics/outputs.md:5 -#: 1c15cff5a4614d88a62c8d2df97029fc -msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/outputs.md:10 -#: 4beae917368545688c01a4a929685cae -msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." -msgstr "" - -#: ../../src/topics/outputs.md:16 -#: 4f4f63b7107e4dc194760802c4581c2a -msgid "The following example demonstrates how to return a file that has been extracted from a tar file." -msgstr "" - -#: ../../src/topics/outputs.md:19 -#: d942035c4c914ccb9de75836af9761c7 -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../src/topics/outputs.md:21 -#: 0e9064cf55fe43588053d37100634538 -msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" -msgstr "" - -#: ../../src/topics/outputs.md:26 -#: aa1dcfc618e74a53b3c579380e5e1558 -msgid "`tar.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:32 -#: 3ec3f4a2d1c547b18780db17fbff060c -msgid "`tar-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:38 -#: 21e598983ce94d22b9d40a77577a6608 -msgid "Next, create a tar file for the example." -msgstr "" - -#: ../../src/topics/outputs.md:45 -#: 62f79a2c055b455d9626ca5a18d1bd72 -msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:51 -#: 19c2b9b13bcc480aa7474301422faab3 -msgid "The field `outputBinding` describes how to set the value of each output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:62 -#: 17bb520489a74f64b76ddbe2ffedcb5e -msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." -msgstr "" - -#: ../../src/topics/outputs.md:65 -#: 9e2b97aa3bfe4eae8524b325bf2ea3f1 -msgid "Capturing Standard Output" -msgstr "" - -#: ../../src/topics/outputs.md:67 -#: 028c844ef208450f994b3949210ca996 -msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:71 -#: 2b758e44e4be4fdf89a5897385db6c59 -msgid "`stdout.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:89 -#: 16395173b7ee468f85ee8450493504de -msgid "Array Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:91 -#: 51e2e929dadc41a78cea98f779e2e2a3 -msgid "You can also capture multiple output files into an array of files using `glob`." -msgstr "" - -#: ../../src/topics/outputs.md:93 -#: b757d4b151ef46fa96897bf00a0d9ab4 -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:99 -#: 2f2f46a81e8946bf8a9b48a5956c82f8 -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:112 -#: 75177c797c704385bfa5ce86e03266c9 -msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." -msgstr "" - -#: ../../src/topics/parameter-references.md:1 -#: 4d05d16c3cb74eb291da7586fa859b90 -msgid "Parameter References" -msgstr "" - -#: ../../src/topics/parameter-references.md:3 -#: c115b7ed044346d6a9c4c06306ee82d8 -msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 -#: 8f83261e3e91424b9a3c38280c643f02 -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../src/topics/parameter-references.md:19 -#: 269af269348e4da5b93cb25dcd10374a -msgid "`tar-param-job.yml`" -msgstr "" - -#: ../../src/topics/parameter-references.md:25 -#: c376ab464fec4ee78a33d42dfed5dc1c -msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/parameter-references.md:36 -#: 53d468d14703494699478e6847d82e34 -msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../src/topics/parameter-references.md:47 -#: 32bd7abe387e4999a0864f6e6a48e435 -msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../src/topics/parameter-references.md:51 -#: 0712e952fe2442daa9ceb0cee79a3ebf -msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." -msgstr "" - -#: ../../src/topics/parameter-references.md:54 -#: ef2b8db0c8d64e41b839b47aae34d0ec -msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." -msgstr "" - -#: ../../src/topics/parameter-references.md:59 -#: f9f45dcc2bcb4fd1a1021d2843137fa3 -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../src/topics/parameter-references.md:61 -#: 4ffbc016a5344e6e9272793d921e4900 -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../src/topics/parameter-references.md:63 -#: 7118718b98c5488c9d9a54e5ec84c055 -msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:69 -#: 20fe8fa105a84171972722158bafbc0d -msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:72 -#: 836fa2a818854cf9af13d674f5bb859c -msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:74 -#: 5d56e1ac063d48c2b140a72db9f78540 -msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:77 -#: 0166655553ac4d8fb868138936176986 -msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:81 -#: e43fe4a9340b458786c51499c75b5556 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:85 -#: 0ba13966a1364d4e9992b5cfeb6871d1 -msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/parameter-references.md:89 -#: feb8bce610be4a3a92053f2e2e5aab76 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:92 -#: 0f5fd76c57e7412097b4ebdeb074f2fd -msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:101 -#: b645dd17256543b0a42d231171140c95 -msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:103 -#: c8d5743769bd4fee93f77a52ba318883 -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/parameter-references.md:107 -#: af6cbb89b7a84bf78b7443b6746484fe -msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/requirements-and-hints.md:5 -#: ad9394b163a94340975a66ea2bba7094 -msgid "Requirements and Hints" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:1 -#: 677bce1f24f449beb2bac5ed8469f624 -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:3 -#: 4c0d14a24b354feabf4b6ad4852f9543 -msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:13 -#: d407e5c9aa9043b0b6ab234348467db0 -msgid "In this example, the software requirement being described is InterProScan version 5.21-60." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:25 -#: f06b60c926204ca88b4355803f1b7b11 -msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:29 -#: 0a7c19b054d2400abd327736b6829670 -msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 -#: cd1773f336544b3688bc76c28e9d1f79 -msgid "Staging Input Files" -msgstr "" - -#: ../../src/topics/staging-input-files.md:3 -#: 6b7bbca601f04f7183bc75988bd6db13 -msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." -msgstr "" - -#: ../../src/topics/staging-input-files.md:9 -#: 069d1dd1f03f4cd79e44f2dcd890b531 -msgid "`linkfile.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:1 -#: 4924b1a69a5f48b0aa6af943b40ffc68 -msgid "Troubleshooting" -msgstr "" - -#: ../../src/topics/troubleshooting.md:3 -#: e100d8d8f23c4d6996ac59c5ad68acf0 -msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." -msgstr "" - -#: ../../src/topics/troubleshooting.md:6 -#: a87dfd0dc0274ff4b34354678f2d49d2 -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:8 -#: 772078ff701a477cae9acb8dda16ef1f -msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." -msgstr "" - -#: ../../src/topics/troubleshooting.md:14 -#: d2d67048e93e40c4820b805f1ba28cc9 -msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." -msgstr "" - -#: ../../src/topics/troubleshooting.md:20 -#: 580477152be041a8ae5c5f546ecbf21d -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:27 -#: 05f8faea082b4fb9b9c22b8eff7eb356 -msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" -msgstr "" - -#: ../../src/topics/troubleshooting.md:35 -#: 4c107fb18fb34c2dba7743118c51e8c8 -msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" -msgstr "" - -#: ../../src/topics/troubleshooting.md:44 -#: 729ea19aa03b49bdadccc6e6f0d2e7d9 -msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." -msgstr "" - -#: ../../src/topics/troubleshooting.md:48 -#: e849cda9fb1d4a48b5b1f9a4e44213a1 -msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." -msgstr "" - -#: ../../src/topics/troubleshooting.md:59 -#: bfc20f529d2d4797b87c63c7b2c05e91 -msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." -msgstr "" - -#: ../../src/topics/using-containers.md:1 -#: 761a900275a044f28ddcebe509a4637a -msgid "Using Containers" -msgstr "" - -#: ../../src/topics/using-containers.md:3 -#: 59af21cf1ee848e993563ad47f7bb248 -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../src/topics/using-containers.md:5 -#: d711ce1ccdcf427aba25a2ab3d11165d -msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 -#: eaaaa01fe0894f479a42a9c3ce199819 -msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." -msgstr "" - -#: ../../src/topics/using-containers.md:18 -#: 92489f186e3f449295b0dc864ebf17f7 -msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../src/topics/using-containers.md:21 -#: 1360c3a2d43b48f3b3e1153bb26b3f30 -msgid "`docker.cwl`" -msgstr "" - -#: ../../src/topics/using-containers.md:27 -#: 2e993e21a3624910b4282bd088694fec -msgid "`docker-job.yml`" -msgstr "" - -#: ../../src/topics/using-containers.md:33 -#: df5b4b041dc944be8580e43012339168 -msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 -#: 92ac2766d118428ea148094c022a8b0d -msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." -msgstr "" - -#: ../../src/topics/using-containers.md:52 -#: e4ddaca03eb449eabbf2d2fce752c367 -msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/using-containers.md:55 -#: 0bc50411a4b748d8864305070d11a304 -msgid "`hello.js`" -msgstr "" - -#: ../../src/topics/using-containers.md:69 -#: 74453227279a46cea3644f3ca7df61b9 -msgid "Notice the CWL runner has constructed a Docker command line to run the script." -msgstr "" - -#: ../../src/topics/using-containers.md:72 -#: 75ce3269886645eda46a6575fca186eb -msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." -msgstr "" - -#: ../../src/topics/workflows.md:1 -#: 1e7e5b46017a476a80d57ab7eb614758 -msgid "Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:3 -#: 1ee41e983ca14a959caa199b1ce12700 -msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../src/topics/workflows.md:13 -#: 070e6a00d09e4675b89afec5d066aec1 -msgid "CWL workflow." -msgstr "" - -#: ../../src/topics/workflows.md:41 -#: fd37ebe3aad9473891cc764a47363f8e -msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." -msgstr "" - -#: ../../src/topics/workflows.md:51 -#: 85176099018c4ae19bed1261e92e6e92 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:81 -#: 952e9a347f444ef496fa0cdf00160ffd -msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../src/topics/workflows.md:91 -#: 2b5ad46ca3024ce1b37e1c92a820aabf -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:150 -#: ea17d17cd08b4c40a842598c8521af56 -msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../src/topics/workflows.md:160 -#: 6e5f1266974d4a32995aaa69fbbfd648 -msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." -msgstr "" - -#: ../../src/topics/workflows.md:165 -#: 20be823f70c348bbaad6bfc8b88201a9 -msgid "Writing Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:167 -#: 02311e5310cb49d19bf2998513f73124 -msgid "This workflow extracts a java source file from a tar file and then compiles it." -msgstr "" - -#: ../../src/topics/workflows.md:170 -#: ca6e4a3fe04145a9a21cc43cc53a07bc -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:179 -#: ../../src/topics/workflows.md:180 -#: 75452467551a46a2b2b3685f1a4aae0d -#: 93efa8e941a7427f949afc794ed16e75 -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../src/topics/workflows.md:180 -#: 39beed65cb114bd78c79aa4a5d6f4398 -msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 -#: dd880d0589fe45dbaf9b7d799402f158 -msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" -msgstr "" - -#: ../../src/topics/workflows.md:185 -#: 671d0bd54bb147518c35f0844a76c61d -msgid "`1st-workflow-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:191 -#: 66de58a51b034f6a8d5dbe742046f817 -msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/workflows.md:205 -#: 564e68d58e364715aa72183cb16b3d72 -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../src/topics/workflows.md:212 -#: 558739ceb3fe40de8ea87ff1e7d3fe9d -msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." -msgstr "" - -#: ../../src/topics/workflows.md:221 -#: fdc601ee1aa54e1f84cd00eed2e44e52 -msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." -msgstr "" - -#: ../../src/topics/workflows.md:233 -#: e4f4a76cee96473d9da3bc1c9e35324a -msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." -msgstr "" - -#: ../../src/topics/workflows.md:248 -#: d524ed5f1e964688af9d74eef8e46e04 -msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:256 -#: c646e4714d78437fb450127b119fbd70 -msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." -msgstr "" - -#: ../../src/topics/workflows.md:261 -#: 8351ddfd726c40159d81c017ef221606 -msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." -msgstr "" - -#: ../../src/topics/workflows.md:267 -#: 456794c7274f4654b54aae8d4073a2df -msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." -msgstr "" - -#: ../../src/topics/workflows.md:278 -#: 6485e8d6814144d1bcbe66bfe4fcbdb9 -msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." -msgstr "" - -#: ../../src/topics/workflows.md:285 -#: a2b9e47cc923466f8bd2fbc4b33fc4fa -msgid "Nested Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:287 -#: 698cc640807247fd8d512c59ce32ee48 -msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../src/topics/workflows.md:297 -#: dd658e10da624918b7dec1ea18bbf432 -msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:300 -#: f6bd95a4fbc44ffdbfec7fcac90f6bb6 -msgid "`nestedworkflows.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:309 -#: ac7b02a71d3544848d4fb539b2a4f115 -msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 -#: 4380dbd066a44102a71c7e42ca7de8d8 -msgid "\"Visualization \"Visualization" -msgstr "" - -#: ../../src/topics/workflows.md:322 -#: da946c9d59f44fb995daa6aadc44031d -msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." -msgstr "" - -#: ../../src/topics/workflows.md:336 -#: 7c73bc555f604afd8491c1619d6905eb -msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." -msgstr "" - -#: ../../src/topics/workflows.md:341 -#: e79ce424410e4682881fe14326955a14 -msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." -msgstr "" - -#: ../../src/topics/workflows.md:347 -#: be8d2b89052e4f9d96ff2bf15526e229 -msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../src/topics/workflows.md:366 -#: 967b064ec4284d0aaf374509915497e1 -msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../src/topics/workflows.md:383 -#: 02d667b922264f8e8021844df0085578 -msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." -msgstr "" - -#: ../../src/topics/workflows.md:389 -#: db8734e07541495188d9ee97eaaaeff3 -msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." -msgstr "" - -#: ../../src/topics/workflows.md:394 -#: 22542da60ac24403827e2e2a14595770 -msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." -msgstr "" - -#: ../../src/topics/workflows.md:398 -#: d10f35716f9c4b878da0f2b4ff3d44aa -msgid "Scattering Steps" -msgstr "" - -#: ../../src/topics/workflows.md:400 -#: 1fd555d1f8ca499ead8d5601eb62266a -msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." -msgstr "" - -#: ../../src/topics/workflows.md:411 -#: f5fc85accf8c4bb9bc701ba0b4ee2e21 -msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:415 -#: e69cb5e87f4b4670abbc1606197d804c -msgid "`scatter-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:421 -#: 15d763c45a2749a8926b1f965db9d97f -msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" -msgstr "" - -#: ../../src/topics/workflows.md:429 -#: c2aac63fc0c347d9833d253039000fa3 -msgid "First of all, notice that the main workflow level input here requires an array of strings." -msgstr "" - -#: ../../src/topics/workflows.md:441 -#: 06a23beb753c4a97b302943f59128d78 -msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." -msgstr "" - -#: ../../src/topics/workflows.md:445 -#: 45985434cfe9438cb558075e1fd73809 -msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../src/topics/workflows.md:450 -#: e92da36d865142289b11d245221ff8d4 -msgid "Using the following input file:" -msgstr "" - -#: ../../src/topics/workflows.md:452 -#: 3ed7a2b9f77b4eadae3bf6e4a98d14b9 -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:458 -#: fd66c4fb9c2a4beea0ed5ed8874fcd61 -msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:466 -#: 65944dc8b32a46a4beb73dbdebb7b01a -msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" -msgstr "" - -#: ../../src/topics/workflows.md:469 -#: 6250fe161ab0421b8799040b79ce695a -msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" -msgstr "" - -#: ../../src/topics/workflows.md:472 -#: cc40c0f1ade34ab3b400a02b59b7ba01 -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:480 -#: 29f53a5d64fa498bad0dbe94b238fd97 -msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" -msgstr "" - -#: ../../src/topics/workflows.md:483 -#: 037fccb419bc4e9f839c665ae31e28ee -msgid "`wc-tool.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:489 -#: fdd4bec90c484a618ed8e4d1199deff8 -msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" -msgstr "" - -#: ../../src/topics/workflows.md:491 -#: 11afb584f37947358963f6510935c5d5 -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:497 -#: a77e0bfb589c40b6a61a9ca559961a7c -msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 -#: 3f4aa12588204fe5b33db590a9446283 -msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" -msgstr "" - -#: ../../src/topics/workflows.md:513 -#: 640c67f3bcd740c59f90c361024acbcc -msgid "`scatter-nested-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:519 -#: 8c4d30cbbea146a584731d164d4ad9ef -msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:522 -#: 5d0fd4f8b58e4a8e8f46902e64e6556b -msgid "Conditional Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:524 -#: e98ab273645340f9a1446183a642e79e -msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../src/topics/workflows.md:527 -#: 37a83ed92d9e44689cfd3a31c2785418 -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:566 -#: 7cebef0a9e1444149b1dc58d30f6c10e -msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../src/topics/workflows.md:573 -#: 0cd2bd98918b4622bc586d50f1ce1fa4 -msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." -msgstr "" - -#: ../../src/topics/workflows.md:587 -#: 92458de979564d19a634bb8d3bf6f586 -msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../src/topics/workflows.md:607 -#: d4ee6cc8903f4e6992439ca2586246ed -msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../src/topics/workflows.md:627 -#: 62b438c4ed8a409f96974f3d59cc5854 -msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." -msgstr "" - -#: ../../src/topics/yaml-guide.md:1 -#: f0f288aeae4f4649ba3615437b531e97 -msgid "YAML Guide" -msgstr "" - -#: ../../src/topics/yaml-guide.md:6 -#: f35023cb05504d1db0cbee41c4e5f371 -msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../src/topics/yaml-guide.md:13 -#: 01564f1d2038489685160f03db92085f -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../src/topics/yaml-guide.md:16 -#: ad662dce1e4149728b8e17f74d8f975f -msgid "Contents" -msgstr "" - -#: ../../src/topics/yaml-guide.md:18 -#: 4f6a57f34f094418b7c13aa07eef95c7 -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:19 -#: 373a6c24de9144e69f37418d6ce8857d -msgid "[Comments](#comments)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:20 -#: f804a8493c8e40178772d94bdc45b43e -msgid "[Maps](#maps)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:21 -#: b3c504b8ab1a42788ef4e3339d27b0dc -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:22 -#: 2c2681fe72e24a5d8d98f0aa8e8c56a2 -msgid "[JSON Style](#json-style)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:24 -#: 571e5c13552c4381bb6de53c02fe5f43 -msgid "Key-Value Pairs" -msgstr "" - -#: ../../src/topics/yaml-guide.md:26 -#: fd789f444d9a4061b4fc61bac70353bb -msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:42 -#: 2cef838551994b078e460c63214517f9 -msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." -msgstr "" - -#: ../../src/topics/yaml-guide.md:51 -#: 2a3a8a553d3c455e9288f63b9a02898d -msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 -#: b0b8def4623a4018b1ac913a9256c0a2 -msgid "Comments" -msgstr "" - -#: ../../src/topics/yaml-guide.md:63 -#: 3f0d4346f0104cc08c059eed9ab4b3a9 -msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:76 -#: 22e0ac963278414d8141ce5ce4031029 -msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" -msgstr "" - -#: ../../src/topics/yaml-guide.md:79 -#: 49cad54646d04adc8e5ac9f0f3c8f895 -msgid "Maps" -msgstr "" - -#: ../../src/topics/yaml-guide.md:81 -#: c8776a4511b24f46bbe0a34d52cf3c8b -msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 -#: 401b053bd08a4286b9059cb6ebf8d679 -msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." -msgstr "" - -#: ../../src/topics/yaml-guide.md:127 -#: 8d48a277f37f458f88c54f362534d7b5 -msgid "Arrays" -msgstr "" - -#: ../../src/topics/yaml-guide.md:129 -#: de90253a11f24f29a4a57348b4f60941 -msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:146 -#: 1e20968f957441c58cabfbc46c21e8ca -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:167 -#: 4cf2e158afb348d7b3fd6274fe888129 -msgid "JSON Style" -msgstr "" - -#: ../../src/topics/yaml-guide.md:169 -#: 44c5c010c97a40068a6b930949dcd8cf -msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:177 -#: c6277b2a7a934f81a91e406ef317a1fb -msgid "and:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:184 -#: 8b3ece04170c447e9b5a8f76374c4c23 -msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." -msgstr "" - -#: ../../src/topics/yaml-guide.md:194 -#: 6b952b7369b447bdb0bf1e9ff8540194 -msgid "Reference" -msgstr "" - -#: ../../src/topics/yaml-guide.md:196 -#: a6024fb7ce664896a6858d5ea3562fb7 -msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/tutorials.po b/locales/pt/LC_MESSAGES/tutorials.po deleted file mode 100644 index f893e551..00000000 --- a/locales/pt/LC_MESSAGES/tutorials.po +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/tutorials.md:1 -#: d32522e2993f4b48a789f46537fa5ebf -msgid "Tutorials" -msgstr "" - -#: ../../src/tutorials.md:5 -#: 63a51dccb29045fd8f78d5e396c6e050 -msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." -msgstr "" - -#: ../../src/tutorials.md:7 -#: cb5f8748a5544be2835467ab07eb7a1c -msgid "Beginner Tutorials" -msgstr "" - -#: ../../src/tutorials.md:9 -#: 685d0cb2faa04703bcef408ecc2b92f4 -msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" -msgstr "" - -#: ../../src/tutorials.md:11 -#: 20f45705145d45fc8420c4119b06a49f -msgid "Advanced Tutorials" -msgstr "" - -#: ../../src/tutorials.md:13 -#: 2bccd19d542d4458a1ba8616236f1840 -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../src/tutorials.md:15 -#: c491c73e4c00476980438ffc79c6e4d3 -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../src/tutorials.md:17 -#: b8485449206542e097584eca7363c8ce -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..3584ce39 --- /dev/null +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -0,0 +1,3820 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Portuguese \n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" + +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "Licenças" + +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." +msgstr "" +"Todo o material instrucional do projeto Common Workflow Language e " +"alterações na estrutura também são disponibilizados sob a [licença Creative " +"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o [texto legal completo da licença CC " +"BY 4.0][cc-by-legal]." + +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "Você tem o direito de:" + +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " +"formato" + +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" + +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "para qualquer fim, mesmo que comercial." + +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" +msgstr "" +"O licenciante não pode revogar estes direitos desde que você respeite os " +"termos da licença." + +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" +"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " +"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " +"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " +"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " +"uso." + +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" +msgstr "" +"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " +"algo que a licença permita. Com o entendimento de que:" + +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." +msgstr "" +"Não tem de cumprir com os termos da licença relativamente a elementos do " +"material que estejam no domínio público ou cuja utilização seja permitida " +"por uma exceção ou limitação que seja aplicável." + +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." +msgstr "" +"Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " +"autorizações necessárias para o uso pretendido. Por exemplo, outros " +"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " +"podem limitar o uso do material." + +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "Software" + +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"Salvo indicação em contrário, os programas de exemplo e outro software " +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" +"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." + +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 +#: eab02dc13915490bb3c9ba744d78b6a7 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +msgid "" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +msgid "" +"The first method involves adding the folder containing your scripts to " +"the `PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +msgid "" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "" + +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +msgid "" +"The second method involves including an input of `type: File` in the " +"script itself:" +msgstr "" + +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +msgid "" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +msgid "" +"Using " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +msgid "" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." +msgstr "" + +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." +msgstr "" + +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +msgid "" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" +msgstr "" + +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +msgid "" +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +msgid "" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "" + +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +msgid "" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +msgid "" +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." +msgstr "" + +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +msgid "" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +msgid "" +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." +msgstr "" + +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +msgid "" +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +msgid "" +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input " +"directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "" +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "" +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows support the creation of FAIR data " +"and adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 +#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "" +"The CWL Specification page in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +msgid "" +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +msgid "" +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +msgid "" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem" +" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " +"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" +"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " +"details on installing WSL2. Your operating system also needs internet " +"access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create " +"and activate a Python virtual environment using the `venv` module, and " +"install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` " +"and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +msgid "" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +msgid "" +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env ` rather than" +" using a hard-coded location, since `/usr/bin/env ` looks for" +" the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +msgid "" +"cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +msgid "" +"The CWL community also maintains a list of editors and viewers: " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: " +"." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models " +"with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for " +"pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +msgid "" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "" +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +msgid "" +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +msgid "" +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +msgid "" +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "" +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +msgid "" +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "" +"For more examples of providing metadata within CWL descriptions, see " +"[the Metadata and Authorship section of this User Guide](../topics" +"/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +msgid "" +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "" +"Each `CommandLineTool` description should focus on a single operation " +"only, even if the (sub)command is capable of more. Don't overcomplicate " +"your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "" +"Custom types should be defined with one external YAML per type definition" +" for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +msgid "" +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +msgid "" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +msgid "" +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +msgid "" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. If a command-line tool is written manually in CWL v1.1+, there is" +" a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " +"Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "" +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f +#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 +#: f924d65fed0c4cb5b0a019b084a8b535 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +msgid "" +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +msgid "" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +msgid "" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +msgid "" +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +msgid "" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number " +"of cores required for the tool to run successfully, as well as details of" +" the version of the software that the description was written for and " +"other useful metadata. These features are discussed further in other " +"chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "" +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains" +" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by " +"the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +msgid "" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 +#: 1acb064f7a4a482aa0174bdc847c6382 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e +#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 +#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +msgid "" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc +#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd +#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 +#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 +#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d +#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f +#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c +#: f760465a49d64d4c8468ad9c4fea62b1 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +msgid "" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +msgid "" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b +#: d555a3d991e344a5a8e1289168d7c6d1 +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c +#: e9fa9430535c424fa3e8be5d460d2ba4 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c +#: b0290d1a477b48119e17cf1fed9d6dff +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 +#: e1cde4aa32c041238ed2596173c6d824 +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf +#: c2a92d3eca7f4ee39cec649170eeea53 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +msgid "" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 +#: 718ceee9973240ec9c100977bbcc8921 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 +#: c07ab08eb75d4528949c56a3d7c12b28 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +msgid "" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +msgid "" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" +" attribute that allows users to load external JavaScript files, or to " +"provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +msgid "" +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +msgid "" +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +msgid "" +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +msgid "" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +msgid "" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*," +" and *null*; complex types are *array* and *record*; in addition there " +"are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "" +"The field `inputBinding` is optional and indicates whether and how the " +"input parameter should appear on the tool's command line. If " +"`inputBinding` is missing, the parameter does not appear on the command " +"line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +msgid "" +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +msgid "" +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +msgid "" +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "" +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +msgid "" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 +#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +msgid "" +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +msgid "" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +msgid "" +"If you use exclusive input parameters combined with expressions, you need" +" to be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as “fasta” (one of the values of the enum), " +"your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +msgid "" +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to a `null` value, which does not match the expected type " +"for the output field (a `string`), resulting in failure when running your" +" workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript" +" expression when using exclusive parameters, or any parameter that allows" +" `null`. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value if none was " +"provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "" +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/) as described in the [Schema Salad specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +msgid "" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like" +" a command line tool or an expression. You can also plot it with the CWL " +"Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx Graphviz directive (this" +" user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +msgid "" +"If you try running it with `cwltool`, the command will fail since " +"`cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +msgid "" +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +msgid "" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +msgid "" +"The `glob` field consists of the name of a file in the output directory. " +"If you don't know name of the file in advance, you can use a wildcard " +"pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +msgid "" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +msgid "" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +msgid "" +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +msgid "" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +msgid "" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +msgid "" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +msgid "" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +msgid "" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +msgid "" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may " +"also help to avoid confusion about which version of a tool the " +"description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a `SoftwareRequirement`, " +"search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "" +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use `InitialWorkDirRequirement` to stage input files into" +" the output directory. In this example, we use a JavaScript expression to" +" extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +msgid "" +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +msgid "" +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +msgid "" +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the " +"container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +msgid "" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that " +"is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +msgid "" +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier " +"examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +msgid "" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "" +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +msgid "" +"This workflow extracts a java source file from a tar file and then " +"compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +msgid "" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a " +"workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +msgid "" +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +msgid "" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +msgid "" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +msgid "" +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +msgid "" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +msgid "" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +msgid "" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +msgid "" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +msgid "" +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +msgid "" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +msgid "" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +msgid "" +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +msgid "" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to " +"the list." +msgstr "" + +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +msgid "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" + diff --git a/locales/setup.pot b/locales/setup.pot deleted file mode 100644 index 961f7927..00000000 --- a/locales/setup.pot +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/setup.md:5 -#: 8395100e210f4ac5a87cc2aeb3d7067c -msgid "This page has moved" -msgstr "" - -#: ../../src/setup.md:9 -#: 1e47ac8e393541d19b9499e307fe69e7 -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." -msgstr "" diff --git a/locales/sphinx.pot b/locales/sphinx.pot index f8448bb7..e7779e0d 100644 --- a/locales/sphinx.pot +++ b/locales/sphinx.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,11 +17,11 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/_templates/sidebar-nav-bs.html:1 -#: 1c343f1abfaa4e14b7f1b645c77c595c +#: d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" msgstr "" #: ../../src/_templates/sidebar-nav-bs.html:3 -#: 3c55f014feb3477889c4df5a158a8804 +#: 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" msgstr "" diff --git a/locales/tutorials.pot b/locales/tutorials.pot deleted file mode 100644 index f989fb64..00000000 --- a/locales/tutorials.pot +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/tutorials.md:1 -#: b963a4be60544dec9a0c34e04aa43371 -msgid "Tutorials" -msgstr "" - -#: ../../src/tutorials.md:5 -#: f9246ba9313948f7b8547822aae2305d -msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." -msgstr "" - -#: ../../src/tutorials.md:7 -#: 9a3d1f4c2d0b438188e84b692f831dc5 -msgid "Beginner Tutorials" -msgstr "" - -#: ../../src/tutorials.md:9 -#: 3c4d6087706b4c90ac69005cebed9adc -msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" -msgstr "" - -#: ../../src/tutorials.md:11 -#: 585908b83f854dd7a28715a4a0f6b1c4 -msgid "Advanced Tutorials" -msgstr "" - -#: ../../src/tutorials.md:13 -#: 8934504b3c924a7d812014c344d58dce -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../src/tutorials.md:15 -#: 0c6b1dbd9f464c698322783bd55d6d6c -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../src/tutorials.md:17 -#: 9a767964b3cb4f619f0b7a7d5d08a97d -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" diff --git a/locales/topics.pot b/locales/user_guide.pot similarity index 57% rename from locales/topics.pot rename to locales/user_guide.pot index 1f40bff2..0a669946 100644 --- a/locales/topics.pot +++ b/locales/user_guide.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -16,274 +16,1273 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 1a006f1604c0405aaa4b93e41edc5184 +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: b61b4d7ed53a436486c1429987a2a21b +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 1bf9e65f1cc249ee93656a53ddd354ca +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 3329dc69c32f4b9092b196d79ae5d0c1 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 -#: a003a3d1de0e4dfe8c777905e55fb9fe -#: e2dc24c683054cd785326de2c3f3f136 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: aca6a0cd24a2411c8cfb1ad392f6d315 +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: bcf37e403eb041269e351d7f98a19587 +#: 9643449da1da46d7861866dce490cbcb msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: c5f68f8a9f34445ebcbd5783f96cb046 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: 4eca90c659ba43158db373d36ee681df +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 -#: 7474eeb128624dc4b1e980dbd0f04ca4 +#: 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 -#: 0c520e5add334609a1afddc559abe19a +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 -#: 125a69207077425fa54f346abc45342d +#: 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 -#: 6ca38a04844c403b836942b2f2f1e1e2 +#: 4dee8504a8e5496081dadc386ab45540 msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 -#: 1da05be0d97d429a84085459ebae54cf +#: 674c238b25e240eda05e22e399f2f78f msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 -#: fb1b2a8c54f34d78ac61dd4b5ffd9063 +#: b651f80f47b4442fbf29454a233697fc msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 -#: a8b1b5caf9904fc5b9eef8c110474b84 +#: 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 -#: 42a5a8cb3b284549aabb817b73ce5810 +#: 3a87a0fb2a364e3da5aaa4017e430b19 msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 -#: eddd878eb0324851997de2a69bcbb43f +#: ecf2b9c0b1664afe9c4e180610610021 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 -#: b05c8ff667174f6798feb811cdd3c41d +#: e24cb13d98014e558b6a6946758359e0 msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 -#: 9dc16d1a6b0546cead6967f5e9b1526a +#: f2b14a92374e449d9fb1e8c86ae0dd61 msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 -#: b8bf85e8523a4553a58face698aa863b +#: 928e3df7ca3e479ca6474a8e72cf36eb msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" #: ../../src/topics/best-practices.md:55 -#: 6fb9a1a2ffe14f39b01af8736a9698eb +#: d355f035676446c88b028f327aeb4829 msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 -#: 0a935aa93e554c0987af7349f94ccd3a +#: 339b852df24242189d6efcd2898a3396 msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 -#: cadb5982a13e4621807ad976cf9b1524 +#: 3ef57e6862f240bebcf193a52397af0a msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." msgstr "" #: ../../src/topics/best-practices.md:69 -#: bd7ab2cc6234458181e9b99938eba824 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 -#: 7beb72d7dd5a405f9be8b6fb6a310f10 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "Custom types should be defined with one external YAML per type definition for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 -#: e5942c4d4b4d4e1a8c0e9ed3da80960e +#: c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 -#: 5a5dbc9b9d2242ba8d15ecf39123694b +#: fae385da16aa443da996fa23ac03d6ae msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." msgstr "" #: ../../src/topics/best-practices.md:82 -#: dd3016d33b7d4340a09a7c8e5aec4f0b +#: 92430be71ecc40e18bbbb80d5576c613 msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." msgstr "" #: ../../src/topics/best-practices.md:85 -#: 45d110a660b348f58a1107476df18cee +#: 387d83db81024f65aa9a890c2d07874a msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 -#: 97a5b141592e4415aa4acef4f6228045 +#: d8e2280a75a74916a1630afaa2fe2ae3 msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 -#: 85f624f8879348e8bb368ec2749925bf +#: f1c1340f9745458980e0fbd641738687 msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 -#: 20a851dae87941c7975173ed9cd1e360 +#: 5424e5472c3d466fa2a3d2022c6cb475 msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 -#: bb19e1b689564a11bb9e72d5f82cf3d9 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 -#: b14199173add4585be62c4e8278b49f4 +#: 12f57b2ba76b492abe1816e06bfb1417 msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 -#: 9e883f18843a41d7b10102bc11655839 +#: e1f657a46ce94a0d83671540e2cc2dab msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 -#: fe3a1468aa864742b92c6e8f4ff1a38f +#: abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 -#: e9dbf14538404cceb02507962a173ee8 +#: 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 -#: a650a7dacbb547db97158a8ac2c9d0dc +#: a5eacdbc9aa142c890b177869da4143d msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 -#: 501217b98c424a319e70ef963de506f6 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 -#: 7143809471454e00880ad8faaf43f141 +#: e3bdaceae8784ab0807b2cf356a98580 msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 -#: 7ad86e42708a465980a56f735644de9f +#: ed521ac365db4a6ba5a1051fbaa2932e msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a8f29712337b4d1daf3190cc8973b8f7 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 534843389795437991fad0b5a702b483 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2052170aa2624feeb2253477895aa838 +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d5ed098a33ae4c1ab2a30eba483ecc6f +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 2b55c028602f41babb6e535b425ba5dc +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 47408669ae8b4432a43d763dba12a466 +#: 9454a330b9324744b89448f2694b1b03 msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: b2e5e925971849a09a8d54d9c649a32d +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "To test the above CWL tool, use this job to provide the input value `message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 #: ../../src/topics/outputs.md:77 -#: 9a39f53bdcc94904a90effb507767645 -#: f296149bf19947528b134b01a4d7ce81 -#: 965fa9769dea4ac9b3dd252e0a3bc603 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 79d8ea95f0c34585a3dec4f83453de60 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 4afab699247b4f619702c4086eb1b6f3 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 693b91423f004118b806bb8ee7952eaf +#: 1741804e33aa43ce88b4320c11ae5973 msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." msgstr "" @@ -292,193 +1291,193 @@ msgstr "" #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 #: ../../src/topics/workflows.md:198 -#: e4a25f04a6fa4001bb1e58cb775cdd84 -#: c771cbc64607412a9164c28934e9e0f5 -#: bdd5a3eac1e3436496e05a13c4f06073 -#: 1e62b28ef0184081b4d6e53f34b753e1 -#: 33edd6deb38740ed98466b6e023b0393 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/custom-types.md:1 -#: a3a8bcdfadc4484ea5e4c13a25b2da85 +#: cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 -#: 7800570badf149b3bb1f81d470dbf4be +#: 67573252cc064b27ab13eebc468ac58a msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 -#: 496313f8ec67403ca78ba66130df261e +#: 73e68b3af9cf41338d843c0c40e50cdc msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 -#: f7cc0d1ac5dd47658093cd0360f90329 +#: ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 -#: 0d563f15c1cc4484b6b2955bdc70e1a9 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 -#: 06425b6cdaf244b198fdde312e864190 +#: a999b1acda2641598086648c64aa3831 msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 -#: 26c3762a637a4492a6c12588544cb0a7 +#: f8c12a58cb0b46a488823c6ae95f25ea msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 -#: 221433aa39104642af8afb70ebd08576 +#: f25a63e0926d4932bbe64b2e4bdabf9e msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 -#: 197bf36a5d7741b3a9ac56c19d4a7686 +#: b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 -#: d9249cf936d24ab3b3fc508d17d94745 +#: fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 -#: 2ff7ce81cd3a492a8549484ba8d1f135 +#: d718630a296545f3a989c8c71e9ddc77 msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 -#: 2bb45c56e2fc49e094be2cf742222e67 +#: 9a97acd430064710bcdf76edbd9f711c msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 -#: e2a4a531c6164f15bc711618db058f52 +#: 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 -#: 90f7960bd24d4481bd05da1d61ef146b +#: 3c821c9c46d841ec89b8a5b1018f3af8 msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 -#: a51814548e44467c841ca65b2ac63b2c +#: bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 -#: fa13573d9c174ca1accf20a449e5984f +#: 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 -#: f2912b17e3be47b0b7186efdb4c4010f +#: 48deb71f361a43e48a56ed483075bca8 msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 -#: 4d9c95d18c1a4880845e7194a99aed3c +#: 716b56506ca7470299899c5d820a9ea2 msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 -#: c656a020978f465b85b8754346ea5b6d +#: b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 -#: ff4d0b6bc0264650a21adc811b8caf4c +#: 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 -#: 77e00be2c0984465af5bf501b4031f32 +#: e3ecac0a8e604f2b98a2a12b0579990a msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 -#: 3d7b7238be974c0487f219cb5c030149 +#: c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 -#: 03a62f421c8241779c0e79f4dbad96cc +#: 007a345b4bad49cf996c4301b8386473 msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 -#: 31a85893835748339b6c84fb98fde14b +#: 2edbd398eadb458b8eacd5fa5496f0a2 msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 -#: 08d9ecd7d3294c5b9dd4db228a1d8d5b +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 -#: d94d6c69aaa64edd9c75624286713c2e +#: efb5fd14988c4e2a8f834ee5369d4102 msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 -#: 020019b8aedb494fad022d19b7106f83 +#: e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 -#: a6b66e0fc0de442e8f72f0d0c37c7e8c +#: 276f688ba7cc471a842f085ca852b1d9 msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 -#: 48b7d9ddac2940c0815e5c855bfca6d9 +#: ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 -#: 894b843f9c064d56913e1a8c48093314 +#: 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 -#: 2319e845caee41a3bc5888c3f1fc28d1 +#: 8b70a1ad70514039b97164fa630c12e4 msgid "Note that requirements can be provided with the map syntax, as in the example above:" msgstr "" #: ../../src/topics/expressions.md:54 -#: 9ea661d749db428eacd2207dc7a01e36 +#: 2f28ab412d2843ffa5f14acdc01fc732 msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 -#: 4ff76250f28144a4a9d8807a9d4ed3b4 +#: d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 -#: 7f9f2df357a740feb89bfbcc44ff4d61 +#: cbec9277b5004e50af2728cbda0df740 msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 -#: 12633ed841dd447a8753faeb4f9e5096 +#: e259f55f8000479bbd8009e25cf0ca6c msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 -#: 4db64481d38c4896a85a8f6038a9931c -#: 1b4ff3eeddde4a9a8018235b9d706567 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 msgid "`arguments`" msgstr "" @@ -488,38 +1487,38 @@ msgstr "" #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 #: ../../src/topics/parameter-references.md:86 -#: 50547062ee404e2ebeae7eeb54b9de4b -#: 88933bc02fa84412944673c3463af1ad -#: 4fde39d8a50e49f09bd28a8598760682 -#: b933cbf847d94c5fb8471918ce8cb4ad -#: 0145c520b85a4bc29302bb654f08f23b -#: a3e322ac8a0d4e2ba9bfbece6b5ae64b +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 -#: d9b166225120432f9a2bf2cc7b6ffdfe -#: 28f8ec2fc5c0436aaba19e9d479aa466 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 -#: b866a0e5897e44329714f4c55eb20d2e -#: e64b5027878346d79f9ab52b3d3b916e +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 -#: ed38ec582fbb48ff9f9cffa7962ef515 -#: 6cc0788250624fd69fa4e3881191ab7f +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 -#: 17eefb5f38534c1b87116c3a061ea1bb +#: 8210b36347a749889450529ecdf4ff0e msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" @@ -531,14 +1530,14 @@ msgstr "" #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 #: ../../src/topics/parameter-references.md:90 -#: ce0572fc81b343e6991c88ca0195149a -#: f8b77ad06ebe43d7b03b2135737902e2 -#: c7953486c99d4c7898c0155a6085dfd5 -#: 46d99b1f7f0747479bd58486cf7941d2 -#: cd0a797b3619404f964ba9efb33756bd -#: 528cd5e0d3994230b719fbfb39b1f13e -#: 324241aae8ff4505ab0467f2a7f27fe2 -#: f4086b1ad2e44c2b9de2636f8bc1eb90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -550,1534 +1549,1574 @@ msgstr "" #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 #: ../../src/topics/parameter-references.md:91 -#: 764d7cf3fb5444d58dc9e0eb6b8fc649 -#: 0450a4b8de3046998d30ce1f09c10daf -#: fd6bf79cbb694dbb89e8731aed733e6c -#: e6048a64e09d46099132fee40a2e0644 -#: 9512391eb96440bd8e48c3754821e3d0 -#: 3e8669bf4a6741f9aba170864b251dac -#: a02ede726d3f4eec9602f72054c0d963 -#: 4ed593dfc39246789f1e4ecdc742323b +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 -#: 304de40206cb43d7b651245586cfa55b +#: 23088850ad02459696f6bbd385109aac msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 -#: 7855471c93bc44aabb1a2b9beb52b56a +#: f02257a822ad46ac93c5981531cc85d5 msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 -#: f0452f324bfa451f9f3264f9a55e0e5d +#: 989a1c4aaa1143be9f53b90cd8b6d500 msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 -#: 6dc476cf8689465ea3993f49a9eead75 -#: 4dfc0be21065471d91def850bc2528fb +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 -#: 09d69778a89044099b3e5d7cf02471bb -#: e3077bdff0dc4dfdae60eb60f3d66d8b +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 -#: b28843f7b57745db9cb3648ef23fda0f -#: 6a745fa266dd42849c95410775b690e0 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 -#: be00ed49197f48ecb7cb244ecc214369 +#: d289541e460147aa933f7878996f8649 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 -#: 90ad2b27f97b4ca089cf23a073cdf17b -#: 38d062892cb04bc7bbf0b56f263079e1 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 -#: c2d2756d617743b886c67160c2face21 +#: 81b4d1f23a3642bfa9bb395b94260cd1 msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 -#: 8681600183d1429cbd1b15639e1a222f -#: 1d49cd7337004fc38f4e8e9aa4270481 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 -#: 24b7f85116cc4d2f904600555aa19b8b -#: c401a68b4f384d3eb13ab3e89a4a7195 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 -#: 0e1f9d22d0714bc5b80e420f63b34cff +#: f495da32f05a4a5ba9539be0a54c1a59 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 -#: 5fed95f16aaf42d4b41c569d9546b7f0 +#: bdb4c68a175047ddbe141ca24960127f msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 -#: b539a931f31d4cfe9d72aa5800115fb2 -#: 48e497c024bc4c38a86dd027aaa4fd2d +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 -#: be638c80121948c99cc9fdb67a5d291e -#: 1fd8fe769ba8497eb8a9520af91ea33e +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 -#: b5f3ad78a233411c97520c1fffdec18f -#: 7854e46c7fd24afd9c1942808521bee1 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 -#: 211bd57896494fca9ea8aa2fc142eea2 -#: 28ec0718d3114bfdaae4524c009da944 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 -#: c6a421f7a0214d89958d4c258b58aac8 -#: 07bd0bc74ad74187bdc24c26041467ca +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 -#: 3afc146cde2e47d5b52e62fbd1f37426 -#: 2225f5acb44a4ce0ad16be5c4f6cba48 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 -#: 9acd61d4d67a4d2c82171a79462fb458 -#: cd7e7fea3b8346268618c31b70581326 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 140e449e46a84e3ca1a604176e583f44 -#: 3d8b717d4568458eb53b0b91695b3de8 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 -#: 76f35653e34b433d8e9fedc6d12ce856 +#: 97b61352363f47cb890e8937c5613fa3 msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 1a2edf61fda8404689e3c0a7389d7d02 -#: 3bced6d84fa6453195be82dbc6d7ec83 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 -#: 0b5aceb6c9d24bd9bfe95cc04fdc61ad +#: 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3523cc46c6324fca9053d6b1dd8c7495 -#: 21eee2c1cb6b430486446d223dcca0eb +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: b4f126415048402ca388c4c63f34ebe5 -#: fdf588cf8cd34d60bfb6cece3ef859e0 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 1b494245c14e4e22918c43ad9f26cc8d -#: df4d781178f2465b8a421651bdd2f66f +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 -#: a88008a23ede4ea49ffcaccba7029d31 +#: 0bc424ef2ca346099f29b937379908a0 msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: a256b51f1e944b7d9659b945d8ab05c9 -#: 23bbd631e73147e3af561eb4a14d2d6c +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 -#: a446842e26e44781ad10cdaad73bc49d +#: 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 -#: 3cc10263ab2f4dbfb6ccb12612b89cf1 +#: 29b73e1dd72744f68377f0a38c10f062 msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 -#: 995f6af5fc244293b34f5d840f01ce1c +#: 38a2afaf4a6c4d04909af22c93f2808d msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 -#: b556a1d134764505aa25003d79a53e88 +#: cd74f34b21af4de9be96fd897efc469b msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 -#: ad23da5452bd46248606f6799ce93db0 +#: f12e371f3f1a4b0cb2cff9800352d48c msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 -#: c63036ac68344465af6c7756be00b60b +#: 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 -#: 2f7f270b0ac24f2f8df506f5dde72cf7 +#: 8f0e8f050e334ac08334e9215e1dcf61 msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 -#: f49272e5e4c1491eb59c79d2dfb88a86 +#: 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 -#: 8b50c892d36d4d178ec4268c7c13887d +#: 7a6be0005a6441feb67f036d005d7885 msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 -#: 9d22117a6f5a434593d5144bf824999f +#: ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 -#: 4fbc454a144a466b9dd7ff74903fc5fb +#: 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 -#: 281b129a76a24b0a818092acd1038757 +#: 06635145b441418aaae84dc804f3d6ac msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 -#: 4dda6ca233d54c12b6ddceabae198495 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 -#: 59d87fecfd7f4438b68e0bcdecdcfb46 +#: 04eaf1f7c630450db318dcd8b7626e15 msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 -#: 0f7e33673ad349e5ad41a078032e5806 +#: c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 -#: 77a7141f897048139ef3785b5f870b43 +#: 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 -#: 14ed183bc7e346598921445c0dea11e0 +#: fd4579a3c9844492b314b5c3c1775fc7 msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 -#: 9406d05bf0ed4774af50fd66d24aa299 +#: 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 -#: f5a9048ef9e047528c291505ef9a2c12 +#: e024bcb70e04412e90e1838426d1b69a msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 -#: 51e8c5a231eb45fb8c15be49b37a7bff +#: a3db21c0b3114802a8a5b610e252ef13 msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 -#: 860a6f01ebac45938abd220758fd1109 +#: 0f5bc8520d6a4dafa37c65343da9702a msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 -#: 32155f96d47f4d76998a401aa9e9591f +#: 5cb830da47464a8b9c3950983fa4d56f msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 -#: a62bbb9251794560ace0e52be3d9ebd3 +#: 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: e301af8f675444c69cfb6b578c02fdc7 -#: 3da1dec243994409bd764b133d4fc243 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 -#: 82c6efcfb5d5410eb316399b7c4f638e +#: 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 -#: 29c3d25c657340a1bab7123a166b78c2 +#: a2ce43b391864e8bbde16328cc19b32b msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 -#: ef8e7bd7e944429da78474d2fc5e0348 +#: aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 -#: 08dd50bc6a5942ec8f3b6c201fc4497f +#: 56ee4dcfff6141d5bef80eb96559876d msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 -#: 78c51215a68f40b280cc21d0e412eacf +#: 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 -#: bb8e2203374a4ae7b833c543ecc563b0 +#: 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 -#: f34aa1e4d08944c497602b2a35f38a50 +#: d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 -#: 2932972efc94447987b02a7707c62656 +#: 96671c56523c4ea9992fb5dfcfa6490e msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 -#: 968f4e83c511425d8faf4c8d0f18097e +#: bcc6246742cb46bfb185e415c4a3431a msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 -#: 2eb89bdbaee04a899a961a7b87f0aef1 +#: 86dce36de687449c88fb5eb9d64eb045 msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 -#: 3781fc7cd22d48bdb5aa4abc0c93b06f +#: cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 -#: f4af4a85efb243728d2ee783393dce14 +#: 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 -#: dbf8350f003a46b984b7432160e6def5 +#: c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 -#: db2993fe83814747a52f9db0b2fcc81e +#: dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 -#: 39fe18bf5d4b4539b2f98e3bf0feea2a +#: 36ab1d9edafc4831bb1bca5f123b04b0 msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 -#: 58e7b0e7d0a149498e846dd2790c0eee +#: 7dc630ea86464b1dba3a4e5079260b3b msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." msgstr "" #: ../../src/topics/inputs.md:44 -#: 4b78c5437904492ea3e692372d2fc163 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 -#: f2626686125d4ec29fb2338373b54c93 +#: 651e032007ea4a119d20c820bb61f86b msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." msgstr "" #: ../../src/topics/inputs.md:53 -#: 46327aca33cb49d1ba61149e94884991 +#: 0b056dde9e87428996e47870b12119da msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" msgstr "" #: ../../src/topics/inputs.md:64 -#: 43f2e7020da94f77bce4e1f852ab11f1 +#: 628124a1670b4b058bb0fb6e495a099c msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" msgstr "" #: ../../src/topics/inputs.md:70 -#: 8342aa3f84624325aff8f7f4de788187 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 -#: 2d54f11f99b245e5b2802b984bc024a5 +#: ec2adb3912bc46e28891229e9e0d9a1c msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 -#: 83a357dc06b343549876035b03b8c5d1 +#: a519be60726a44af9941fdce04735353 msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." msgstr "" #: ../../src/topics/inputs.md:109 -#: 0461538fa12a44c5a9d230a928ae930d +#: cb8fc8c4c79e467eac5fab4ca685201e msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 -#: 2b2552958f404447b711d09650d22395 +#: a26cc105716f47cb807174c9003153b0 msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 -#: 82c97e60f8634bd6b4d3e88524722412 +#: cc159dd5fe5748caac838862f5b8c4d1 msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 -#: 0ae1393a80e94b899023c29f4af6084b +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." msgstr "" #: ../../src/topics/inputs.md:142 -#: 74339f624bba49d6b68e1dfc4724f673 +#: 6812698e9ad84d3385de5e88e9dde0b3 msgid "The `baseCommand` field will always appear in the final command line before the parameters." msgstr "" #: ../../src/topics/inputs.md:146 -#: 3a4473864ec04d2e9a0d550b2051f717 +#: 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 -#: 575661b36a2040699956f897bd6cc614 +#: d1f02be278754267893dfce5a940997d msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 -#: 3d18a704f5a94e2889e847c32a78aaab +#: 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 -#: fceca2b53d0646b2ae9f1cf9dbefe2fc +#: 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 #: ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 -#: cba49054785b4ec2a7acd3aaa2e165d8 -#: 647c0e302af841d7b1789447281d7344 -#: d23de44d5d5b4bc7b32f3726afa97500 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/inputs.md:178 -#: dd867685663f4728b9fbe446a9b14a3d +#: 75d59e395c66416cae9b352db5081516 msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 -#: 67bf2c2cbbc44f6eb870af3a3a852676 +#: 874c6f19abbf45d7ab7d30a378c4048d msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 -#: 94d66455bfd04697814495e116176ffe +#: 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 -#: 39a9d3583f29451d8035158c54266ed6 +#: dea0d4b681f94e73b13965dcfe75cf7d msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 -#: eba6af5cf8224d198fc04f090362307c +#: ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 -#: b48377cceff342e793e982c9fa2095d3 +#: d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 -#: b64ef70d944c461b8ec7219e14e47795 +#: 750474486a84482292eeba45f118287f msgid "In the first example, you can't provide `itemA` without also providing `itemB`." msgstr "" #: ../../src/topics/inputs.md:217 -#: 73cd08a2226f4cbe99fcde2d3636d640 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 -#: 3c33bffa2c574ef888b041c1e6735b8e +#: 1eb0e39bb6d04b8cab300f44a79f3add msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 -#: 23bd067b32724dad9daba1e924757d86 +#: bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 -#: 1be92fc3d0b44ea089273cfcd47318ef +#: 4b2ab812f62c4f949dd25c8527f2411c msgid "In the third example, only `itemD` is provided, so it appears on the command line." msgstr "" #: ../../src/topics/inputs.md:255 -#: 3d08125883b74f49bba042ed58d34648 +#: b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 -#: 7636c7e8b6e04d7089ba1cb10c4c475d +#: 2c3b884cb1c54521900cc90782e8a58d msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 -#: e1c95ce96db043eb86ff9b3ae595017b +#: a1073b6306044dffb414319ae01f68bb msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." msgstr "" #: ../../src/topics/inputs.md:265 -#: e6588c4b8fa64959b2dcac52403a6415 +#: 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 -#: e7f85cb69a5342889525fbb81b44c86c +#: 9a1d92334685449386dfa3b3a899ed48 msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 -#: 71756719e0274300a839b38c8b4ea986 +#: fb623af4c480411b8fde28d01c981411 msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 -#: 88bf75fce3064eaf823b5d88be0ce053 +#: e98e165f6bba40809c90473d72f9d592 msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 60374713dea84fff92b89b4ebaa8d7ac +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: 7616d5ea746f47ac972183150b97e8b0 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 0ca022c095334ec4a9fe41cb732e11a1 +#: 80af387fe3ff4e2da999903385bd602b msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 1c807f8fd1c540ae8802092fbcec7159 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: c51956eb3ece432ea0ed5b676b2f037a +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: 45e6ab3a53b94f5b90136d68c1c0e479 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 7e05dc23d6be4428b4a414b3a65c4727 +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 -#: 96e7266ef25b429da42337c3582cc201 +#: 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 -#: 9cb6959a877f4590bccb977416753410 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." msgstr "" #: ../../src/topics/operations.md:7 -#: 7b54a3cd870d4b038dff685064bbca1a +#: 5565c1b2d8a349169a305a9b26b4574d msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 -#: 0d661c96ac2d41ee94641a397aa3bdf7 +#: 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 -#: 94d39b79923a4a65b1a6ce5c464528c6 +#: 88160cef4cfa4add9020aa89511a5749 msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 -#: 56801121f70b4cb2ab6207e254ec8bbf +#: 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 -#: 42418ff882d44c1b9584fb9f7887f744 +#: 730ba1434a1445ae847ec6153b6a3b72 msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 -#: 1118de96d202444d9bb4db74ebe4792d +#: 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 -#: aca51d371db84aa79418c79a18310055 +#: a25d0b1e13324b40a6b8fcd227948c4f msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 -#: 3473e6d2942e4546a2c1590edeb502f8 +#: da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 -#: c210ad12f61047b68302e67da9b5dae0 +#: 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 -#: 1c15cff5a4614d88a62c8d2df97029fc +#: d661df070e3040869da412d07a71f716 msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/outputs.md:10 -#: 4beae917368545688c01a4a929685cae +#: a11585474d3849cca5467512ed964743 msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 -#: 4f4f63b7107e4dc194760802c4581c2a +#: 2682f9ca8e604a0c9986f7746fdec960 msgid "The following example demonstrates how to return a file that has been extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 -#: d942035c4c914ccb9de75836af9761c7 +#: 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 -#: 0e9064cf55fe43588053d37100634538 +#: 22447a560f6f4317bf67bd7c4336126c msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" msgstr "" #: ../../src/topics/outputs.md:26 -#: aa1dcfc618e74a53b3c579380e5e1558 +#: f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 -#: 3ec3f4a2d1c547b18780db17fbff060c +#: ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 -#: 21e598983ce94d22b9d40a77577a6608 +#: dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 -#: 62f79a2c055b455d9626ca5a18d1bd72 +#: 52703d6b7f914097934bfad13663abeb msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/outputs.md:51 -#: 19c2b9b13bcc480aa7474301422faab3 +#: 5e1c79df657d4a6e84e055dd6b300a5d msgid "The field `outputBinding` describes how to set the value of each output parameter." msgstr "" #: ../../src/topics/outputs.md:62 -#: 17bb520489a74f64b76ddbe2ffedcb5e +#: 329d2809dfae4f90bc638f5f03a47ee3 msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 -#: 9e2b97aa3bfe4eae8524b325bf2ea3f1 +#: 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 -#: 028c844ef208450f994b3949210ca996 +#: c6bcf7c6a8774dd6be41cc775848c3b8 msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 -#: 2b758e44e4be4fdf89a5897385db6c59 +#: 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 -#: 16395173b7ee468f85ee8450493504de +#: 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 -#: 51e2e929dadc41a78cea98f779e2e2a3 +#: 9647019d8c37466886e7aab6f176634d msgid "You can also capture multiple output files into an array of files using `glob`." msgstr "" #: ../../src/topics/outputs.md:93 -#: b757d4b151ef46fa96897bf00a0d9ab4 +#: b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 -#: 2f2f46a81e8946bf8a9b48a5956c82f8 +#: cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 -#: 75177c797c704385bfa5ce86e03266c9 +#: cc067051f22f433bbece08f60933e002 msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 -#: 4d05d16c3cb74eb291da7586fa859b90 +#: a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 -#: c115b7ed044346d6a9c4c06306ee82d8 +#: dbfe2c1123144316aa026374b0f353d3 msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 -#: 8f83261e3e91424b9a3c38280c643f02 +#: 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 -#: 269af269348e4da5b93cb25dcd10374a +#: 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 -#: c376ab464fec4ee78a33d42dfed5dc1c +#: 074cf5d912854d8c864607cc24b15302 msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 -#: 53d468d14703494699478e6847d82e34 +#: 0290af3e3cbb4b32b0450c8771f3bf95 msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 -#: 32bd7abe387e4999a0864f6e6a48e435 +#: b54240bb94f746bba7511633aa969db0 msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 -#: 0712e952fe2442daa9ceb0cee79a3ebf +#: 8b70a072aa87414c88e89a3e19af0a51 msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 -#: ef2b8db0c8d64e41b839b47aae34d0ec +#: eea20f89c45f424a888178df53713b28 msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 -#: f9f45dcc2bcb4fd1a1021d2843137fa3 +#: cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 -#: 4ffbc016a5344e6e9272793d921e4900 +#: 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 -#: 7118718b98c5488c9d9a54e5ec84c055 +#: 7647e0229a924f988cf02b7812a55c06 msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 -#: 20fe8fa105a84171972722158bafbc0d +#: 9d663249666045618a0d3acddb85a9a9 msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 -#: 836fa2a818854cf9af13d674f5bb859c +#: 5fed4984f6784347b4cbe0630b1dd2c2 msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 -#: 5d56e1ac063d48c2b140a72db9f78540 +#: dbf6153cd02542a6a01c172803122b7f msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 -#: 0166655553ac4d8fb868138936176986 +#: b6250cf6fa8a4a0c94b33302e0decca5 msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 -#: e43fe4a9340b458786c51499c75b5556 +#: fa6ca3bbc6784380a03a950a6f49a180 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 -#: 0ba13966a1364d4e9992b5cfeb6871d1 +#: b92b516e537a4773ad67b4af586e7a25 msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 -#: feb8bce610be4a3a92053f2e2e5aab76 +#: 467a701228504d06b971b79a59c69064 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 -#: 0f5fd76c57e7412097b4ebdeb074f2fd +#: 2634f989eb304009a8568d70ed42786c msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: b645dd17256543b0a42d231171140c95 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: c8d5743769bd4fee93f77a52ba318883 +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: af6cbb89b7a84bf78b7443b6746484fe +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: ad9394b163a94340975a66ea2bba7094 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: 677bce1f24f449beb2bac5ed8469f624 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 4c0d14a24b354feabf4b6ad4852f9543 +#: 574d93d1d592458a985f259519c036cb msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: d407e5c9aa9043b0b6ab234348467db0 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "In this example, the software requirement being described is InterProScan version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f06b60c926204ca88b4355803f1b7b11 +#: 02e40154eac74ecc98d0447d03475b44 msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 0a7c19b054d2400abd327736b6829670 +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 -#: cd1773f336544b3688bc76c28e9d1f79 +#: b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 -#: 6b7bbca601f04f7183bc75988bd6db13 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 -#: 069d1dd1f03f4cd79e44f2dcd890b531 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 -#: 4924b1a69a5f48b0aa6af943b40ffc68 +#: 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 -#: e100d8d8f23c4d6996ac59c5ad68acf0 +#: fbe0c65b444441f785d0054176d036a6 msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 -#: a87dfd0dc0274ff4b34354678f2d49d2 +#: 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 -#: 772078ff701a477cae9acb8dda16ef1f +#: 9a710602e00c4934ae3a3b471aa68458 msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 -#: d2d67048e93e40c4820b805f1ba28cc9 +#: 21b5be7270a14f0987240c81d1ec879b msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 -#: 580477152be041a8ae5c5f546ecbf21d +#: 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 -#: 05f8faea082b4fb9b9c22b8eff7eb356 +#: cfe9d8241fe84bd5b74042a5625d933f msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 -#: 4c107fb18fb34c2dba7743118c51e8c8 +#: 764d933cc4da446abd8dd8f913f05dac msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 -#: 729ea19aa03b49bdadccc6e6f0d2e7d9 +#: c93efc6d4e004859981ee7f5fa28ed03 msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 -#: e849cda9fb1d4a48b5b1f9a4e44213a1 +#: 546601da44cb49bd9611b1c85807fd90 msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 -#: bfc20f529d2d4797b87c63c7b2c05e91 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 -#: 761a900275a044f28ddcebe509a4637a +#: eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 -#: 59af21cf1ee848e993563ad47f7bb248 +#: 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 -#: d711ce1ccdcf427aba25a2ab3d11165d +#: e07f33d01b804663a25ffb08aad74821 msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." msgstr "" #: ../../src/topics/using-containers.md:15 -#: eaaaa01fe0894f479a42a9c3ce199819 +#: 7a644506619a4f08958ec7d4540cd557 msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 -#: 92489f186e3f449295b0dc864ebf17f7 +#: b5195b7d8eaa419fb2b90cb33a57783a msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 -#: 1360c3a2d43b48f3b3e1153bb26b3f30 +#: 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 -#: 2e993e21a3624910b4282bd088694fec +#: 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 -#: df5b4b041dc944be8580e43012339168 +#: 2713594c937d4c528fc8d04d9e9819ed msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 -#: 92ac2766d118428ea148094c022a8b0d +#: cf94c1424fc2413c85647fd1ee73d951 msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 -#: e4ddaca03eb449eabbf2d2fce752c367 +#: dc0452107c604e29bdf32bb289fe5db8 msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 -#: 0bc50411a4b748d8864305070d11a304 +#: 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 -#: 74453227279a46cea3644f3ca7df61b9 +#: 483181f498fc4d968b5fe6ef427709f7 msgid "Notice the CWL runner has constructed a Docker command line to run the script." msgstr "" #: ../../src/topics/using-containers.md:72 -#: 75ce3269886645eda46a6575fca186eb +#: 7487485d6aa4458089a4b4bdf107ea64 msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 -#: 1e7e5b46017a476a80d57ab7eb614758 +#: 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 -#: 1ee41e983ca14a959caa199b1ce12700 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" #: ../../src/topics/workflows.md:13 -#: 070e6a00d09e4675b89afec5d066aec1 +#: f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 -#: fd37ebe3aad9473891cc764a47363f8e +#: 5870ac44e4c24b8daf5f06c49f95ce04 msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 -#: 85176099018c4ae19bed1261e92e6e92 +#: a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 -#: 952e9a347f444ef496fa0cdf00160ffd +#: 93188ed43ee949cc98b3ea679ce14feb msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 -#: 2b5ad46ca3024ce1b37e1c92a820aabf +#: 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 -#: ea17d17cd08b4c40a842598c8521af56 +#: 1cc17ad26e9c474b895ba5cd20c8b66a msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 -#: 6e5f1266974d4a32995aaa69fbbfd648 +#: 24aca0bea4d94e3593b844cf0586cffe msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 -#: 20be823f70c348bbaad6bfc8b88201a9 +#: 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 -#: 02311e5310cb49d19bf2998513f73124 +#: 9c56528acd5f49deb139e034dfbfac7c msgid "This workflow extracts a java source file from a tar file and then compiles it." msgstr "" #: ../../src/topics/workflows.md:170 -#: ca6e4a3fe04145a9a21cc43cc53a07bc +#: 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 #: ../../src/topics/workflows.md:180 -#: 75452467551a46a2b2b3685f1a4aae0d -#: 93efa8e941a7427f949afc794ed16e75 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 -#: 39beed65cb114bd78c79aa4a5d6f4398 +#: a2dd833fdca4443181648e41051a5232 msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 -#: dd880d0589fe45dbaf9b7d799402f158 +#: 7e40cc9f9e1341c195e843c009575b94 msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" msgstr "" #: ../../src/topics/workflows.md:185 -#: 671d0bd54bb147518c35f0844a76c61d +#: 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 -#: 66de58a51b034f6a8d5dbe742046f817 +#: 6fcf8ad3d1bd49afa4a105622437bd59 msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 -#: 564e68d58e364715aa72183cb16b3d72 +#: 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 -#: 558739ceb3fe40de8ea87ff1e7d3fe9d +#: def35d6021394def80a53ae49a2cdbde msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 -#: fdc601ee1aa54e1f84cd00eed2e44e52 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 -#: e4f4a76cee96473d9da3bc1c9e35324a +#: c84d4450bc6a475dbf34e0b22cea9130 msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 -#: d524ed5f1e964688af9d74eef8e46e04 +#: cca9665f6daa44b49233baf34ab9fcc7 msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." msgstr "" #: ../../src/topics/workflows.md:256 -#: c646e4714d78437fb450127b119fbd70 +#: 547edbf5fa424b8286cc21674ff159b0 msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 -#: 8351ddfd726c40159d81c017ef221606 +#: 7ca248888b9d484cb544cd76ba538662 msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 -#: 456794c7274f4654b54aae8d4073a2df +#: ae6b240718104380b08db5552d7355ea msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 -#: 6485e8d6814144d1bcbe66bfe4fcbdb9 +#: e5a8b7f84be64020b191099f3fad30ed msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 -#: a2b9e47cc923466f8bd2fbc4b33fc4fa +#: f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 -#: 698cc640807247fd8d512c59ce32ee48 +#: 12a06d8358534102b202965d4258c18e msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 -#: dd658e10da624918b7dec1ea18bbf432 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" msgstr "" #: ../../src/topics/workflows.md:300 -#: f6bd95a4fbc44ffdbfec7fcac90f6bb6 +#: 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 -#: ac7b02a71d3544848d4fb539b2a4f115 +#: b7f93705e5b8416696be01850072e8c0 msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 -#: 4380dbd066a44102a71c7e42ca7de8d8 +#: e87045829b344089ab59dc27063ddd7a msgid "\"Visualization \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 -#: da946c9d59f44fb995daa6aadc44031d +#: 42ef2f145b824d69b63abc1da175c216 msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 -#: 7c73bc555f604afd8491c1619d6905eb +#: c61cedf543664d388183e04b3939cc39 msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." msgstr "" #: ../../src/topics/workflows.md:341 -#: e79ce424410e4682881fe14326955a14 +#: 9e39e3f1501c4fcaab3e8962e090f6be msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 -#: be8d2b89052e4f9d96ff2bf15526e229 +#: 03e2f767c4da461982fc3c0f3ba94762 msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" #: ../../src/topics/workflows.md:366 -#: 967b064ec4284d0aaf374509915497e1 +#: 3bea5822b8694e2aa32c446e1c54a045 msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 -#: 02d667b922264f8e8021844df0085578 +#: 426023bd6e3a471cbb30dbda3d6f9e57 msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 -#: db8734e07541495188d9ee97eaaaeff3 +#: 0d498cd4caf54c15891ca1afe58e2727 msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 -#: 22542da60ac24403827e2e2a14595770 +#: b2d75045e02741b4850f5ff1243f7858 msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." msgstr "" #: ../../src/topics/workflows.md:398 -#: d10f35716f9c4b878da0f2b4ff3d44aa +#: cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 -#: 1fd555d1f8ca499ead8d5601eb62266a +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 -#: f5fc85accf8c4bb9bc701ba0b4ee2e21 +#: 5fa79c62049a447c8328ebf9db54ebf4 msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 -#: e69cb5e87f4b4670abbc1606197d804c +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 -#: 15d763c45a2749a8926b1f965db9d97f +#: 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 -#: c2aac63fc0c347d9833d253039000fa3 +#: f1cb55fc59824cc18a95fd6dcb32cf4c msgid "First of all, notice that the main workflow level input here requires an array of strings." msgstr "" #: ../../src/topics/workflows.md:441 -#: 06a23beb753c4a97b302943f59128d78 +#: d947c54933d64aad90df392a1cedd63f msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 -#: 45985434cfe9438cb558075e1fd73809 +#: 651d35997332404186aa6d5711da4a3d msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 -#: e92da36d865142289b11d245221ff8d4 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 -#: 3ed7a2b9f77b4eadae3bf6e4a98d14b9 +#: 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 -#: fd66c4fb9c2a4beea0ed5ed8874fcd61 +#: b662c1a5a4424c8d8350a806356acc61 msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 -#: 65944dc8b32a46a4beb73dbdebb7b01a +#: 04d6babfd87343d7a5f13867ea02b65f msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 -#: 6250fe161ab0421b8799040b79ce695a +#: 2eaacf1a90204a2b9bd621344560f2a1 msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 -#: cc40c0f1ade34ab3b400a02b59b7ba01 +#: 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 -#: 29f53a5d64fa498bad0dbe94b238fd97 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 -#: 037fccb419bc4e9f839c665ae31e28ee +#: e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 -#: fdd4bec90c484a618ed8e4d1199deff8 +#: e3a7182f00f440b8b5461da91194a64b msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" msgstr "" #: ../../src/topics/workflows.md:491 -#: 11afb584f37947358963f6510935c5d5 +#: 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 -#: a77e0bfb589c40b6a61a9ca559961a7c +#: b5338f39e8c74ff28e139da68089a742 msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 -#: 3f4aa12588204fe5b33db590a9446283 +#: f6d92156d67c4a339bcfd194cff897df msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 -#: 640c67f3bcd740c59f90c361024acbcc +#: 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 -#: 8c4d30cbbea146a584731d164d4ad9ef +#: d80ab383eec9402faba997b548fe42eb msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 -#: 5d0fd4f8b58e4a8e8f46902e64e6556b +#: f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 -#: e98ab273645340f9a1446183a642e79e +#: 49217c02f58c43ff9ec00f10da8d4e84 msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." msgstr "" #: ../../src/topics/workflows.md:527 -#: 37a83ed92d9e44689cfd3a31c2785418 +#: 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 -#: 7cebef0a9e1444149b1dc58d30f6c10e +#: 8dbd56473f8c40c0bb12a48be06117e3 msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 -#: 0cd2bd98918b4622bc586d50f1ce1fa4 +#: 78d7f3ede2c746d482042adef050b2c4 msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 -#: 92458de979564d19a634bb8d3bf6f586 +#: cbbf93c70fe04ba7932ba25758ddc611 msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 -#: d4ee6cc8903f4e6992439ca2586246ed +#: cfa1c1fde4454df283f87cc54a9c59ec msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 -#: 62b438c4ed8a409f96974f3d59cc5854 +#: 1a8be2950cbb475bbb2617e005f0fac9 msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 -#: f0f288aeae4f4649ba3615437b531e97 +#: 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 -#: f35023cb05504d1db0cbee41c4e5f371 +#: 5d83c56102e141cc978500f678dd0c1c msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 -#: 01564f1d2038489685160f03db92085f +#: c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 -#: ad662dce1e4149728b8e17f74d8f975f +#: fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 -#: 4f6a57f34f094418b7c13aa07eef95c7 +#: 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 -#: 373a6c24de9144e69f37418d6ce8857d +#: b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 -#: f804a8493c8e40178772d94bdc45b43e +#: b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 -#: b3c504b8ab1a42788ef4e3339d27b0dc +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 -#: 2c2681fe72e24a5d8d98f0aa8e8c56a2 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 -#: 571e5c13552c4381bb6de53c02fe5f43 +#: 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 -#: fd789f444d9a4061b4fc61bac70353bb +#: cda73485875d4c8e9464679a20558616 msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 -#: 2cef838551994b078e460c63214517f9 +#: 98cae24919b74c088a5d89706aec581b msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 -#: 2a3a8a553d3c455e9288f63b9a02898d +#: b4b0940b4b5743c09637b36b964202d0 msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 -#: b0b8def4623a4018b1ac913a9256c0a2 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 -#: 3f0d4346f0104cc08c059eed9ab4b3a9 +#: 9ca3554d771d45998e88aaede525b227 msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 -#: 22e0ac963278414d8141ce5ce4031029 +#: 3fca839cede94cfd8e4f605c73ba699d msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 -#: 49cad54646d04adc8e5ac9f0f3c8f895 +#: da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 -#: c8776a4511b24f46bbe0a34d52cf3c8b +#: 3ded0f125249485c921994b6e6b93ac9 msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 -#: 401b053bd08a4286b9059cb6ebf8d679 +#: 53ece35d309a4c8d99f1efb2122a7092 msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 -#: 8d48a277f37f458f88c54f362534d7b5 +#: d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 -#: de90253a11f24f29a4a57348b4f60941 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 -#: 1e20968f957441c58cabfbc46c21e8ca +#: fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 -#: 4cf2e158afb348d7b3fd6274fe888129 +#: 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 -#: 44c5c010c97a40068a6b930949dcd8cf +#: 87bafb845c714b109874f6137b84462d msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 -#: c6277b2a7a934f81a91e406ef317a1fb +#: 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 -#: 8b3ece04170c447e9b5a8f76374c4c23 +#: fcd05b1ef31a4046946a2399c7fc5575 msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 -#: 6b952b7369b447bdb0bf1e9ff8540194 +#: f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 -#: a6024fb7ce664896a6858d5ea3562fb7 +#: 859368c1f25c4a4aad57abfd046c63f5 msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" diff --git a/src/conf.py b/src/conf.py index 60ece96c..990751ba 100644 --- a/src/conf.py +++ b/src/conf.py @@ -236,5 +236,5 @@ } gettext_uuid = True -gettext_compact = True +gettext_compact = "user_guide" locale_dirs = ['locales/'] From 3a715f91e821d471ddf4883a3c5543c29eaf12ac Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 25 Jan 2023 15:35:18 +0100 Subject: [PATCH 40/49] add Weblate to README --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index de079218..d6817cc9 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,8 @@ [![Syntax Check](https://app.travis-ci.com/common-workflow-language/user_guide.svg?branch=main)](https://app.travis-ci.com/common-workflow-language/user_guide) +[![Translation status](https://hosted.weblate.org/widgets/commonwl/-/user-guide/svg-badge.svg)](https://hosted.weblate.org/engage/commonwl/) + This is the source of the official user guide for the Common Workflow Language standards. Releases are published at from the `release` branch. From a8098340780f4db905c755358391ddc75417727a Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Thu, 26 Jan 2023 14:55:11 +0100 Subject: [PATCH 41/49] convert license to RST to restore indirect links (#366) --- LICENSE.md | 63 -- LICENSE.rst | 59 ++ locales/es/LC_MESSAGES/user_guide.po | 1380 +++++++++++++------------ locales/pt/LC_MESSAGES/user_guide.po | 1385 +++++++++++++------------- locales/user_guide.pot | 1358 ++++++++++++------------- src/LICENSE.md | 2 - src/LICENSE.rst | 1 + src/conf.py | 2 +- src/index.md | 2 +- 9 files changed, 2098 insertions(+), 2154 deletions(-) delete mode 100644 LICENSE.md create mode 100644 LICENSE.rst delete mode 100644 src/LICENSE.md create mode 100644 src/LICENSE.rst diff --git a/LICENSE.md b/LICENSE.md deleted file mode 100644 index 75596a51..00000000 --- a/LICENSE.md +++ /dev/null @@ -1,63 +0,0 @@ -# Licenses - -## Instructional Material - -All Common Workflow Language project instructional material and changes -to the structure are also made available under the [Creative Commons Attribution -license][cc-by-human]. The following is a human-readable summary of -(and not a substitute for) the [full legal text of the CC BY 4.0 -license][cc-by-legal]. - -You are free: - -* to **Share**---copy and redistribute the material in any medium or format -* to **Adapt**---remix, transform, and build upon the material - -for any purpose, even commercially. - -The licensor cannot revoke these freedoms as long as you follow the -license terms: - - - -* **Attribution**---You must give appropriate credit (mentioning that - your work is derived from work that is Copyright © the Common Workflow - Language project, and, where practical, linking to - https://www.commonwl.org/ ), provide a [link to the - license][cc-by-human], and indicate if changes were made. You may do - so in any reasonable manner, but not in any way that suggests the - licensor endorses you or your use. - -* **No additional restrictions**---You may not apply legal terms or -technological measures that legally restrict others from doing -anything the license permits. With the understanding that: - - * You do not have to comply with the license for elements of the - material in the public domain or where your use is permitted by an - applicable exception or limitation. - * No warranties are given. The license may not give you all of the - permissions necessary for your intended use. For example, other - rights such as publicity, privacy, or moral rights may limit how you - use the material. - -## Software - -Except where otherwise noted, the example programs and other software -provided by Common Workflow Language project are made available under the -[OSI][osi]-approved -[Apache 2.0 license][apache-2.0-license]. - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - - - - -[cc-by-human]: https://creativecommons.org/licenses/by/4.0/ -[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode -[apache-2.0-license]: https://opensource.org/licenses/Apache-2.0 -[mit-license]: https://opensource.org/licenses/mit-license.html -[osi]: https://opensource.org diff --git a/LICENSE.rst b/LICENSE.rst new file mode 100644 index 00000000..cc6a19b0 --- /dev/null +++ b/LICENSE.rst @@ -0,0 +1,59 @@ +Licenses +======== + +Instructional Material +---------------------- + +All Common Workflow Language project instructional material and changes +to the structure are also made available under the `Creative Commons +Attribution license `_. The following is a human-readable summary of (and +not a substitute for) the `full legal text of the CC BY 4.0 license `_. + +You are free: + +- to **Share**—copy and redistribute the material in any medium or + format +- to **Adapt**—remix, transform, and build upon the material + +for any purpose, even commercially. + +The licensor cannot revoke these freedoms as long as you follow the +license terms: + +- **Attribution**—You must give appropriate credit (mentioning that + your work is derived from work that is Copyright © the Common + Workflow Language project, and, where practical, linking to + https://www.commonwl.org/ ), provide a `link to the license `_, and + indicate if changes were made. You may do so in any reasonable + manner, but not in any way that suggests the licensor endorses you or + your use. + +- **No additional restrictions**—You may not apply legal terms or + technological measures that legally restrict others from doing + anything the license permits. With the understanding that: + + - You do not have to comply with the license for elements of the + material in the public domain or where your use is permitted by an + applicable exception or limitation. + - No warranties are given. The license may not give you all of the + permissions necessary for your intended use. For example, other + rights such as publicity, privacy, or moral rights may limit how + you use the material. + +Software +-------- + +Except where otherwise noted, the example programs and other software +provided by Common Workflow Language project are made available under +the `OSI`_-approved `Apache 2.0 license `_. + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an “AS IS” BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +.. _cc-by-human: https://creativecommons.org/licenses/by/4.0/ +.. _cc-by-legal: https://creativecommons.org/licenses/by/4.0/legalcode +.. _OSI: https://opensource.org +.. _Apache-2.0: https://opensource.org/licenses/Apache-2.0 diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index ba080ed4..3fa6daab 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,149 +9,113 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"POT-Creation-Date: 2023-01-25 16:53+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Spanish \n" "Language: es\n" +"Language-Team: Spanish \n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n != 1;\n" -"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.rst:2 dcdc2e8da0ec4d9e9453601fdd83bac5 msgid "Licenses" -msgstr "Licencias" +msgstr "" +"Licencias" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.rst:5 3e165520ca56481b8f8d494a8d471de3 msgid "Instructional Material" -msgstr "Material didáctico" +msgstr "" +"Material didáctico" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." +#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " -"cambios en la estructura también están disponibles bajo la [licencia " -"Creative Commons Attribution][cc-by-human]. Lo que sigue es un resumen " -"legible por humanos (y no un sustituto) del [texto legal completo de la " -"licencia CC BY 4.0][cc-by-legal]." +"cambios en la estructura también están disponibles bajo la `licencia " +"Creative Commons Attribution `_. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del `texto legal completo de la " +"licencia CC BY 4.0 `_." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.rst:12 b7a7a0fb40344fe087c1cc3ec19308aa msgid "You are free:" msgstr "Usted es libre de:" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 +msgid "to **Share**—copy and redistribute the material in any medium or format" msgstr "" -"**Compartir**---copiar y redistribuir el material en cualquier medio o " +"**Compartir**—copiar y redistribuir el material en cualquier medio o " "formato" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" +#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 +msgid "to **Adapt**—remix, transform, and build upon the material" +msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.rst:18 430ff4de74924bc3a3b2c7e809ea4456 msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e -msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms:" +#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia." -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 -msgid "" -"**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." +#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 +msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" -"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " -"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " -"Language Project» y, cuando sea práctico, con un enlace a https://www." -"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " -"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " -"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " -"licenciante." +"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su" +" trabajo se deriva de un trabajo que tiene «Copyright © The Common " +"Workflow Language Project» y, cuando sea práctico, con un enlace a " +"https://www.commonwl.org/ ), brindar un `enlace a la licencia `_, e indicar si se han realizado cambios. Puede hacerlo en cualquier" +" forma razonable, pero no de forma tal que sugiera que usted o su uso " +"tienen el apoyo de la licenciante." -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 -msgid "" -"**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" +#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 +msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" -"**No hay restricciones adicionales**---No puede aplicar términos legales ni " -"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " -"permitido por la licencia. Con el entendimiento de que:" +"**No hay restricciones adicionales**---No puede aplicar términos legales " +"ni medidas tecnológicas que restrinjan legalmente a otras a hacer " +"cualquier uso permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 -msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." +#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limit msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 -msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." +#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " -"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " -"publicidad, privacidad, o derechos morales pueden limitar la forma en que " -"utilice el material." +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como" +" publicidad, privacidad, o derechos morales pueden limitar la forma en " +"que utilice el material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.rst:44 3d7ca3f2cede4d5f998bf014bd970748 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " -"la [OSI][Osi]." +"disponibles bajo la `licencia Apache 2.0 `_ aprobada " +"por la `OSI`_." -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." +#: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 +#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 +#: dfc7702e073140c985cf47272a20214d msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -160,30 +124,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -191,94 +155,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -286,22 +250,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -310,25 +274,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef msgid "" msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -336,26 +300,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 msgid "" msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -364,77 +328,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -443,11 +407,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -458,22 +422,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -482,11 +446,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -494,7 +458,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -502,15 +466,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -521,18 +485,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -542,18 +506,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -562,24 +526,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: 9bba7c4f783942e4a299603430601363 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: e2140e0f0e7747ef8383887c20a7945a msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -588,39 +552,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 15bf490724cd46dcbcfab44633c5a9a2 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 51d52d051e654a8395239f88df7c9d8c msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: eb496cc818524fa7bae5a22ddd00a19c msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: c4a22d12e7f149ff901d27de32b9361d msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 7618de899a7043989d77baacf62eb7b2 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: 6f1544a220664b79b04bf008058b5a91 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: fbd14ac9a2f541478a320ed4cbc69e13 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -629,7 +593,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: da4dba50d25d4533b3dbb92f54d32a30 msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -638,7 +602,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: ce11c9f8d65c4268984d0384d95144cc msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -648,7 +612,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 3a201aa497e84f70855bb2251e7e3281 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -657,24 +621,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: b78f7fa2be1c4bb090f6da895457ad1e msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: f7e95d264ffa4e2db0864faccd9e5a0e msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 3f1e5b01e49a4dc1b1c99936a4589afc msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 03c3048f38ae4938a484cf02001877b3 msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -684,7 +648,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: f9715b5ec65c405c849bb030c1927060 msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -693,12 +657,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 442662f50e9e4620970ce32b1b127969 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: 2b34c786af3840e88f29d214e19dc837 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -712,7 +676,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: dd6aadff8cf54ce78ea6b317afbaddb0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -721,7 +685,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: fe7f1f0b28434f8aaf0f6ac6589a83f0 msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -730,71 +694,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: d10cf45b3c7f49dc98bc0e5d1246f224 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 -#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 +#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 8badec9987ba40609cf1f626172b2b2d msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: c75a8b4bf0e24781bf6713cf6f013cd1 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 79b146ffe6d74e1b8f6019251dc4b7c2 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 07cca9a33d8f4b77ac6ad35ca8b95655 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: 31db11c8ddf2423192a8b2063b3e91c2 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: d81dd96143ea444aa78ff45cfa0584b3 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -804,11 +768,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -816,29 +780,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -848,11 +812,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -860,7 +824,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -868,26 +832,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -898,23 +862,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -925,32 +889,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -958,30 +922,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -991,47 +955,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1039,7 +1003,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1047,57 +1011,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1105,11 +1069,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1117,11 +1081,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1129,32 +1093,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1162,21 +1126,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1184,46 +1148,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1231,19 +1195,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 32f86f911ebe4a4c94975f81742333f3 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: d5f1ad2b95ad46d48f8f2ca5e357bb5d msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: c53ceee943ad4acea779e072b9137889 msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1254,37 +1218,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: 7dfe9dffbf5744299bf232599644c7f6 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed +#: 991172e201ec4796992a349dee44f090 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: 1f3c23a4769043ca985b8ddfed19391d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: f81b43c7cb194a1cad8672129223c833 msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: a20073a8f5374eb1bc8531ff33e622b6 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: d08869beca3a4774baf1097b63e79474 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1295,11 +1259,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1307,13 +1271,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1329,7 +1293,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1339,43 +1303,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1383,13 +1347,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1401,44 +1365,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1446,31 +1410,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1478,52 +1442,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: 12cf5f2264504c44a2173e858bb2c283 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: 7694f9cabfe04308bbddd2c88ae6d9b9 msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1532,17 +1496,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: b557dc4f8ef549b98f59412a918643de msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 3011eb003c084285b30cfa56a8da45b6 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1550,7 +1514,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: ce78b2d147054da895beba66d0ecdab4 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1560,7 +1524,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: a973846ec5a946eeaff02c5b00997da9 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1568,13 +1532,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 +#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d +#: ccec7f73b9d948e79a6cdf32bc124092 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: 22948f19cb78485f8f86244686a35c09 msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1582,7 +1546,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 001d9579bfce438e865377fb9c2df776 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1594,7 +1558,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: e62618db8995428bb3f260e03ac8f459 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1604,19 +1568,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f -#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 +#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 +#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 +#: e9801b2142cd45368a73ef9b121c1d08 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1625,21 +1589,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1648,13 +1612,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1665,15 +1629,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1681,7 +1645,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1691,26 +1655,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1718,32 +1682,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1751,7 +1715,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1760,67 +1724,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 +#: c12625211cc542b68cb51365a63eef00 msgid "`arguments`" msgstr "" @@ -1828,32 +1792,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e -#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 -#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 +#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe +#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: e7f1993580f0425098a719e83a64cc7f msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff +#: c158e9ee5fbf4e868b152a0a5880092f msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a +#: 92697d3179ec48898eaea9aba3c24dcd msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 +#: d6722e3093884ad7b62696fbb2f48fdc msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1864,11 +1828,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc -#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd -#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 -#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 +#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 +#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef +#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 +#: c610220d06484d589313dc29faf8222c msgid "`format`" msgstr "" @@ -1877,51 +1841,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 -#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d -#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f -#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 +#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 +#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da +#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c +#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b +#: f71216a4b35e4157aece5ffa2602d8bf msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b +#: ba1fff3ebb274dfba845b3ee20ebd71f msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 +#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f +#: 722d3bd7184841639b9f9a38914002da msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 +#: 7b46d408e7e7481b91a950b2d4010c9a msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1930,32 +1894,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff +#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 +#: e9fc5f7fa4474dfc95039b94167fe894 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 +#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 +#: 61744122b7d7494890cbe6b2fb72b9f7 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 +#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 +#: e0c7ccc8f8664cf794cbb7330355f3fe msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1963,61 +1927,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 +#: c9534670f5f04769aa3749c3778eb705 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 +#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 +#: 7b0887a8caed41b2acccf7021bb323d3 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd +#: e5e8b8c75f0f43cbb6e160e5bf810c6e msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 +#: fe3b9fb45e01490498c5a35c012b3de8 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 +#: ddf82b12b12d416fb65f3ce3f51bbdf0 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 +#: af14fda3cca645fbb2f3c5825fe0788e msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 +#: fec70bb106ad4d95a2d55ebdcf711afc msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -2025,33 +1989,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2059,22 +2023,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2082,7 +2046,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2092,54 +2056,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2148,15 +2112,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2165,11 +2129,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2177,7 +2141,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2186,34 +2150,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2221,11 +2185,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2234,80 +2198,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2315,7 +2279,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2323,7 +2287,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2331,14 +2295,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2346,7 +2310,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2354,7 +2318,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2364,13 +2328,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2381,17 +2345,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2401,23 +2365,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 -#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 +#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2427,7 +2391,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2438,11 +2402,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2450,46 +2414,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2497,18 +2461,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2516,7 +2480,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2524,7 +2488,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2534,12 +2498,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 71628ebe908b4cd28dd1fa17e3d2e2fb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: f123ca244c23413c91405a4b84887525 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2554,7 +2518,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 23299ae1bec94b00a32a8af7eeac350f msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2562,17 +2526,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 2495a9f2032a47c188338cb81ba429eb msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 3fd2f3cf7bdf44089df2ce3122534801 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: d5a5b8b490b640439db92da949266e4e msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2582,15 +2546,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 5935ed94331d4b2f8ce597f31edea843 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2598,56 +2562,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2655,7 +2619,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2664,17 +2628,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2682,71 +2646,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2755,11 +2719,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2772,40 +2736,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2813,45 +2777,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2859,13 +2823,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2873,43 +2837,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 943ba46512ce48fe8c5b62327734c503 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: bbcd43d5af7d44108aeb65075a6bd2be msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 834295755af841a78e466eea43864861 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: a6b626489bfa468e8f059ab3aa669201 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: e1dbea105aa845c38cb1f90b43847271 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: e9640f47d40e45bca184eb30700df648 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2919,14 +2883,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 0456efb3718b4356ad2b277ee16de967 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: f7e97f926505407f8f8e9a427e055e43 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2935,7 +2899,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 +#: ec597ff8f6ee47bc815b069335869f1f msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2951,11 +2915,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2965,26 +2929,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2993,7 +2957,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -3003,18 +2967,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -3022,7 +2986,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -3030,7 +2994,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3040,7 +3004,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3050,15 +3014,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3071,35 +3035,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3112,23 +3076,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3136,44 +3100,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3181,33 +3145,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3220,34 +3184,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3255,7 +3219,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3264,7 +3228,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3275,7 +3239,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3283,7 +3247,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3293,13 +3257,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3309,11 +3273,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3321,17 +3285,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3339,7 +3303,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3361,7 +3325,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3370,7 +3334,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3380,7 +3344,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3388,14 +3352,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3404,7 +3368,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3413,7 +3377,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3421,11 +3385,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3436,7 +3400,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3444,23 +3408,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3468,7 +3432,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3476,59 +3440,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3546,7 +3510,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3554,38 +3518,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3594,7 +3558,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3602,62 +3566,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3667,7 +3631,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3676,7 +3640,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3687,28 +3651,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3719,7 +3683,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3732,11 +3696,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3747,26 +3711,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3776,52 +3740,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index 3584ce39..3ed0733d 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -9,142 +9,115 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-25 16:53+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Portuguese \n" "Language: pt\n" +"Language-Team: Portuguese \n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.16-dev\n" +"Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.rst:2 75de2be8809847b8bf1ccd42aa694a24 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.rst:5 2edd71801f6245ef821887a74f21b94c msgid "Instructional Material" msgstr "" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." +#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." msgstr "" "Todo o material instrucional do projeto Common Workflow Language e " -"alterações na estrutura também são disponibilizados sob a [licença Creative " -"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " -"humanos de (e não um substituto para) o [texto legal completo da licença CC " -"BY 4.0][cc-by-legal]." +"alterações na estrutura também são disponibilizados sob a `licença " +"Creative Commons Attribution `_. O seguinte é um resumo " +"legível por humanos de (e não um substituto para) o `texto legal completo" +" da licença CC BY 4.0 `_." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.rst:12 90cc755d172e4c82b882b4ee620fe652 msgid "You are free:" msgstr "Você tem o direito de:" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 +msgid "to **Share**—copy and redistribute the material in any medium or format" msgstr "" -"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " -"formato" +"**Compartilhar**—copiar e redistribuir o material em qualquer suporte " +"ou formato" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" +#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 +msgid "to **Adapt**—remix, transform, and build upon the material" +msgstr "**Adaptar**—remixar, transformar, e criar a partir do material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.rst:18 430ff4de74924bc3a3b2c7e809ea4456 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e -msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms:" +#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " "termos da licença." -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 -msgid "" -"**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." +#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 +msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" "Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " "trabalho deriva de um trabalho que é «Copyright © The Common Workflow " -"Language project», e, quando prático, criar uma ligação para https://www." -"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " -"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " -"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " -"uso." +"Language project», e, quando prático, criar uma ligação para " +"https://www.commonwl.org/ ), fornecer um `link para a licença `_, e indicar se foram feitas alterações. Você pode fazê-lo de " +"qualquer forma razoável, mas não de uma forma que sugira que o " +"licenciante o apoia ou aprova o seu uso." -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 -msgid "" -"**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" +#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 +msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" -"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " -"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " -"algo que a licença permita. Com o entendimento de que:" +"**Sem restrições adicionais**—Você não pode aplicar termos jurídicos ou" +" medidas de caráter tecnológico que restrinjam legalmente outros de " +"fazerem algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 -msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." +#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" "Não tem de cumprir com os termos da licença relativamente a elementos do " -"material que estejam no domínio público ou cuja utilização seja permitida " -"por uma exceção ou limitação que seja aplicável." +"material que estejam no domínio público ou cuja utilização seja permitida" +" por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 -msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." +#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" "Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " "autorizações necessárias para o uso pretendido. Por exemplo, outros " -"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " -"podem limitar o uso do material." +"direitos, tais como direitos de imagem, de privacidade ou direitos " +"morais, podem limitar o uso do material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.rst:44 3d7ca3f2cede4d5f998bf014bd970748 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." msgstr "" "Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" -"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." +"fornecido pelo projecto Common Workflow Language são disponibilizados sob" +" a `licença Apache 2.0 `_ aprovada pela `OSI`_." -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +#: ../../LICENSE.rst:50 9c4d58a1129a4d4eb4db1bfabbeddb6e msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." +"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT" +" WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the" +" License for the specific language governing permissions and limitations " +"under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 +#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 +#: dfc7702e073140c985cf47272a20214d msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -153,30 +126,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -184,94 +157,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -279,22 +252,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -303,25 +276,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef msgid "" msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -329,26 +302,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 msgid "" msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -357,77 +330,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -436,11 +409,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -451,22 +424,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -475,11 +448,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -487,7 +460,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -495,15 +468,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -514,18 +487,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -535,18 +508,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -555,24 +528,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: 9bba7c4f783942e4a299603430601363 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: e2140e0f0e7747ef8383887c20a7945a msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -581,39 +554,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 15bf490724cd46dcbcfab44633c5a9a2 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 51d52d051e654a8395239f88df7c9d8c msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: eb496cc818524fa7bae5a22ddd00a19c msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: c4a22d12e7f149ff901d27de32b9361d msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 7618de899a7043989d77baacf62eb7b2 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: 6f1544a220664b79b04bf008058b5a91 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: fbd14ac9a2f541478a320ed4cbc69e13 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -622,7 +595,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: da4dba50d25d4533b3dbb92f54d32a30 msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -631,7 +604,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: ce11c9f8d65c4268984d0384d95144cc msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -641,7 +614,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 3a201aa497e84f70855bb2251e7e3281 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -650,24 +623,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: b78f7fa2be1c4bb090f6da895457ad1e msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: f7e95d264ffa4e2db0864faccd9e5a0e msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 3f1e5b01e49a4dc1b1c99936a4589afc msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 03c3048f38ae4938a484cf02001877b3 msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -677,7 +650,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: f9715b5ec65c405c849bb030c1927060 msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -686,12 +659,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 442662f50e9e4620970ce32b1b127969 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: 2b34c786af3840e88f29d214e19dc837 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -705,7 +678,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: dd6aadff8cf54ce78ea6b317afbaddb0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -714,7 +687,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: fe7f1f0b28434f8aaf0f6ac6589a83f0 msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -723,71 +696,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: d10cf45b3c7f49dc98bc0e5d1246f224 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 -#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 +#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 8badec9987ba40609cf1f626172b2b2d msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: c75a8b4bf0e24781bf6713cf6f013cd1 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 79b146ffe6d74e1b8f6019251dc4b7c2 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 07cca9a33d8f4b77ac6ad35ca8b95655 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: 31db11c8ddf2423192a8b2063b3e91c2 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: d81dd96143ea444aa78ff45cfa0584b3 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -797,11 +770,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -809,29 +782,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -841,11 +814,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -853,7 +826,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -861,26 +834,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -891,23 +864,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -918,32 +891,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -951,30 +924,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -984,47 +957,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1032,7 +1005,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1040,57 +1013,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1098,11 +1071,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1110,11 +1083,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1122,32 +1095,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1155,21 +1128,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1177,46 +1150,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1224,19 +1197,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 32f86f911ebe4a4c94975f81742333f3 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: d5f1ad2b95ad46d48f8f2ca5e357bb5d msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: c53ceee943ad4acea779e072b9137889 msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1247,37 +1220,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: 7dfe9dffbf5744299bf232599644c7f6 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed +#: 991172e201ec4796992a349dee44f090 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: 1f3c23a4769043ca985b8ddfed19391d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: f81b43c7cb194a1cad8672129223c833 msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: a20073a8f5374eb1bc8531ff33e622b6 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: d08869beca3a4774baf1097b63e79474 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1288,11 +1261,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1300,13 +1273,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1322,7 +1295,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1332,43 +1305,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1376,13 +1349,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1394,44 +1367,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1439,31 +1412,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1471,52 +1444,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: 12cf5f2264504c44a2173e858bb2c283 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: 7694f9cabfe04308bbddd2c88ae6d9b9 msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1525,17 +1498,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: b557dc4f8ef549b98f59412a918643de msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 3011eb003c084285b30cfa56a8da45b6 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1543,7 +1516,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: ce78b2d147054da895beba66d0ecdab4 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1553,7 +1526,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: a973846ec5a946eeaff02c5b00997da9 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1561,13 +1534,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 +#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d +#: ccec7f73b9d948e79a6cdf32bc124092 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: 22948f19cb78485f8f86244686a35c09 msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1575,7 +1548,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 001d9579bfce438e865377fb9c2df776 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1587,7 +1560,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: e62618db8995428bb3f260e03ac8f459 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1597,19 +1570,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f -#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 +#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 +#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 +#: e9801b2142cd45368a73ef9b121c1d08 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1618,21 +1591,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1641,13 +1614,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1658,15 +1631,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1674,7 +1647,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1684,26 +1657,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1711,32 +1684,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1744,7 +1717,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1753,67 +1726,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 +#: c12625211cc542b68cb51365a63eef00 msgid "`arguments`" msgstr "" @@ -1821,32 +1794,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e -#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 -#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 +#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe +#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: e7f1993580f0425098a719e83a64cc7f msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff +#: c158e9ee5fbf4e868b152a0a5880092f msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a +#: 92697d3179ec48898eaea9aba3c24dcd msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 +#: d6722e3093884ad7b62696fbb2f48fdc msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1857,11 +1830,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc -#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd -#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 -#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 +#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 +#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef +#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 +#: c610220d06484d589313dc29faf8222c msgid "`format`" msgstr "" @@ -1870,51 +1843,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 -#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d -#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f -#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 +#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 +#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da +#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c +#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b +#: f71216a4b35e4157aece5ffa2602d8bf msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b +#: ba1fff3ebb274dfba845b3ee20ebd71f msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 +#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f +#: 722d3bd7184841639b9f9a38914002da msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 +#: 7b46d408e7e7481b91a950b2d4010c9a msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1923,32 +1896,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff +#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 +#: e9fc5f7fa4474dfc95039b94167fe894 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 +#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 +#: 61744122b7d7494890cbe6b2fb72b9f7 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 +#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 +#: e0c7ccc8f8664cf794cbb7330355f3fe msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1956,61 +1929,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 +#: c9534670f5f04769aa3749c3778eb705 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 +#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 +#: 7b0887a8caed41b2acccf7021bb323d3 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd +#: e5e8b8c75f0f43cbb6e160e5bf810c6e msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 +#: fe3b9fb45e01490498c5a35c012b3de8 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 +#: ddf82b12b12d416fb65f3ce3f51bbdf0 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 +#: af14fda3cca645fbb2f3c5825fe0788e msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 +#: fec70bb106ad4d95a2d55ebdcf711afc msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -2018,33 +1991,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2052,22 +2025,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2075,7 +2048,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2085,54 +2058,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2141,15 +2114,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2158,11 +2131,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2170,7 +2143,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2179,34 +2152,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2214,11 +2187,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2227,80 +2200,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2308,7 +2281,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2316,7 +2289,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2324,14 +2297,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2339,7 +2312,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2347,7 +2320,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2357,13 +2330,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2374,17 +2347,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2394,23 +2367,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 -#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 +#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2420,7 +2393,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2431,11 +2404,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2443,46 +2416,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2490,18 +2463,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2509,7 +2482,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2517,7 +2490,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2527,12 +2500,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 71628ebe908b4cd28dd1fa17e3d2e2fb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: f123ca244c23413c91405a4b84887525 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2547,7 +2520,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 23299ae1bec94b00a32a8af7eeac350f msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2555,17 +2528,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 2495a9f2032a47c188338cb81ba429eb msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 3fd2f3cf7bdf44089df2ce3122534801 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: d5a5b8b490b640439db92da949266e4e msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2575,15 +2548,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 5935ed94331d4b2f8ce597f31edea843 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2591,56 +2564,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2648,7 +2621,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2657,17 +2630,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2675,71 +2648,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2748,11 +2721,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2765,40 +2738,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2806,45 +2779,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2852,13 +2825,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2866,43 +2839,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 943ba46512ce48fe8c5b62327734c503 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: bbcd43d5af7d44108aeb65075a6bd2be msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 834295755af841a78e466eea43864861 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: a6b626489bfa468e8f059ab3aa669201 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: e1dbea105aa845c38cb1f90b43847271 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: e9640f47d40e45bca184eb30700df648 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2912,14 +2885,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 0456efb3718b4356ad2b277ee16de967 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: f7e97f926505407f8f8e9a427e055e43 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2928,7 +2901,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 +#: ec597ff8f6ee47bc815b069335869f1f msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2944,11 +2917,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2958,26 +2931,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2986,7 +2959,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2996,18 +2969,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -3015,7 +2988,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -3023,7 +2996,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3033,7 +3006,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3043,15 +3016,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3064,35 +3037,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3105,23 +3078,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3129,44 +3102,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3174,33 +3147,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3213,34 +3186,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3248,7 +3221,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3257,7 +3230,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3268,7 +3241,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3276,7 +3249,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3286,13 +3259,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3302,11 +3275,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3314,17 +3287,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3332,7 +3305,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3354,7 +3327,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3363,7 +3336,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3373,7 +3346,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3381,14 +3354,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3397,7 +3370,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3406,7 +3379,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3414,11 +3387,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3429,7 +3402,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3437,23 +3410,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3461,7 +3434,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3469,59 +3442,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3539,7 +3512,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3547,38 +3520,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3587,7 +3560,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3595,62 +3568,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3660,7 +3633,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3669,7 +3642,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3680,28 +3653,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3712,7 +3685,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3725,11 +3698,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3740,26 +3713,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3769,52 +3742,64 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" +#~ msgid "" +#~ "Unless required by applicable law or " +#~ "agreed to in writing, software " +#~ "distributed under the License is " +#~ "distributed on an \"AS IS\" BASIS, " +#~ "WITHOUT WARRANTIES OR CONDITIONS OF ANY" +#~ " KIND, either express or implied. See" +#~ " the License for the specific " +#~ "language governing permissions and limitations" +#~ " under the License." +#~ msgstr "" + diff --git a/locales/user_guide.pot b/locales/user_guide.pot index 0a669946..a806cea1 100644 --- a/locales/user_guide.pot +++ b/locales/user_guide.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"POT-Creation-Date: 2023-01-25 16:53+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -16,1273 +16,1273 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" -#: ../../LICENSE.md:2 -#: 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.rst:2 +#: 75de2be8809847b8bf1ccd42aa694a24 msgid "Licenses" msgstr "" -#: ../../LICENSE.md:4 -#: 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.rst:5 +#: 2edd71801f6245ef821887a74f21b94c msgid "Instructional Material" msgstr "" -#: ../../LICENSE.md:6 -#: 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +#: ../../LICENSE.rst:7 +#: 3c0a9704ed8f4367893242a4f75d703f +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." msgstr "" -#: ../../LICENSE.md:12 -#: 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.rst:12 +#: 90cc755d172e4c82b882b4ee620fe652 msgid "You are free:" msgstr "" -#: ../../LICENSE.md:14 -#: 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.rst:14 +#: e5246890525144bda8547106b6643382 +msgid "to **Share**—copy and redistribute the material in any medium or format" msgstr "" -#: ../../LICENSE.md:15 -#: 18a3a0aec35743848c97bc178f9c94ff -msgid "to **Adapt**---remix, transform, and build upon the material" +#: ../../LICENSE.rst:16 +#: 4d96baa7ca7a4240b75be213696558ba +msgid "to **Adapt**—remix, transform, and build upon the material" msgstr "" -#: ../../LICENSE.md:17 -#: b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.rst:18 +#: e19adbba09d14d069534251a7ef70993 msgid "for any purpose, even commercially." msgstr "" -#: ../../LICENSE.md:19 -#: 6021e65292a149d5b15e14491f3eb05e +#: ../../LICENSE.rst:20 +#: 8bc6672f4a33428296226112a1be6fbe msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" -#: ../../LICENSE.md:24 -#: 8fb7a2946c384364814c6ec3910997d3 -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.rst:23 +#: be38276e7b374f57b9997391bf898a62 +msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" -#: ../../LICENSE.md:32 -#: 8161753b7526445db319210044566200 -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.rst:31 +#: f00d5c3846034c2ea116c2f74786d9fc +msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" -#: ../../LICENSE.md:36 -#: 15314ba527864eaa834cf1185cfcc4e3 +#: ../../LICENSE.rst:35 +#: 1798d65c10104040923c2fea2199bab2 msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" -#: ../../LICENSE.md:39 -#: b351ddf9847d48b1a2a87fc78eaba4d2 +#: ../../LICENSE.rst:38 +#: c65198b804f8436ba783643d51bc72d9 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" -#: ../../LICENSE.md:44 -#: a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.rst:44 +#: 4777f6a958394b138c5b68eee0367734 msgid "Software" msgstr "" -#: ../../LICENSE.md:46 -#: 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.rst:46 +#: 7dec2236137f4de5ac7df7a8c8eaf98b +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." msgstr "" -#: ../../LICENSE.md:51 -#: 0f68eafafaef4b54accba7e13bfaa702 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.rst:50 +#: 9c4d58a1129a4d4eb4db1bfabbeddb6e +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 #: ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 -#: d4f35995b0f6494d9771a4be0a82538f -#: d6ccd4b546254f56a597d67dd4fdc5d6 +#: bdd540403a5746ff99edf2dcad0e3122 +#: 5ad4be9b62d54c95a913795b514676fd +#: dfc7702e073140c985cf47272a20214d msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." msgstr "" #: ../../src/episodes.md:5 #: ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc -#: 436cfca6f857469bbff7c652df32160f +#: f1b89ae4325343f783bce8b7c9971047 +#: 810c4e8dd79247d6a6fd51a8f65d3975 msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 -#: cc11f5d29206492d9f2f0922882b6159 +#: 3060770b3bef41d7bcfcdfb413d7689c msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." msgstr "" #: ../../src/faq.md:1 -#: e2ed894d325a4f50a5e2dc69da5531a1 +#: 48bb9f628b344ba1a3b67ae1cb264e3c msgid "FAQ" msgstr "" #: ../../src/faq.md:11 -#: 61edb787dab04ca2ad3ed07616d878a0 +#: 7e3684e9672643738846756e1ebafd18 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 -#: d5321589e7ed4f0db3c630cc39800791 +#: 187ceabb7fd9480bb8cf0f2da47f65ef msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 -#: fc62427c0a004810b055dee90ec5e2d9 +#: b548b76bcc85420a9b30792386105139 msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 -#: 1c6b8a4194a14611b4061b1540c3807f +#: 9ce692b78ead47e4b0f8cdae8837d35b msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 -#: bc7ad10c929848a3a9a240a3c501d299 +#: 6df1201c159343da9e7515379980d6a0 msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 -#: 7225a993d281421b95c8e3df2846a0e3 +#: f9ab1d0dc1c842b6abb5385268c1d3bd msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 -#: 7ef1dbb81993473f948d9c6f3c64b381 +#: 9f6a84ab6a9343b6ad7db826f8964362 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 -#: 450edf800a18423195bea4fe8793a2cb +#: fa50e4fa990b42d1ba4c0f4ae1e5caa1 msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 -#: 1a8cc75ea6174b9297871b2e58971077 +#: 3a871012fcfd4f3ebeca0cb86ec93435 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 -#: a7d84f740a714ec588503ee084fbbc34 +#: d954edfff2584288ac8c600733070d2e msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" msgstr "" #: ../../src/faq.md:97 -#: 569d553abe85450c9d1c37456bf412f4 +#: af6b1e37d6be4450a761854480ec9aab msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." msgstr "" #: ../../src/faq.md:104 -#: 95f5dbbd21084a318413b9528fb867be +#: 31f4a2d43062493ca64c648f80afc8e9 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 -#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: 41c54e71b6cd4f63b2a619a515240d34 msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." msgstr "" #: ../../src/faq.md:115 -#: 8d86baa239364f799d4f9d5ea2b0e314 +#: 8edc3541ad134ab5a1d23c724f1f0a4e msgid "The second method involves including an input of `type: File` in the script itself:" msgstr "" #: ../../src/faq.md:135 -#: f2c109998c76434893ff16b17fdb2bd0 +#: ac0ea81eba8842a18801ab03cbf80a57 msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 -#: c2c752b86bf94d6fb3751f4dd81bc7a7 +#: 52be1a5640234feabe958ff7ade33653 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 -#: 2c38cc58cbb340bc935a5f00e96ba95c +#: c6db734d5aef4f4f99676bdebf9c83c9 msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 -#: ce6db54bd0f54839a5beb948530a21f0 +#: a9f7b47c0dd741739795da39bf114879 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 -#: d06cbf89028b4638ad54c2529bcbfa25 +#: e3fdd9228b924905a4a1f4b2b7ad7159 msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 -#: d53fb28dcad04e7788cba9e280a2343c +#: 3f7cda1437cc48f18745a827ebb74582 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 -#: d9e30e11533b4d53a144f5df7041268d +#: 5aeaba2cae64442e816bbd458aee833a msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 -#: 941077158ec54ae19bfa2e2ad6662da1 +#: 5af827a402834978addd82c70be6b5ab msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 -#: 937cb94a370640c788fbc3fe0b19f2e5 +#: 6d69e42bd8e443c4b19d80807c7efd6b msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 -#: a1d57e15656548128a76a8b975c564c9 +#: 404640397b6e40c2a2cd5cf85ab3b1c0 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 -#: c8c235a9bf6240628f0b5493ffebf7e0 +#: 1682c2486e224770b62269709a8663cf msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." msgstr "" #: ../../src/faq.md:229 -#: 3da4dcb043eb4423a53a14182949d9cd +#: 9078fc009bc145808813c9cc2b734b58 msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 -#: 89b90d3bf1ea4ebd88482d435241fac5 +#: d4b5a54a400c409cb7984428f6a03ec8 msgid "To make an input parameter optional, add a question mark to the type declaration." msgstr "" #: ../../src/faq.md:247 -#: a854006054ce4ffe94bbfa73bdbecbf2 +#: 9e8dbee6e8f84d08b1a54fffa06394ef msgid "" msgstr "" #: ../../src/faq.md:248 -#: f80eb714e9df417fbba555b5dd5f4d8c +#: 1d846bfb5f054d09a4afad1da8e4b642 msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 -#: 10af80fa13af4158aec7060550485350 +#: 2d0e95fec8084787b734388d60188574 msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 -#: ad1c26711ccd4efd8fdb25f9293d33fd +#: eccc4a364330470fa474dcaaa3433390 msgid "" msgstr "" #: ../../src/faq.md:268 -#: 49e2095b51f84f609f5d4bc088ad9745 +#: e945f6a337af4e4686bed482a4fe6c39 msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 -#: 52b8538177c64090af51f5f6a696c28c +#: 8a3efaa0ad1548428bcfd6e01d135cdc msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." msgstr "" #: ../../src/faq.md:322 -#: f96c9257e3734b8aa0cc5e065f74f944 +#: cdab644adc5643708870fb08c06cbfca msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 -#: 7dc0540508084a3495ff3b2ac90fd323 +#: 089a5a0b076b44aeaab4d69ee3c79f97 msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." msgstr "" #: ../../src/faq.md:342 -#: b53dc77466b24a67b52b8aadf4fab724 +#: 561172559c6f41a68819608fd9e58bb0 msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 -#: cf4e7f3977ae4f9b877072c2b1c4b533 +#: c5ee4946d2e840abaa3dc796a62652c7 msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 -#: 99b37739ef18443ca7c0e715a131e0c7 +#: 4f2069a2113c414db18eca95550e9e09 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 -#: 9b00b5a55ee941e1adbfe89e133791e3 +#: 31f3390e6771414ba7bf57c044c4b0c4 msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 -#: 07922147f7ab487ba2a1e7c43c9f410c +#: 3b77ce4930ae46d5be9f6965e8c54727 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 -#: 7a11806f0c7045b48fe58a271f814797 +#: 06f36bbe4d3840229b7374f27b86ae80 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 -#: fdaec25650ab4b0fb1c527610e24ae5a +#: 3cb2f70d00274a4dafd972ccd8c519c2 msgid "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 -#: 182959fc9f4746d082994e07d05c8cde +#: 093a1529262043ef84a99675054938e0 msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 -#: cc7752e9989e4a6d957682f479d6fc60 +#: 45b6d9acbfaa47e5984184f7da554d0a msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 -#: 6db1ebd2d6c74ceca889662cd7df5cd5 +#: 5705c9bacca5405ca6f14315a5575db8 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 -#: 3de2513c7d7b4569ba63f7e6d29137b7 +#: 82bfc285b59a439ca97d3278997f0fce msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 -#: ae3a9188706649e28f97bc4ec34c0821 +#: 181d5130101d45ccb22aebae3d154c2f msgid "The file is here" msgstr "" #: ../../src/faq.md:410 -#: e1ac97ab6ad3449b8c54933d25257f73 +#: e864390b5ddb423aaa10e9d33d257dc1 msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 -#: f6c402f7f6974edbbb5582c8e22f3869 +#: fe637c32fb15427a9045679b5da42ec5 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 -#: 190099a242a645c9b9f8bc3ce89d920d +#: 1f8004b9df8547029d82e57f9abdc979 msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 -#: 06a4f6ffc2da4d43b453d4784b42efd3 +#: 70990dc5a0034099921ceb89c89e2dcc msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 -#: 1901c34201054a9cae199b0dbb8b945e +#: f679e26f18d9455f945fd13361a9c906 msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 -#: 2d498470524d47f18f9936ace6acebb0 +#: fcd0273dbdd84e728cfd8fbe239f2a01 msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 -#: d7b044f5224a48eda09bc949cf645193 +#: 173ddbd1e7c64927a8dcb12a2a2140f8 msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" #: ../../src/index.md:1 -#: 2754519265eb426b940bbbd2b8d64e1e +#: 662fe273e2fb4042b688512955e450a1 msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 -#: f8d6e4cd54cb42c88182a43171d97bab +#: a15b52205f0145feaac298510e4d678a msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" #: ../../src/index.md:7 -#: 132d40fee3b84469afa80d5ff613bf77 +#: 512aa0c7166b429e8116f71eef007f79 msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 -#: 0f47157605a34ea58770ea898deebae4 +#: b1b19e17a18540939cb3bb7f8a700cab msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 -#: 6d269e8d70184034bcb56385a6ca198f +#: d58b36ac43ac44139897be752fbb1f87 msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 -#: ed74c9a4b623464480e2c184668fcec0 +#: 6726cf3585a646a8b4cbeb543cf84a38 msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" #: ../../src/index.md:23 -#: cfa67cf5521b414da6f7d34cbed283f7 +#: 2e504aa7c46a426fa959e7254e9a84a5 msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 -#: ee6b82bd86264e4bb1e8e4065b1e6b9c +#: e7be0df0838b432d9c7f296d777f120b msgid "Table of Contents" msgstr "" #: ../../src/introduction/basic-concepts.md:1 -#: e208c8a7506e41dcac9a403c5d2850c1 +#: 173e0816db20432c8d9dba1de5393dee msgid "Basic Concepts" msgstr "" #: ../../src/introduction/basic-concepts.md:3 -#: ac62d326a68145b695e46b714d4e8156 +#: 30eacc583f6841719e2142d283811d97 msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." msgstr "" #: ../../src/introduction/basic-concepts.md:10 -#: 984e6676b9d04c7092bc492f195dfb91 +#: 791b8f38a14147bbaa174c7eb595f17e msgid "The CWL Specification" msgstr "" #: ../../src/introduction/basic-concepts.md:21 -#: cbe1d761da5b403d9605fa1fb8e62fdf +#: 1a3989dcbb9844b39d84bf6df6b352ed msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." msgstr "" #: ../../src/introduction/basic-concepts.md:25 -#: 3a71b269bd3c49eb913cf69b60373c24 +#: db1bbc6e980f404f9f3fcd08e92ee9a3 msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." msgstr "" #: ../../src/introduction/basic-concepts.md:33 -#: b171b72c48d44050a3416a7a42c4021d +#: acc7887c65974114996f700a38a7eccc msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." msgstr "" #: ../../src/introduction/basic-concepts.md:37 -#: b3df1607e9d242d78b22dc44335fbe2d +#: d2476d9bcff44f21b8d84a3a0d87a246 msgid "Implementations" msgstr "" #: ../../src/introduction/basic-concepts.md:39 -#: 078b58ffc1cc4d25a7c4eea3bb76e025 +#: f86415e4d78e48c4a8a76ced81221b98 msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." msgstr "" #: ../../src/introduction/basic-concepts.md:44 -#: c3869b4ec5ff47d99e8da79770722e04 +#: c5524d73708c4c779980528864506fd4 msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." msgstr "" #: ../../src/introduction/basic-concepts.md:51 -#: 2482c84831fc4dfab629e7bfcfb41cbf +#: ac46a9f8850a434bac5bc2b41ee6294e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: 9bba7c4f783942e4a299603430601363 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: e2140e0f0e7747ef8383887c20a7945a msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 15bf490724cd46dcbcfab44633c5a9a2 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 51d52d051e654a8395239f88df7c9d8c msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: eb496cc818524fa7bae5a22ddd00a19c msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: c4a22d12e7f149ff901d27de32b9361d msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 7618de899a7043989d77baacf62eb7b2 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: 6f1544a220664b79b04bf008058b5a91 msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: fbd14ac9a2f541478a320ed4cbc69e13 msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: da4dba50d25d4533b3dbb92f54d32a30 msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: ce11c9f8d65c4268984d0384d95144cc msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 3a201aa497e84f70855bb2251e7e3281 msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: b78f7fa2be1c4bb090f6da895457ad1e msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: f7e95d264ffa4e2db0864faccd9e5a0e msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 3f1e5b01e49a4dc1b1c99936a4589afc msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 03c3048f38ae4938a484cf02001877b3 msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: f9715b5ec65c405c849bb030c1927060 msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 442662f50e9e4620970ce32b1b127969 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: 2b34c786af3840e88f29d214e19dc837 msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: dd6aadff8cf54ce78ea6b317afbaddb0 msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: fe7f1f0b28434f8aaf0f6ac6589a83f0 msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: d10cf45b3c7f49dc98bc0e5d1246f224 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 #: ../../src/introduction/quick-start.md:94 -#: 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf -#: 3439764fab0e49d2bcb7c9fbae556e65 +#: ebf339ed376a4d3b89b15b4d5afe593b +#: 332b6e8b831e4bc5aed3745938230a57 +#: ce7fc63b808d4499b9bf9828c2dafe35 msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 8badec9987ba40609cf1f626172b2b2d msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: c75a8b4bf0e24781bf6713cf6f013cd1 msgid "The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 79b146ffe6d74e1b8f6019251dc4b7c2 msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 07cca9a33d8f4b77ac6ad35ca8b95655 msgid "The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: 31db11c8ddf2423192a8b2063b3e91c2 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: d81dd96143ea444aa78ff45cfa0584b3 msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." msgstr "" #: ../../src/introduction/index.md:1 -#: 1769a0cbf4de4d77879c1f202cd11af9 +#: c54984605872472190ae7771809a20db msgid "Introduction" msgstr "" #: ../../src/introduction/index.md:3 -#: 950370f0a36048b38e1bde9b78f80816 +#: 01a237b8ec2f46c9acd31d142591ce75 msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." msgstr "" #: ../../src/introduction/prerequisites.md:1 -#: f01faaf1b253407cbbc2f353c24774f3 +#: 3fb9888b666945eab1e3ff109646c574 msgid "Prerequisites" msgstr "" #: ../../src/introduction/prerequisites.md:6 -#: 353b14f06ee845d0a06a829643e31534 +#: 5fb0486762354f93853fff209f835c08 msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." msgstr "" #: ../../src/introduction/prerequisites.md:12 -#: b5a0607096814c0aa577f977c3b57c54 +#: 5f1e7a608e0b455196d191c845a5c98e msgid "CWL Implementations" msgstr "" #: ../../src/introduction/prerequisites.md:14 -#: ff2bb4c6504b456bac7ca9c514414dbf +#: 7ba4b5c51be24f5392949d06ee42e018 msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." msgstr "" #: ../../src/introduction/prerequisites.md:19 -#: cbbcce4c2a96471b8b0ae3593ad59de4 +#: e2d3e6dd13b14d819a504c35da6fe8e7 msgid "Operating System" msgstr "" #: ../../src/introduction/prerequisites.md:21 -#: 5089fdba8aed4113983fa86e698df98b +#: 91251d1f0efb4d4cb083b4517ff3107a msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" msgstr "" #: ../../src/introduction/prerequisites.md:24 -#: dbaa4bae22fe4d05b18d7351967ddbc3 +#: 6ad263e267514c5fb05794d3d76d418d msgid "Linux" msgstr "" #: ../../src/introduction/prerequisites.md:25 -#: c05187af85be41b782678b79627f8fbf +#: 8a3bfd72dccf4a8c874a96aebcbe5cb7 msgid "macOS" msgstr "" #: ../../src/introduction/prerequisites.md:26 -#: beb6cf4d7c154eb9b6d7fe024a318ed7 +#: 5195706d9c6c4573aff135fd539759a2 msgid "Windows" msgstr "" #: ../../src/introduction/prerequisites.md:29 -#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: 9c4506915e4c40599527bc1d2b18645b msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." msgstr "" #: ../../src/introduction/prerequisites.md:35 -#: 56d78c95daa54135b6aa9b2bfdc34d01 +#: 37d9eb784ec1425786158f98e3f63890 msgid "CWL Runner" msgstr "" #: ../../src/introduction/prerequisites.md:41 -#: 0f2704bf1f7148be95e999e312899f11 +#: 572f493a985141a1b92dafbdba92790d msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." msgstr "" #: ../../src/introduction/prerequisites.md:46 -#: 86264c9e56104ecea9146407c379aae2 +#: 9606d3c4849f4b17b2e55a298210f055 msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" msgstr "" #: ../../src/introduction/prerequisites.md:51 -#: 0a0f0e5151ab4c498b4f8a12c016f28d +#: 754fc59967d94ffa935284676d55ffed msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" #: ../../src/introduction/prerequisites.md:62 -#: f7aaafeee230400da056464c853582c2 +#: 2905c6362d4146e8b35bc74744841972 msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." msgstr "" #: ../../src/introduction/prerequisites.md:65 -#: 5eced7e4cd084e8a806b1d3b12d0c000 +#: 091278ece252483a9838fb771de3e04e msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:67 -#: 040c019b6e844eda8c8c2b210852516b +#: 0928a5c668c3414a945bc9eda147892c msgid "`true.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:73 -#: 6391e08e0bde49f4b21286d8fdb97433 +#: 56f3c481762848298214a88e559fc0f9 msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" msgstr "" #: ../../src/introduction/prerequisites.md:79 -#: cdef47fca304479c9a9df75afc0afb35 +#: 710c266ab4a5477b84d6ea987420fa20 msgid "Validating `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:84 -#: d41c4bc740aa474ea09a7cbd267c8840 +#: cc353db5da2546bb88a77ce1a202ff9d msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" #: ../../src/introduction/prerequisites.md:86 -#: 24d7be55d3994f0b82c38da47918e0c9 +#: b62df08ec96f4cdb887600079856dd76 msgid "Running `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:91 -#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: 97e02557293440d1a58ba659dad21113 msgid "Cwl-runner Python Module" msgstr "" #: ../../src/introduction/prerequisites.md:93 -#: 096d0a50f69e48bd9915238d1b4264c1 +#: 0935c3ff01634c75b5c91546dc36c7b9 msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." msgstr "" #: ../../src/introduction/prerequisites.md:101 -#: f9df974a8e2645a6918e67466bd1fdc2 +#: cfb37fd605164a8d9cc75bf892ce97c0 msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" #: ../../src/introduction/prerequisites.md:104 -#: 71ebe91d4bda473abe87578929433212 +#: 5f06a7a6aae343d989a5b30979c600f6 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" #: ../../src/introduction/prerequisites.md:111 -#: 746c6fc9c29d466494458a08d4c96672 +#: 5f956260f3874b6dbeaf3ad7ecc09c9a msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." msgstr "" #: ../../src/introduction/prerequisites.md:115 -#: b9cc5a843a0f49daad56e9303657bdd5 +#: d35e4effec554a638d6c3047ef3fd05f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:120 -#: 34ab40437ab646488ba3ee86cd7fe071 +#: 15a1f944a0d642729d3736ed1c907074 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:125 -#: 705807fae182425dbf4244dbf2be1226 +#: fa34c808bb494ddfa3f3926bc42e650c msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" #: ../../src/introduction/prerequisites.md:129 -#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: 0c15f62eb7534e809f625f3fa213e92d msgid "`true_shebang.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:135 -#: 164c438baab54ec19bbb4584a10dd411 +#: d67719a6f0ce4ba1bb6152a10507b729 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" #: ../../src/introduction/prerequisites.md:137 -#: bf8be77af6154326b28442c5d2e2b852 +#: 1c96e75281844bfab0578bab2e816854 msgid "Making `true.cwl` executable." msgstr "" #: ../../src/introduction/prerequisites.md:144 -#: 695184d1b45a42f393e2da99c3721773 +#: bece1fc3c3f842b0b30d8f1b7fbfc200 msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." msgstr "" #: ../../src/introduction/prerequisites.md:148 -#: 7c4f45b3e7b549e186126693aa4a3d4f +#: a7caa36b0f83448b91ef2e76e30abc51 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" #: ../../src/introduction/prerequisites.md:154 -#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: 39321e93e9994fcca20b425aa45c2894 msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," msgstr "" #: ../../src/introduction/prerequisites.md:161 -#: eec6c07455384630809ff1c532bfe7d4 +#: 601cf500d76c4e0287af4429a46b36d2 msgid "Text Editor" msgstr "" #: ../../src/introduction/prerequisites.md:163 -#: f6b39b12bd5c495cb53e2795bf9200ed +#: b286d5359e184ef58054c72df4014629 msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" #: ../../src/introduction/prerequisites.md:167 -#: 2fdb62a13f9447bc89183426260ce781 +#: e14423edd829401faed0950772123240 msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" msgstr "" #: ../../src/introduction/prerequisites.md:171 -#: 1f07135156254f74a6b043bf33d00cc3 +#: 889c44360bd54a0e85e7f0e61aa6593c msgid "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" #: ../../src/introduction/prerequisites.md:172 -#: de344f356b1c466d9131cdbd4d7353a3 +#: 7b9bff73624947ac90a99c7880e2e911 msgid "cwl-plugin for IntelliJ - " msgstr "" #: ../../src/introduction/prerequisites.md:174 -#: 3f9324ede11441f58d93875867034cf0 +#: c5ff687c86ef4ccaae25d8bcfbd5f873 msgid "The CWL community also maintains a list of editors and viewers: " msgstr "" #: ../../src/introduction/prerequisites.md:177 -#: 6ce8b81560e341c580d316d69202b268 +#: 0a610a9632064deb824afd0719429d3a msgid "Docker" msgstr "" #: ../../src/introduction/prerequisites.md:181 -#: 40cfd559d6a848d1aae354d3bdaa8e9c +#: ec0c47438a5242cb99dffa7a4997e95a msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." msgstr "" #: ../../src/introduction/prerequisites.md:185 -#: 8a9a50b0ebe847ce90593881ffe0d69c +#: aae94ac2114641f186eac0f4117223eb msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." msgstr "" #: ../../src/introduction/prerequisites.md:191 -#: 923cf9dd6d6c417aabe42f9fa62ffa35 +#: 209e072724ed4d27b37e9bff6d55d811 msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." msgstr "" #: ../../src/introduction/prerequisites.md:198 -#: 9390b03889de44638141d705e0ef8322 +#: 3bf47876e3694e6cadb05123326459cb msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." msgstr "" #: ../../src/introduction/prerequisites.md:199 -#: 12042e411482458f8c35a2491f9433e0 +#: 459a65b8e67c4a9aaa03138c1abe94ad msgid "The Python `venv` module: " msgstr "" #: ../../src/introduction/quick-start.md:1 -#: cdd4196f9aa34beba115901ec97913b6 +#: 898eb29ac7714c69840b795633953a05 msgid "Quick Start" msgstr "" #: ../../src/introduction/quick-start.md:3 -#: c43d9675ed134b78b02acb5a102a764a +#: 2a658bd2d8ce4533ab7e056fc3a3ffcf msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." msgstr "" #: ../../src/introduction/quick-start.md:7 -#: 280936bb2a22469799b2c9e9ba22adee +#: 32dd2e28cf0f40b6930750f0162355eb msgid "“Hello World”" msgstr "" #: ../../src/introduction/quick-start.md:12 -#: cb203354977d42a58112d09357f62565 +#: 471c47d311074ecfac071b6d52d9cfb6 msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" msgstr "" #: ../../src/introduction/quick-start.md:16 -#: 9e51962a7e5c47248f3e20703ae101eb +#: 5078140028ea4d04973cb9cd20f0607e msgid "`hello_world.cwl`" msgstr "" #: ../../src/introduction/quick-start.md:22 -#: 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ab127d4ba0a44526ab129587a8160923 msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." msgstr "" #: ../../src/introduction/quick-start.md:27 -#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: d5cc6b4295a74f3586f022b0227759b3 msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." msgstr "" #: ../../src/introduction/quick-start.md:32 -#: 498a43362a4749f3b8b433709d34a1d5 +#: 585a4fe583ce44e180a062742b3b0849 msgid "Installing a CWL Runner" msgstr "" #: ../../src/introduction/quick-start.md:34 -#: f3e56aedd56b4b93bdc3894273e8c144 +#: 0d81b0c9ea58420789d1d71cca32ce88 msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" msgstr "" #: ../../src/introduction/quick-start.md:39 -#: 81481f5b82e4488398f87f0a169bd359 +#: ea4ab0782d8049d8b1b89cea4ae60048 msgid "Installing `cwltool` with `pip`." msgstr "" #: ../../src/introduction/quick-start.md:47 -#: a81342e756d24c40acc15835d0a768f2 +#: f6f3b7453a254f828bd4c9e9fef92bed msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." msgstr "" #: ../../src/introduction/quick-start.md:51 -#: c12cf89f8b9a421ebd05330326e219b3 +#: 3bf9050175d4444ebbbabe219412574f msgid "Running \"Hello World\"" msgstr "" #: ../../src/introduction/quick-start.md:53 -#: 9b68bcb1a41849dc9601ab47c5bbb0fe +#: e03f72a14dcf4bf38ce8232598ca761d msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" msgstr "" #: ../../src/introduction/quick-start.md:57 -#: ce04027dfcfe4b7b91ea3c2136b18b23 +#: 3dcfb2facd324dccb3084c02487625dc msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:62 -#: 0d8a788402914ebd8f09a5ca80650011 +#: b8531da183964b02bca19f818ec076d4 msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" msgstr "" #: ../../src/introduction/quick-start.md:65 -#: 6d0b679efab24813a7a3b709ade940d1 +#: 7ba1ddebeb2843179fe99fc410b193c6 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" #: ../../src/introduction/quick-start.md:70 -#: 2ea056ab04b6419a9faf350de22a17f2 +#: a6dc303e9d284b60bf1102212505ca27 msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" msgstr "" #: ../../src/introduction/quick-start.md:74 -#: 1a44a545434b448aa956005deeed90a8 +#: 59ac7830ae3e4d7cb1bf503e8c90fe30 msgid "`hello_world-job.json`" msgstr "" #: ../../src/introduction/quick-start.md:80 -#: e76bfcc0c9f84bcdb3f6d5277869a88c +#: 6d1d6f42ada2418ba0a1de1371825b9f msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" msgstr "" #: ../../src/introduction/quick-start.md:82 -#: d4cdbe870a6f4a68b542ca719d989062 +#: 1cd924fe8ace4a82ad8701f37b5e7d84 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:88 -#: b6d59e4b9c854abab1b3f7a0fa26f504 +#: aa297c52cd964291a47bb91c0135156b msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." msgstr "" #: ../../src/introduction/quick-start.md:96 -#: 5535b98e8b1342f09f003ec6db2b44b1 +#: 28b02c90397745bfbacc03c3b1034939 msgid "Continue reading the next sections of this User Guide!" msgstr "" #: ../../src/introduction/quick-start.md:97 -#: 77e43c7117fd4c52b140f0dd52cc3963 +#: ef2a4f39f01049b891868b84d968c0dd msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" #: ../../src/introduction/quick-start.md:98 -#: 7282abfa7155497ca47c30f9abfb6474 +#: 89e3fa8dceda4f0cb1cfdfd1f17fe4df msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." msgstr "" #: ../../src/introduction/quick-start.md:99 -#: 176d8d47830f4031bb95dc231ebf1303 +#: 7cd178223ba94d1ab3ee8cc5f13a8dcf msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" #: ../../src/introduction/quick-start.md:100 -#: 82a7ca3703bc4f0daa18942a1ac8943b +#: 46f6f8d050ce4f8c897056167d9707a7 msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" #: ../../src/introduction/quick-start.md:101 -#: d039a9d6461c44628d4660c00d9ce6ff +#: 5ee00ee409b746dc951ca1d4c360e624 msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." msgstr "" #: ../../src/introduction/quick-start.md:102 -#: fbc3383d9e1c4eaca7931c3cc4f1752b +#: d4af972281174b8999eab55ee0ab1a0e msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" #: ../../src/setup.md:9 -#: 1330bd38c4b5495f890b98c669f81a9d +#: 80401cfffae042ab9ec4b3754af04b25 msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 32f86f911ebe4a4c94975f81742333f3 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: d5f1ad2b95ad46d48f8f2ca5e357bb5d msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: c53ceee943ad4acea779e072b9137889 msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: 7dfe9dffbf5744299bf232599644c7f6 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 -#: 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: 00709fa451134ee09a0d808e101f28ed +#: 991172e201ec4796992a349dee44f090 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: 1f3c23a4769043ca985b8ddfed19391d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: f81b43c7cb194a1cad8672129223c833 msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: a20073a8f5374eb1bc8531ff33e622b6 msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: d08869beca3a4774baf1097b63e79474 msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 -#: 612c4a66c36a43d4ac5d74c1757d6845 +#: 109b773789024b2b9c063a6169c6169f msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 -#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: 959fa04f88e54d42b9b774cc95d85ee0 msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 -#: 4bcb84707acb40a0bfe2ea0853cb10b7 +#: 64674980c3f24c45bbfbf3f957dda55e msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 -#: 4dee8504a8e5496081dadc386ab45540 +#: 90f2e4265919446a902e17627f4420e2 msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 -#: 674c238b25e240eda05e22e399f2f78f +#: 6b5f91a749fd44b5acfd6071c9913342 msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 -#: b651f80f47b4442fbf29454a233697fc +#: 5fe2962837b14f0e9989063be4a506c3 msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 -#: 263a127a77cf4c41af76854f22f1f260 +#: 4e1bdea962ed4618884cb9d1d59d7509 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 -#: 3a87a0fb2a364e3da5aaa4017e430b19 +#: 37eff4ca02e843259f6ffa38e4a87a04 msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 -#: ecf2b9c0b1664afe9c4e180610610021 +#: ae47231c203d40a98c10045038ea9b65 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 -#: e24cb13d98014e558b6a6946758359e0 +#: 018a6d5dbf1044559b365c7b9017eb3f msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 -#: f2b14a92374e449d9fb1e8c86ae0dd61 +#: e073d8f990c44b09a73d642cfe49bebd msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 -#: 928e3df7ca3e479ca6474a8e72cf36eb +#: e04fae88d9b64493ac69eaee24585098 msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" #: ../../src/topics/best-practices.md:55 -#: d355f035676446c88b028f327aeb4829 +#: b26b9c9b1c4346a297a31c9721f0172a msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 -#: 339b852df24242189d6efcd2898a3396 +#: b50500c3c3f54b16a535a16175a44653 msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 -#: 3ef57e6862f240bebcf193a52397af0a +#: 623f3a804199449bb85e23e00c8bb507 msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." msgstr "" #: ../../src/topics/best-practices.md:69 -#: f1a7c4f896a04a80b0c5f6a1db61ff8c +#: effea0b1356447c0899ca0746667ea31 msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 -#: 1ac4c3d8c3e44bd1af3fc5df70051926 +#: 00e8ef87864c4ca2b2c1c0548b02b38d msgid "Custom types should be defined with one external YAML per type definition for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 -#: c858f64e66f048a5b0032ef3e4d83694 +#: 6e6f48d70b894a6c959ca30fe6bad772 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 -#: fae385da16aa443da996fa23ac03d6ae +#: 02fe08760a4a4ab49e96f4e51316a81d msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." msgstr "" #: ../../src/topics/best-practices.md:82 -#: 92430be71ecc40e18bbbb80d5576c613 +#: 172ed7915a654964ba63f860b2d65330 msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." msgstr "" #: ../../src/topics/best-practices.md:85 -#: 387d83db81024f65aa9a890c2d07874a +#: 4d0a2871a7484e21b3c39c4dbaaa63fc msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 -#: d8e2280a75a74916a1630afaa2fe2ae3 +#: 1eea9f1e284447718141f5417b6bb433 msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 -#: f1c1340f9745458980e0fbd641738687 +#: 509411d353fe4314b087b81b09ea960b msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 -#: 5424e5472c3d466fa2a3d2022c6cb475 +#: a54bc80bf08243bba67d98dd682ee134 msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 -#: 3f4e98f6bfa141feba8c4b120e3d03e8 +#: 69ecdaea24ef42eebef9d86e5d716b11 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 -#: 12f57b2ba76b492abe1816e06bfb1417 +#: 3cc5847468d1478bb5589dee68147189 msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 -#: e1f657a46ce94a0d83671540e2cc2dab +#: 98c6bc409420485095ae65d6b0b9a3a0 msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 -#: abb83f0097654a43bd78639d3dbb2bc8 +#: ebe23e5378514f888a9ec32a2adb1e98 msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 -#: 3b1a9ae3412f4d6e96a39b9a16934232 +#: 387cfe85604f424f8d31c4a4c9c15edb msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 -#: a5eacdbc9aa142c890b177869da4143d +#: 7b1d65754e854693bb60289c97d3fb5d msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 -#: 1849b8f3ae1c4a84ae59a78ffd6b371e +#: f440cef729c8410281432307a4da8d55 msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 -#: e3bdaceae8784ab0807b2cf356a98580 +#: 4fbb8ceb1b59480583ac611142167049 msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 -#: ed521ac365db4a6ba5a1051fbaa2932e +#: b87869204838415bbf694214e3680593 msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: 12cf5f2264504c44a2173e858bb2c283 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: 7694f9cabfe04308bbddd2c88ae6d9b9 msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: b557dc4f8ef549b98f59412a918643de msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 3011eb003c084285b30cfa56a8da45b6 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: ce78b2d147054da895beba66d0ecdab4 msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: a973846ec5a946eeaff02c5b00997da9 msgid "To test the above CWL tool, use this job to provide the input value `message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 #: ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb -#: 2699fbc4376148af91b7a5a6cdac467c -#: ca03defa3ad14cf698171cb09e3055c1 +#: ccec7f73b9d948e79a6cdf32bc124092 +#: 9e8eb1542db640ff9e300649ce50dc9d +#: 294fd83a97a64249bac38f7482159372 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: 22948f19cb78485f8f86244686a35c09 msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 001d9579bfce438e865377fb9c2df776 msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: e62618db8995428bb3f260e03ac8f459 msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." msgstr "" @@ -1291,193 +1291,193 @@ msgstr "" #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 #: ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 -#: 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 -#: d6255506eebe44be94c5ce703c44a513 -#: 7bbd2d738fc54649aeb10f8d2bc38b6f +#: 98e0548845fa447fb05a29c9fc2f17b5 +#: e9801b2142cd45368a73ef9b121c1d08 +#: 457756c4e9544f068af897113358cc89 +#: de5e8aad4e3046bf9bfc2ad8ccba17d0 +#: 6d5ae75431424ea788c3440606f22940 msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/custom-types.md:1 -#: cb34fd4c8cb04053ada491a227651048 +#: ee2bca9bdbb74b60a706c3118d6a17ba msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 -#: 67573252cc064b27ab13eebc468ac58a +#: e63ae9694f40438d872d141ae824a42d msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 -#: 73e68b3af9cf41338d843c0c40e50cdc +#: 750fdd4c270e46a09f79e867358f7414 msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 -#: ef5f35acb97f4ddfad7b688712f53484 +#: b3f688cc82444ef7a7a0aa63dac39cac msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 -#: 7015dfa99a6f4cfb87ebf0ed61e8043c +#: 3638be18b4f64cf08053d512e590dda3 msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 -#: a999b1acda2641598086648c64aa3831 +#: 7d5b9c21739c48f18c13614ca6967f6b msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 -#: f8c12a58cb0b46a488823c6ae95f25ea +#: 8fea29993f944d8d8d3181afa29bd0a6 msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 -#: f25a63e0926d4932bbe64b2e4bdabf9e +#: 02d0b648d70f49d7892f690be06df585 msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 -#: b0a4df0fd3ca42338cff4689235dcf4e +#: 0743bef42b9a42328849c8c2f9da9eed msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 -#: fecfbb44456640d8ba05e519bf2ff564 +#: 85c5d0cbbc6243a6823f5eeac0f85dd9 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 -#: d718630a296545f3a989c8c71e9ddc77 +#: be848f30769543eb9c0be55263e3f758 msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 -#: 9a97acd430064710bcdf76edbd9f711c +#: cbff44a64ba4432cb59a82f82c2f0103 msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 -#: 59014808cbef4c02aaef03129d8a29b0 +#: 617f1c0084cf42d9be4c7a8fa5a48432 msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 -#: 3c821c9c46d841ec89b8a5b1018f3af8 +#: cee79afa3c6f43c29ef05e06b7843d35 msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 -#: bfdebb32440a4034beb42135e38884e8 +#: 225903b11efa417989df42de86ad2451 msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 -#: 777d4a52f7554eff84db2df6d4d0f729 +#: 1a5f058290064c1cad05e63eb127fcbb msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 -#: 48deb71f361a43e48a56ed483075bca8 +#: 74ad8d69cf294ae880dbbe28e25b3545 msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 -#: 716b56506ca7470299899c5d820a9ea2 +#: 5293e8ee9b3b4f59947cfc164ef111c4 msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 -#: b63e6f5a2e89431c8fc7d04f47fd69fe +#: ffa1955c759942c68e7589429e5ea86b msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 -#: 39727e9058f24b62b8746a46d3f812c2 +#: 038bc0ba5f6a405a8255a7be76979baf msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 -#: e3ecac0a8e604f2b98a2a12b0579990a +#: fae1c63de02e48c0969a98e4c49b2e06 msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 -#: c8d648b765ec499a8e9c464590838492 +#: 7093a94695524851a5463193f0701b78 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 -#: 007a345b4bad49cf996c4301b8386473 +#: dc8274ecb15948c29a31db89b12a58bd msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 -#: 2edbd398eadb458b8eacd5fa5496f0a2 +#: cec8eef8a5aa49778ecedd4195ab9f2c msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 -#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: df100967597043c78112bf43b520cfab msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 -#: efb5fd14988c4e2a8f834ee5369d4102 +#: 59ccf4daba39406581a6bc2d9bb1b7d2 msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 -#: e833649b951841c49397796f996d29f3 +#: 570cc75699dd4e0a987fc9aca9a01ee4 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 -#: 276f688ba7cc471a842f085ca852b1d9 +#: 9e123723048546d495ed5110d7177708 msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 -#: ebf399ea4d5f47b9be03e24f04c69f2d +#: 26543894f6e04270b89ab702451bcc89 msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 -#: 65e0cdd505b944caa40f65e612cdddfc +#: f403c1d4e43a4aa0aef8488d2b5a6262 msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 -#: 8b70a1ad70514039b97164fa630c12e4 +#: 249dffb569a944c897ce5862e5f28fad msgid "Note that requirements can be provided with the map syntax, as in the example above:" msgstr "" #: ../../src/topics/expressions.md:54 -#: 2f28ab412d2843ffa5f14acdc01fc732 +#: 1641c96aca2f4923885fe8a509eb3a49 msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 -#: d957f55a6377422c9834f85d45e35009 +#: bc63405a0d964df2bd9493996abc48fe msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 -#: cbec9277b5004e50af2728cbda0df740 +#: 5c191d1420db4e26aca31c1b1e34cb75 msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 -#: e259f55f8000479bbd8009e25cf0ca6c +#: d6a5c65e824a4bbc94578df9597d4716 msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 -#: 1acb064f7a4a482aa0174bdc847c6382 -#: 0222780b98ac48e89b1b4f57c9df8590 +#: a7ff51fe564748229a88a0d3044dbc17 +#: c12625211cc542b68cb51365a63eef00 msgid "`arguments`" msgstr "" @@ -1487,38 +1487,38 @@ msgstr "" #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 #: ../../src/topics/parameter-references.md:86 -#: ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 -#: 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 -#: e4e68011dc5f42e4918c747afa7d764b -#: d44e3cfa661840eb851782e24caf1b68 +#: 3a64ccbbf70447d1a813a725e528b6fe +#: 5fb932af34a54a0ea691260d43053eba +#: 2a2286a9c8494e3b88db35bf63230f33 +#: e7f1993580f0425098a719e83a64cc7f +#: 05c34a5a2e404a14b9d284a9d0c73bd3 +#: e5b0293e6fcd4e9b8d7be3fc9fc127d3 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 -#: 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: 2fd5b42cafe34d3185888de041818dff +#: c158e9ee5fbf4e868b152a0a5880092f msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 -#: 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: 92697d3179ec48898eaea9aba3c24dcd +#: 3f29e4a3087847e9af6f19166a8def9a msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 -#: 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: d6722e3093884ad7b62696fbb2f48fdc +#: c0eaef93bc3743279549bcfb8b014ca3 msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 -#: 8210b36347a749889450529ecdf4ff0e +#: 37c493fdc2f0410a9748f8faf09ce5b5 msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" @@ -1530,14 +1530,14 @@ msgstr "" #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 #: ../../src/topics/parameter-references.md:90 -#: d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 -#: 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 -#: b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb -#: bd61499b71e64164878dea08d6d7141e -#: ed875a006df64f9e8a55fa5e9fa87404 +#: 9cfb6ca1255241aa9e5928ea981286e9 +#: 4ff7326e660f42d8b45c3353005554f8 +#: 04e3eefe4ec445cb90c2fa42344aaed5 +#: 07611b01b06a4afb808322a0dccccf30 +#: 6020618711d449a48618c11215453487 +#: c358a25b1f9543598b90d3df7c012b85 +#: c610220d06484d589313dc29faf8222c +#: 7b132c6e720f4256859757778f5c4fef msgid "`format`" msgstr "" @@ -1549,1574 +1549,1574 @@ msgstr "" #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 #: ../../src/topics/parameter-references.md:91 -#: 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 -#: 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 -#: bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c -#: cd7a0190511d4613b09600a3b1e9d55f -#: 47def3b078e2402182039be0227090ae +#: e193aebe7124444c90be1f6cad81482a +#: 74652fdbeaf14d82b9c5053e322504da +#: 93d2b17bb236426286ffd51bbecda61d +#: a44c278bde5849aeac122c981294332c +#: 6dfc264200a9496f9d2458fc759993d8 +#: f71216a4b35e4157aece5ffa2602d8bf +#: 662b36e3505f4ac3bb5070bb6e055217 +#: ee3d416cc68c4f11a79849bb67395f1b msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 -#: 23088850ad02459696f6bbd385109aac +#: a3c775a0f04b4541a9b712bfe2e4e69a msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 -#: f02257a822ad46ac93c5981531cc85d5 +#: ef16c4a9a7ea415fa399297b63b9710c msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 -#: 989a1c4aaa1143be9f53b90cd8b6d500 +#: 2592e429c74c4ff5b8ba68a36f060c1a msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 -#: 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: 5cca4c2ad617400eb6efad4066b1839b +#: ba1fff3ebb274dfba845b3ee20ebd71f msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 -#: d555a3d991e344a5a8e1289168d7c6d1 -#: 44b3f123c9b04a308c1161b742a7b34b +#: 6914526c0a7c43a2a05438519508ee0f +#: 722d3bd7184841639b9f9a38914002da msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 -#: e9fa9430535c424fa3e8be5d460d2ba4 -#: 0e306cc923974d1db83fdfb45105a11c +#: 737b0f9392154241ae5b56c6caa823f5 +#: 7b46d408e7e7481b91a950b2d4010c9a msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 -#: d289541e460147aa933f7878996f8649 +#: f09e7371708b4c0685eef2a314791ccd msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 -#: b0290d1a477b48119e17cf1fed9d6dff -#: 446f1190af7a40a0913ff04ce7aa938c +#: aa6ca1def2024c98b9d5542de1a81425 +#: e9fc5f7fa4474dfc95039b94167fe894 msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 -#: 81b4d1f23a3642bfa9bb395b94260cd1 +#: 6c37a1ff939748bf83a86c07c3d017fe msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 -#: e1cde4aa32c041238ed2596173c6d824 -#: 557694f82e314baa9ccafba14d6ff2c9 +#: 3a8126b0a0334df890b2be2c693ea5d5 +#: 61744122b7d7494890cbe6b2fb72b9f7 msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 -#: c2a92d3eca7f4ee39cec649170eeea53 -#: 3c939769ede94602a67fc50c435741cf +#: 93cb9015dacc4b50a4ef177ce4ece2e7 +#: e0c7ccc8f8664cf794cbb7330355f3fe msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 -#: f495da32f05a4a5ba9539be0a54c1a59 +#: 58a1773b1cf546d7890010fdebd47388 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 -#: bdb4c68a175047ddbe141ca24960127f +#: 230f3227ed1144f7abe0f8c231bebbd5 msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 -#: 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: c9534670f5f04769aa3749c3778eb705 +#: 5c77dc9f8afe4dd88933943030e836f2 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 -#: 718ceee9973240ec9c100977bbcc8921 -#: 2b25152f6df5494a8632f3ce631c20d8 +#: 4ec8bbac5fb14371a6a4cd53d7cd6450 +#: 7b0887a8caed41b2acccf7021bb323d3 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 -#: c07ab08eb75d4528949c56a3d7c12b28 -#: 846cd427ae25410eae7c920b237edcb0 +#: aceedfb558b246bc87eb3eaedea187fd +#: e5e8b8c75f0f43cbb6e160e5bf810c6e msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 -#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: fe3b9fb45e01490498c5a35c012b3de8 +#: 266dfb5fe6a842078baf66073cac9623 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 -#: 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: 85f424cbfc85460f9da310aee1ff0b82 +#: ddf82b12b12d416fb65f3ce3f51bbdf0 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 -#: 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: 966e88656ae5402a975022ee60646283 +#: af14fda3cca645fbb2f3c5825fe0788e msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 -#: 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: fec70bb106ad4d95a2d55ebdcf711afc +#: 09120baec1464afb8aed4edd773bf509 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b -#: e3b76f42c924489f9a0bcf5a7b636d23 +#: c98db5b115ee4c4abb211481fe7214b0 +#: 2e128858cd06466680fc6bbfb577b818 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 -#: 97b61352363f47cb890e8937c5613fa3 +#: 1dc4148caef748428a7d13caff37b1b1 msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e -#: a258554d462f4f5f83ece28d5b2fc584 +#: 8caf296626024598b4450311ade09e56 +#: 568406e34c8642578396177b40043014 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 -#: 8d0b142bb7ed4e61b8fb03de197240ce +#: 947b1ca132a54ed39745cd12ebcd65e1 msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b -#: 9d4889c8cec24351a7a9e3c547e331b6 +#: 3af8e4ce750048e6b9de12d26b9647a6 +#: f56fb5fa08994fe08cc8ae8c193828d9 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +#: c6dbe0a66b9f47e5b4b47c44d9f54519 +#: 063e2ae9a0eb404e8c277ef7090eb6bc msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 -#: 6abeba392b0444b19f92a19f178a4682 +#: 72acfeef964841e7b65937b62b5850f0 +#: 39c6edc2866542cfa7da9f842fd3edd0 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 -#: 0bc424ef2ca346099f29b937379908a0 +#: 5fa512d352d945e7a3e0d59b0987cd1b msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd -#: 949c376120d8441796ec9c89364f8851 +#: 79755be159fb45b0ad06cecce623ce2c +#: 520bf799546b4700a4f38f950ffd913b msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 -#: 10d36a1adfd04144b401c993b12b4094 +#: 81e91df082834d2cab7ef1f62d8ba57a msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 -#: 29b73e1dd72744f68377f0a38c10f062 +#: e6bfd1dc2e324992b6c3332c11ae3445 msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 -#: 38a2afaf4a6c4d04909af22c93f2808d +#: acf10261df2944ec890d754fd56c6b28 msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 -#: cd74f34b21af4de9be96fd897efc469b +#: bda6b8f398554b0c946c2c7d96308a42 msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 -#: f12e371f3f1a4b0cb2cff9800352d48c +#: 454c02c3918647039c90ae387005dea6 msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 -#: 49d0fda2fc144e0b8b7c92afc1d8945e +#: e1fad28bf9cb4c4c85eb74dd520ba107 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 -#: 8f0e8f050e334ac08334e9215e1dcf61 +#: 9835d0b399b84a0084fe5a4d9e7e6405 msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 -#: 26c74b11bb1849cea0763bb74ec43e42 +#: 410ba7a5ac6349a98460c6337ee5c4fb msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 -#: 7a6be0005a6441feb67f036d005d7885 +#: d2daf50d7f3d4de18331c8fd2c8a5786 msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 -#: ed590f9e6f4f425da886b110295c45db +#: 8f2015c12b2b4d5d9a800ddeaf428f25 msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 -#: 093235307d6f47d4858e559b780ef5e5 +#: f0ff919ffc12439d89d7b40f51ade84c msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 -#: 06635145b441418aaae84dc804f3d6ac +#: 307a17a893fc4dafaec2a63a95704644 msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 -#: 973a9b257b1a4f0dbd4444d4f11dadd7 +#: 7f393e86b114470f8dda47b2deec63aa msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 -#: 04eaf1f7c630450db318dcd8b7626e15 +#: c3f459b87b96435583637b3f1573e658 msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 -#: c4098489fbb049789f022cd3e5c3d49b +#: 9f676022eb2744839ca2109920250cb6 msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 -#: 5979e4ae5c424276bdbc47f69b379d0f +#: ede7285f77864fb0aee6cfecc2c97fa0 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 -#: fd4579a3c9844492b314b5c3c1775fc7 +#: c55fb184bc614ee2b6e5e64611e5df9b msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 -#: 3f038e7371f84ed9b4547358dfb55a11 +#: 66b522f46ce242149386e79f63b32cf8 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 -#: e024bcb70e04412e90e1838426d1b69a +#: 64a20285785d48ca86227a0cf6353ad4 msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 -#: a3db21c0b3114802a8a5b610e252ef13 +#: 5f71bbe2c74e4260b79d4d9230d35397 msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 -#: 0f5bc8520d6a4dafa37c65343da9702a +#: 63bfff437e3348428f7e33ece7ec55e7 msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 -#: 5cb830da47464a8b9c3950983fa4d56f +#: 6ce83d9c06e4436881aa47d94ef41e0b msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 -#: 0535d5de416b4ea3b2f5996583deecc1 +#: 55006c594abf4e70a38e979568fadcf4 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 -#: fb47f73c38cf4ec59bd3021866a631f8 +#: 12ba2083a9ae4c78bf502ab762a29c7d +#: 5c8f1709fe61423bba3ceaca2fc7cf09 msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 -#: 74b28c1b09c6429b82e462e4ec61808e +#: 1a1905ff2d624eca952c8a53b3bee678 msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 -#: a2ce43b391864e8bbde16328cc19b32b +#: 368ff92476b14f5c8331260eafc5acb5 msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 -#: aebee48b742c4145a600fd2daf8c75dc +#: 5d530afa23f349a79f54d51d40724747 msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 -#: 56ee4dcfff6141d5bef80eb96559876d +#: 16f965f86712483aa7f95dfa3f944a17 msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 -#: 8d3a6d83e2e54c56995893c41590b7ff +#: dc629e2c90ed458b96107a6994676434 msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 -#: 5abcdebfa1cb401bb8892553be285fd3 +#: cf2f077cf8044079a7005e6e508dcd8c msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 -#: d3a55f71dc244026a97902de9ed819ea +#: 129e1d2a71894d28b009f4846754a75d msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 -#: 96671c56523c4ea9992fb5dfcfa6490e +#: d6791bbe575042b9a7282c69407dd907 msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 -#: bcc6246742cb46bfb185e415c4a3431a +#: e8da87f8bb664334adf831995601f462 msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 -#: 86dce36de687449c88fb5eb9d64eb045 +#: de6c322618304207b6d1364d1ec2dc13 msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 -#: cd9cea15f57b492ba4098237cd7c5bed +#: 43bdcf6dc1b14030bff27fa53289c02c msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 -#: 8bdb875b63104f699efe28ea0abb1e3d +#: 056510b42ea64717996ab49c307bda86 msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 -#: c6a0151a68494c0cb0176781e65e252e +#: 6852f5dbd9094c99bb68f2a88f76c9bc msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 -#: dc5e6b5e01d64226bd5dbbf3175fe010 +#: f33b6800367248b7927d97ad7b4be5b5 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 -#: 36ab1d9edafc4831bb1bca5f123b04b0 +#: 8ad812d7e88f4cbba83228ffb1711576 msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 -#: 7dc630ea86464b1dba3a4e5079260b3b +#: cc680bbf091a46f8b4b3dbe6324c040a msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." msgstr "" #: ../../src/topics/inputs.md:44 -#: ae37901a8dbe48a59e27ab4e2e6e2d30 +#: 446ac81f078d46289a18f494748f482c msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 -#: 651e032007ea4a119d20c820bb61f86b +#: 3d6d958d111943f3a2139b4dbb7810db msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." msgstr "" #: ../../src/topics/inputs.md:53 -#: 0b056dde9e87428996e47870b12119da +#: ba0ec9157709430c822f4e91459288e2 msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" msgstr "" #: ../../src/topics/inputs.md:64 -#: 628124a1670b4b058bb0fb6e495a099c +#: 2565f8fd4a15429e887aeb71eacdff1e msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" msgstr "" #: ../../src/topics/inputs.md:70 -#: 10ca6321ce3e4b08ab6a5bb380b19c11 +#: 659ed5c64fb546399b741553a347b8e8 msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 -#: ec2adb3912bc46e28891229e9e0d9a1c +#: 3d87e69d41374fbab23b26d36c1aee03 msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 -#: a519be60726a44af9941fdce04735353 +#: 07bc81683e2c4ac68b379462bae95207 msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." msgstr "" #: ../../src/topics/inputs.md:109 -#: cb8fc8c4c79e467eac5fab4ca685201e +#: 3e304da2150f448d9e39715ac5f5deaa msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 -#: a26cc105716f47cb807174c9003153b0 +#: fd8a98686e3c4c609f79ae427f1558d3 msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 -#: cc159dd5fe5748caac838862f5b8c4d1 +#: f1a2e1bbb1104a4fab5a7f04cac845c7 msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 -#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: 6a7f0ccd227e4f90a8c8ca96744bda68 msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." msgstr "" #: ../../src/topics/inputs.md:142 -#: 6812698e9ad84d3385de5e88e9dde0b3 +#: 1f79d115d8a145189638c68c3095396c msgid "The `baseCommand` field will always appear in the final command line before the parameters." msgstr "" #: ../../src/topics/inputs.md:146 -#: 9654e65b1c0642dbb5d4f34edb211989 +#: 6e1b3e2d90184e34925891099d2b5cc1 msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 -#: d1f02be278754267893dfce5a940997d +#: 4f6df7f13e42448eb4a53f03bc477b56 msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 -#: 01f30e38dfdd452dba3a996073936e16 +#: dbc0b52627514ad0908969d0b4ddfdf4 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 -#: 787d4bfb093c4ad287b902084706b751 +#: f173dd96ad124470a53573c86a8df203 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 #: ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 -#: 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 -#: 9db68837918a4a349f32f15f12697a1d +#: e0098a77080d4349b05ceb7735a5fdf5 +#: af25945b530048b685891b1de4e35e72 +#: cb07caa4ff0149b3ae832be53f8d76f6 msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/inputs.md:178 -#: 75d59e395c66416cae9b352db5081516 +#: 2445d2c7c2794fd3ad8b6ed8b4a9440b msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 -#: 874c6f19abbf45d7ab7d30a378c4048d +#: 4459819ba75647d185986a3386939494 msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 -#: 5d7d7a28cc5d4862803032aec78174d9 +#: 8f163bd34ded4785b6e28c8e2147e0dd msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 -#: dea0d4b681f94e73b13965dcfe75cf7d +#: 1799e11a7b9c4929a3d1379d7ea45d03 msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 -#: ddf598abf4f34aca9fffa045860fbf96 +#: 9510c0b431a44b5e84e0b583de7c5446 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 -#: d52a8089920e45bd89d582533b50e3a1 +#: efb4eb6f5e994b50a52fa2c707dad1ce msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 -#: 750474486a84482292eeba45f118287f +#: 34599c6f10ce4104be2359a1b37f91cb msgid "In the first example, you can't provide `itemA` without also providing `itemB`." msgstr "" #: ../../src/topics/inputs.md:217 -#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: 0663ea7918994d3f9c45c652a3ed12db msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 -#: 1eb0e39bb6d04b8cab300f44a79f3add +#: a98dda6ca4b14edba467de638bba28fc msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 -#: bc21ee10bff843689cc98ac6630edcea +#: 10d0e9f8df8c47788703073b17529bc8 msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 -#: 4b2ab812f62c4f949dd25c8527f2411c +#: 9a0e1a130fba4d24a9168ca3e455cd23 msgid "In the third example, only `itemD` is provided, so it appears on the command line." msgstr "" #: ../../src/topics/inputs.md:255 -#: b771302d1bec4050a9417b080eef76c9 +#: 992a8c801ceb4233acf56b6bff315188 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 -#: 2c3b884cb1c54521900cc90782e8a58d +#: 9027d23fa7074b789c3b86ca5ea17fa4 msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 -#: a1073b6306044dffb414319ae01f68bb +#: 68b47710a8ea4b978428b42c627944e9 msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." msgstr "" #: ../../src/topics/inputs.md:265 -#: 4a31c733092142b1af834eab1747c224 +#: d33e4cac65d14111a89c838c4d1759b9 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 -#: 9a1d92334685449386dfa3b3a899ed48 +#: 24cea1cf7d774b6ab56959f289cab39d msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 -#: fb623af4c480411b8fde28d01c981411 +#: b866867d6f8e4d3999b62a85e6884ebc msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 -#: e98e165f6bba40809c90473d72f9d592 +#: 80c49ed168b14d25b2f09b3b0186b44f msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 71628ebe908b4cd28dd1fa17e3d2e2fb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: f123ca244c23413c91405a4b84887525 msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 23299ae1bec94b00a32a8af7eeac350f msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 2495a9f2032a47c188338cb81ba429eb msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 3fd2f3cf7bdf44089df2ce3122534801 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: d5a5b8b490b640439db92da949266e4e msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 5935ed94331d4b2f8ce597f31edea843 msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 -#: 8acf361cf77c4d45ba3f2e344146259f +#: 5feb559552194ba58da7206c601292fe msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 -#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: b7124ba4df9042baadc1641ee09545d6 msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." msgstr "" #: ../../src/topics/operations.md:7 -#: 5565c1b2d8a349169a305a9b26b4574d +#: d34b698c62114041a64e0abce25ca935 msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 -#: 49cf614893d8438299b3bca384eb40cf +#: cba2c31262bd450cbafc7ca77f4fb8fa msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 -#: 88160cef4cfa4add9020aa89511a5749 +#: b01be5f632104096b5af6193aab34d90 msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 -#: 2f73a786b5d94dc0b23ed0cdd185afc8 +#: 60a6a02c1367403db6df3ec10f75eb69 msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 -#: 730ba1434a1445ae847ec6153b6a3b72 +#: 314ea7bc35154f41b2af5fa6683ca389 msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 -#: 98d9b8d867594543890af99e77e24edb +#: d81e679b13474f74bc5e1ce1e31c2bc6 msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 -#: a25d0b1e13324b40a6b8fcd227948c4f +#: d7fb27131ee44bfc82f698ee44b2bae0 msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 -#: da077da5eb8a4ffebfde041fc16300de +#: b8ef11eafd1d46e088f1277f4ac372bc msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 -#: 1b3016f0462f42deb42ddaa33f28bf3d +#: d2382ed1f644459594655d5b5b4d838a msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 -#: d661df070e3040869da412d07a71f716 +#: 6651632d977b44479b721174fffeda2d msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/outputs.md:10 -#: a11585474d3849cca5467512ed964743 +#: bee5f532554241088764ac9e56abbe85 msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 -#: 2682f9ca8e604a0c9986f7746fdec960 +#: 0c7c506f38be421399073871f64e99b0 msgid "The following example demonstrates how to return a file that has been extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 -#: 7e3fa7baf0f549ec89457e7004ac9545 +#: 8b60286e56cc42a8ab5f751a97adf771 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 -#: 22447a560f6f4317bf67bd7c4336126c +#: fa0ad674f15348339a1eee771a6ba9e2 msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" msgstr "" #: ../../src/topics/outputs.md:26 -#: f1ee2e00b0cc4112b51c9df3a919b73f +#: 177b5f1b95a34fb9b2eb42f733d79ac8 msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 -#: ad8e1acb251246d2a47c39b20d4e483a +#: a08a6d8aca8e490482e127a8fd5e650e msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 -#: dc200c6960ae4476a772645d021f14b8 +#: c2c60f68b1e045f88844076e191fda9b msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 -#: 52703d6b7f914097934bfad13663abeb +#: 6d939f62526e4e6d95acb57d72f60a84 msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/outputs.md:51 -#: 5e1c79df657d4a6e84e055dd6b300a5d +#: c48edd9034364b81ad42540a98b51d91 msgid "The field `outputBinding` describes how to set the value of each output parameter." msgstr "" #: ../../src/topics/outputs.md:62 -#: 329d2809dfae4f90bc638f5f03a47ee3 +#: 9ebe0186a7124dfaa30e558e8f59653a msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 -#: 96df2d45e42441d49ce193ccbfab78a3 +#: 9381b7d7c9904df0a5e16dac29c2e08f msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 -#: c6bcf7c6a8774dd6be41cc775848c3b8 +#: 2aa9c6916e3546b7b92fa64bb83275d1 msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 -#: 9d86c03ab44841c785b924cc44727e31 +#: 63afb7a597fc4e459b6a7dbd40bbf6ff msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 -#: 2fb58c2feaa84970bb5274c49f4b5b64 +#: 7418915470f041c9af5bd39ea652de36 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 -#: 9647019d8c37466886e7aab6f176634d +#: f82db001b58c4969b2d8bc1dcbd7cf8a msgid "You can also capture multiple output files into an array of files using `glob`." msgstr "" #: ../../src/topics/outputs.md:93 -#: b9eaf21f5e014eefaae301c47dafd144 +#: 26d9f0b28d384617a8e490c1f8e26e52 msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 -#: cffff6c43b4945daa3b2a49763bc50ae +#: cf46c971b31b4e10bf0fefb4cd028c2f msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 -#: cc067051f22f433bbece08f60933e002 +#: a4347983fb9945a4a2773af88e426dc9 msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 -#: a190a6440ec34898990cdac05d809f22 +#: c5489e0633114372b273098ee2c9ffd9 msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 -#: dbfe2c1123144316aa026374b0f353d3 +#: 75de9fd63393429daf1ca10a85339aa7 msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 -#: 280f1a07d0ae41d7a4674504f832fcf0 +#: 8b5d0ada32d645be9359f43a431f5f91 msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 -#: 5c64d938862747cb9fb52515a656ce27 +#: 2ed93dc8778e44209194f41b9ad193d5 msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 -#: 074cf5d912854d8c864607cc24b15302 +#: a80dd6d9920540e9880514e04035af86 msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 -#: 0290af3e3cbb4b32b0450c8771f3bf95 +#: 9de300f7b9da49f59d1c9fd96dec4a8b msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 -#: b54240bb94f746bba7511633aa969db0 +#: a61f52d3c1024c3692899e05fcea4bee msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 -#: 8b70a072aa87414c88e89a3e19af0a51 +#: dafc9ba578c14fd79d075160e6b7bd6b msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 -#: eea20f89c45f424a888178df53713b28 +#: 28ca6cae42904559bcec98fb9d2b07cb msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 -#: cb4ea13f5db84c0da43df3f7f2478d78 +#: 616c9ff9fcae489285f0bbbc67f07d29 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 -#: 6d3fb423e6c4434697cd113fb27e28ad +#: ac17acd83ddb43dc9fb7a5e595ab1153 msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 -#: 7647e0229a924f988cf02b7812a55c06 +#: 156573324cde41ee8b3c47deabf43db8 msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 -#: 9d663249666045618a0d3acddb85a9a9 +#: c9725be01e8a401fb3ad9ff01339f81e msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 -#: 5fed4984f6784347b4cbe0630b1dd2c2 +#: 6797335256e2412cbbe7636507931455 msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 -#: dbf6153cd02542a6a01c172803122b7f +#: 05a5f0fcb7454cb697e3d810d55fac26 msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 -#: b6250cf6fa8a4a0c94b33302e0decca5 +#: 406e68280b5c4ee494632f94b635b7ad msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 -#: fa6ca3bbc6784380a03a950a6f49a180 +#: 2d6e2a4ff391494591bbdf8dbcc4a6ae msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 -#: b92b516e537a4773ad67b4af586e7a25 +#: e71a974b29624210a107fc2d097d4196 msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 -#: 467a701228504d06b971b79a59c69064 +#: b59df98754e24654bfef0b1fe1d91660 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 -#: 2634f989eb304009a8568d70ed42786c +#: d2bccbff1ce646348fe38c776ad183e1 msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 943ba46512ce48fe8c5b62327734c503 msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: bbcd43d5af7d44108aeb65075a6bd2be msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 834295755af841a78e466eea43864861 msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: a6b626489bfa468e8f059ab3aa669201 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: e1dbea105aa845c38cb1f90b43847271 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: e9640f47d40e45bca184eb30700df648 msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 0456efb3718b4356ad2b277ee16de967 msgid "In this example, the software requirement being described is InterProScan version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: f7e97f926505407f8f8e9a427e055e43 msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 +#: ec597ff8f6ee47bc815b069335869f1f msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 -#: b85eb83e05e845d7a179f1b1d74db444 +#: 7467a7f6f26a459ba4ce83e4e6dfcc2b msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 -#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 -#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: a03372581fa44f9b8e3e088a4099cdd9 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 -#: 0f7508ce59754a7eb230dea6042244c6 +#: 36e082be73464be0ad5d0b681cc510da msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 -#: fbe0c65b444441f785d0054176d036a6 +#: 4464455b51ad4873ac13c4a63ee5fb54 msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 -#: 1b6b7a75cc754775bf9dd80c0941e8da +#: ed7ff0753d1743a995f4cfedd6e5dcc2 msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 -#: 9a710602e00c4934ae3a3b471aa68458 +#: 4c2dd10dd66446058477a52fb8d2c602 msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 -#: 21b5be7270a14f0987240c81d1ec879b +#: 978b6a5fd5fa425fa9a18d9f0e8788da msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 -#: 0490b1fab86749e49b473949c52bbe8b +#: 000c0d6ae8bf414d9293b9f13fd2e448 msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 -#: cfe9d8241fe84bd5b74042a5625d933f +#: 7e91b8811be14f8e80df39ac4c5bd316 msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 -#: 764d933cc4da446abd8dd8f913f05dac +#: d42799cc5bd4484bb6beb309a61e103e msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 -#: c93efc6d4e004859981ee7f5fa28ed03 +#: 48bb0f6666ac48648c7d969608b3bd48 msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 -#: 546601da44cb49bd9611b1c85807fd90 +#: f8876044db184cbaaca56579d0c773df msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 -#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: a5a3d408dbe34cfda4dd0b2abe67e7d7 msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 -#: eff5f28ca83c458a9b07faf7a81f7e91 +#: 4c240a18c4e6441189489011242c1efd msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 -#: 2e634f3737d04d279ae78ceee4b0a664 +#: e37e76ef376a4ee695e600998906ec1c msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 -#: e07f33d01b804663a25ffb08aad74821 +#: 51a307b0ba7c4c1d89309ba8d2250471 msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." msgstr "" #: ../../src/topics/using-containers.md:15 -#: 7a644506619a4f08958ec7d4540cd557 +#: 13cc38d72d34468fa4eb6d91f23ff105 msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 -#: b5195b7d8eaa419fb2b90cb33a57783a +#: 42a48398d3ef4b03bd7395120f2cfb42 msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 -#: 7921a837ee744c5aa9a5bda04b0c8db1 +#: d59387b433bc4ecfaf7e72026624db02 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 -#: 387e9bc9381a4450af54aff77e4df6a2 +#: d963418ccc0b4803bbc758d718ccb5aa msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 -#: 2713594c937d4c528fc8d04d9e9819ed +#: a224d1510c9e46aab23d8bdc03c349dd msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 -#: cf94c1424fc2413c85647fd1ee73d951 +#: 0a82f8a45b0546aaac4c976dcc98014a msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 -#: dc0452107c604e29bdf32bb289fe5db8 +#: bc418a2a535e49359c4cd44b373bbe02 msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 -#: 1a5596243cec4c948d9b6bf0bb12fad0 +#: a799fba2322944cea00e413c08066536 msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 -#: 483181f498fc4d968b5fe6ef427709f7 +#: 35379c6b972940bd8451f10b74dd793e msgid "Notice the CWL runner has constructed a Docker command line to run the script." msgstr "" #: ../../src/topics/using-containers.md:72 -#: 7487485d6aa4458089a4b4bdf107ea64 +#: 2d5265525ad544a0b64ad2cf07aacc26 msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 -#: 7394e7690f934043af617436b40845f0 +#: e2521b89596d42f8a87a3207fd6c32f2 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 -#: b9ae9e9a896048caad7e6c38a5bc1bd1 +#: 3676f23b63e142cb8e5715ae07216a47 msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" #: ../../src/topics/workflows.md:13 -#: f228fb7953ea48ed99d89880205f4620 +#: 00725aed13a440ca8b3c4f9155fbee99 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 -#: 5870ac44e4c24b8daf5f06c49f95ce04 +#: 2e38a4f9072b4ad9bbb74f943d22084d msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 -#: a913c76d06164fa18718a8a6a7dcf0d6 +#: 2b9f4035ea864b6db50c861a1819289d msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 -#: 93188ed43ee949cc98b3ea679ce14feb +#: 28e9064780e7418a8e02a22f92e34404 msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 -#: 36618126a4df4326b236ebe2ea42cffa +#: 66ce14a10d2d4dc497d3ed71e11ed8b8 msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 -#: 1cc17ad26e9c474b895ba5cd20c8b66a +#: 8dc00528c3d2426c8a3492a8191f1d81 msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 -#: 24aca0bea4d94e3593b844cf0586cffe +#: f9ef5e258f7c4971a8543d1dfed711a8 msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 -#: 46cc4859856e4367a9e5e68eecd48b73 +#: 324bc51071d743ea80124c23880ddc0a msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 -#: 9c56528acd5f49deb139e034dfbfac7c +#: d8c13e01976b43a1af34c11a7bc36897 msgid "This workflow extracts a java source file from a tar file and then compiles it." msgstr "" #: ../../src/topics/workflows.md:170 -#: 55ab007d472f43388e4c77aae8f165e7 +#: 43910a8ab4484e529a17df418b1aedbb msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 #: ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa -#: 307b6618a92948fca4203ccb497c77e6 +#: eab3ac7490f24645bbf0babb20aa9df0 +#: 56917e39cfa34470a7a88b52b1f955d9 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 -#: a2dd833fdca4443181648e41051a5232 +#: 7ad12d67e815400c94080804b9285629 msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 -#: 7e40cc9f9e1341c195e843c009575b94 +#: 457d5a31c79143acae2683d95d27f7a3 msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" msgstr "" #: ../../src/topics/workflows.md:185 -#: 26c51dcb76364ed780376aecb7cbacda +#: a2a73901bf634547900d08b9a1ac8889 msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 -#: 6fcf8ad3d1bd49afa4a105622437bd59 +#: f347d80e62384b14acf6423675e5359a msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 -#: 71cb81fa4511495b80422244849979e4 +#: 2a845a4f3f98428fb82f3ca7ce038a6e msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 -#: def35d6021394def80a53ae49a2cdbde +#: e2007c74d5f449a882809d6b91c010bf msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 -#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: 7f5e53ee7cf94be2bff45ef64db28a24 msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 -#: c84d4450bc6a475dbf34e0b22cea9130 +#: a0d076b7b8b048478580c99ef0c8429f msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 -#: cca9665f6daa44b49233baf34ab9fcc7 +#: 7fd926c18ad548e98845e9b5134dd6f2 msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." msgstr "" #: ../../src/topics/workflows.md:256 -#: 547edbf5fa424b8286cc21674ff159b0 +#: 789fbd47f8564cceb430ef3c0bc90e9b msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 -#: 7ca248888b9d484cb544cd76ba538662 +#: 45c4d0492d6143ca9cebe81e9b2cf3ae msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 -#: ae6b240718104380b08db5552d7355ea +#: 73bd3da2af8545928d5ea71d0f7454f6 msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 -#: e5a8b7f84be64020b191099f3fad30ed +#: 15ce3d2700424f0fbb280d602ccebcf6 msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 -#: f0b04849253c4693904512ddd7f9ce84 +#: af4268f19202436eb0a7e8c6bed5e386 msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 -#: 12a06d8358534102b202965d4258c18e +#: 94a4eadca6b949d79de2990a0150eee8 msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 -#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: 09c1619e8cbd4febbb637f7e99ad5890 msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" msgstr "" #: ../../src/topics/workflows.md:300 -#: 49ed137fe996452a8534c68d100db941 +#: 677ea7a27eb64568ab3689142d6efe70 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 -#: b7f93705e5b8416696be01850072e8c0 +#: 097e6d47f9394e62b80110700492783a msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 -#: e87045829b344089ab59dc27063ddd7a +#: e93affce8c104bf6977182047c1f1077 msgid "\"Visualization \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 -#: 42ef2f145b824d69b63abc1da175c216 +#: 06c9e04ba890473b851240a0fa9c3b12 msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 -#: c61cedf543664d388183e04b3939cc39 +#: 0380dc1fe3aa48e4b62283b7b2a611d8 msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." msgstr "" #: ../../src/topics/workflows.md:341 -#: 9e39e3f1501c4fcaab3e8962e090f6be +#: 49b251f7a313492ea60504b00109e526 msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 -#: 03e2f767c4da461982fc3c0f3ba94762 +#: 7ee55702d7dd4679a24ff052f6f0cbeb msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" #: ../../src/topics/workflows.md:366 -#: 3bea5822b8694e2aa32c446e1c54a045 +#: 85d7e2e270874aa6b9f477cec0f48154 msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 -#: 426023bd6e3a471cbb30dbda3d6f9e57 +#: 570e94513c984c09ad6aa255f534216d msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 -#: 0d498cd4caf54c15891ca1afe58e2727 +#: a107258662fb4bd4a9a3d8754e34d1e9 msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 -#: b2d75045e02741b4850f5ff1243f7858 +#: fc1a6502d831458ab8371a575cea47e2 msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." msgstr "" #: ../../src/topics/workflows.md:398 -#: cfa765264a27411ab914de569aa3dac4 +#: 2d10806bf1ce4e26b92adda61efc0862 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 -#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: 046c5e134de94b629cc22d416f3c9182 msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 -#: 5fa79c62049a447c8328ebf9db54ebf4 +#: 52fa22d3277940049fbb589a3ea73433 msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 -#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: 6043beb96c2c49648011ec556aa9e986 msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 -#: 3a67d77a2e7b4c0bb61cc3585ceae942 +#: 5ac4310515124e2986724425bed5651f msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 -#: f1cb55fc59824cc18a95fd6dcb32cf4c +#: 7958e91d5c2f4046aa9d2070a900f9ae msgid "First of all, notice that the main workflow level input here requires an array of strings." msgstr "" #: ../../src/topics/workflows.md:441 -#: d947c54933d64aad90df392a1cedd63f +#: 2db234d776fe4fd38bab07245dcb783a msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 -#: 651d35997332404186aa6d5711da4a3d +#: 7cfb17230e284ee7b6e2a00efe8eeb74 msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 -#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: 4311ac98544e4fb0b2f4b24985710a01 msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 -#: 842b926ae34542cb9023021f137b08be +#: 780f9c72e6c34c39918642c7e2477355 msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 -#: b662c1a5a4424c8d8350a806356acc61 +#: cc4a7316db644b438cbaa181ad9ef2d3 msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 -#: 04d6babfd87343d7a5f13867ea02b65f +#: dfc461a03fe8487794837904febb8b63 msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 -#: 2eaacf1a90204a2b9bd621344560f2a1 +#: 1e83485b00b64dfaba897bd8d772e0f0 msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 -#: 242993d42b164ee5abe7ca10d45856de +#: d0321d6805ec4d3abf3877d02a0a417f msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 -#: 4a94e5f7e1bc4d628702140e4e51d6d3 +#: d7d77e807b3048c7bdf89558f76804cb msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 -#: e61d93b848184c8e8e573928427b4d0a +#: 8d9b8be147fc4a71922dde858842e543 msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 -#: e3a7182f00f440b8b5461da91194a64b +#: 34b7705416a745a6a42e6d402c0757ed msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" msgstr "" #: ../../src/topics/workflows.md:491 -#: 99fa96caacaa45cb97aded9a24fcac6d +#: 257adcee9da64d5c987f3b64efd20ab0 msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 -#: b5338f39e8c74ff28e139da68089a742 +#: fa6ed5d0c14f42f4aa3c5144648db22c msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 -#: f6d92156d67c4a339bcfd194cff897df +#: 333e8ce458d54de394526769f96d12d2 msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 -#: 1c9e386922324ec8a59306572c19fb8b +#: b819e8a5df6e4fa495924095709669ef msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 -#: d80ab383eec9402faba997b548fe42eb +#: f1955468a1364d44a930db77c9c4b495 msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 -#: f7d2827d97db4bf4ab84b5d6621c3b48 +#: 8c3b9b645a204d02b2c73a205e8ec296 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 -#: 49217c02f58c43ff9ec00f10da8d4e84 +#: 4d88b9c186cd4502adbf752e8a70b6ce msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." msgstr "" #: ../../src/topics/workflows.md:527 -#: 20b9f181420c401d8615c17a10027517 +#: 9927673564024ba5833b5ac271737857 msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 -#: 8dbd56473f8c40c0bb12a48be06117e3 +#: 84f4ed7ce2004742b8db9087104a469a msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 -#: 78d7f3ede2c746d482042adef050b2c4 +#: 2b5f9757adca4490a149c7f45e14fcb5 msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 -#: cbbf93c70fe04ba7932ba25758ddc611 +#: 0418de720813442f81ecff293c9448b5 msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 -#: cfa1c1fde4454df283f87cc54a9c59ec +#: 524eec63be8248ae982939c975ef50a2 msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 -#: 1a8be2950cbb475bbb2617e005f0fac9 +#: 5e99f9912cc549a7890e2934425eb943 msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 -#: 5f09d4d897cf457d80b9a11b8c01747e +#: b0121ee087d6424fbb0ea5957a7b0b8c msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 -#: 5d83c56102e141cc978500f678dd0c1c +#: 49e9f6b3a06840289decf3f557860f87 msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 -#: c38438fbf9a04e729ec2e3c962435289 +#: ed9eebec0b3d4b72ba65507d37757a37 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 -#: fdb9cc750cec43ee962517e637dc5fea +#: bf9b255a24a84f3ba989a223492b8f41 msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 -#: 08da9cd8056b4ddd8f5150cc85ba72ee +#: e79fa0b7f8b14810a3a20908ef92bc55 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 -#: b027fc234ed943bbb00d4c6bc03c040a +#: 290e2035f903417cbecb5dc5f09d6ebe msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 -#: b8befec0d8684638aaa616a659e0100c +#: d420730151534f1a89076588a3358f09 msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 -#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: a6b5378bbe1e4bee9e37a765bddf75f7 msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 -#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: 6e4d9465dc2b454d96b02d7ad1817795 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 -#: 98056c5cfd5640ad9de0679360797cc7 +#: a649d4af5f434dac9395e013ec4836bb msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 -#: cda73485875d4c8e9464679a20558616 +#: 446190a298834b73bda068286e8490cf msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 -#: 98cae24919b74c088a5d89706aec581b +#: 2f35c012ff174721bffe66a3f58a804f msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 -#: b4b0940b4b5743c09637b36b964202d0 +#: 43127c98c9d94aedac61cee67929c1a6 msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 -#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: dc4fe561203c4c38a9caea5bd6eff2cd msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 -#: 9ca3554d771d45998e88aaede525b227 +#: f924e4896db2424d99ce8c9da14c599a msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 -#: 3fca839cede94cfd8e4f605c73ba699d +#: bf7646f5f925485c842a6d34140e40b8 msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 -#: da34c635707345b2a5e85a2fcd30bbaf +#: c483e61dec8949fa96bb893d422888a0 msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 -#: 3ded0f125249485c921994b6e6b93ac9 +#: 85fcb523d0e34a499eae04d304887f7b msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 -#: 53ece35d309a4c8d99f1efb2122a7092 +#: 83d47c8736a34f3cbf09e3997845e4f4 msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 -#: d74321b111d84ae7a515f2f17dd39e23 +#: c698fb3d37bc403e9aeb679b8fc0e15e msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 -#: 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ae8af2f0eeda4aec97201211dfa965c7 msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 -#: fd64dd818ec64bb6aa9a11586a5747f6 +#: 2ee87aa465cd41fda16a61e242f8c9d0 msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 -#: 8c06e542dd4144fa83388d8142552c8d +#: 0a6fd4469ff24b61b3ad001b09eead18 msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 -#: 87bafb845c714b109874f6137b84462d +#: b96ba19bce9341d39c46054e1f10fe8f msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 -#: 5ab9ddf613a540a2b8228e37600cc5dc +#: 903f30af3d0c45cfb61063936a8097a7 msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 -#: fcd05b1ef31a4046946a2399c7fc5575 +#: ede8db7c0a58432e8a1c416e937a06d2 msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 -#: f4b8fc8236044fada420def13a02813d +#: c8b53615476a4a1fbef2420d93bac94e msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 -#: 859368c1f25c4a4aad57abfd046c63f5 +#: ea03cb5525cc491f9feb5c4780b38fee msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." msgstr "" #: ../../src/tutorials.md:1 -#: 2203c93f02ac4514a43508ecb98dfcc5 +#: 92fd3a5e31714eab859dd630af2e78cf msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 -#: 5d92464923c245818c070fbef102be89 +#: de660ecdb5b44c97a0e519d00b232497 msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." msgstr "" #: ../../src/tutorials.md:7 -#: 8a5cd557dab5456bb41cdc24af73b50c +#: 5afc1e1288e74ed0985e61e5164479c7 msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 -#: 13d7e2e92e96432787c712cf6a595424 +#: 862dc7ac81e54b1fb3d4c2f961b8810e msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 -#: 0abdd85c9b964a4e89ba3d80a6c78d6f +#: e2c94c0e1c7048d38cd7aa2c465a859d msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 -#: 3cbf1f69a5514fd3bee90e68b201190f +#: b63253780f51467a95207d820d13ac39 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 -#: 68c97a7065634d02956f3f5c1d4eeb9f +#: 6d06ca7ed5df4560aaed286f4fe33928 msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 -#: a67c7e0eaf4e4d27b3e5db303333a088 +#: 5448df4a6a8f431d80e269bcd480e19e msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/src/LICENSE.md b/src/LICENSE.md deleted file mode 100644 index 84798e58..00000000 --- a/src/LICENSE.md +++ /dev/null @@ -1,2 +0,0 @@ -```{include} ../LICENSE.md -``` diff --git a/src/LICENSE.rst b/src/LICENSE.rst new file mode 100644 index 00000000..68c5792f --- /dev/null +++ b/src/LICENSE.rst @@ -0,0 +1 @@ +.. include:: ../LICENSE.rst diff --git a/src/conf.py b/src/conf.py index 990751ba..921ced1e 100644 --- a/src/conf.py +++ b/src/conf.py @@ -237,4 +237,4 @@ gettext_uuid = True gettext_compact = "user_guide" -locale_dirs = ['locales/'] +locale_dirs = ['../locales/'] diff --git a/src/index.md b/src/index.md index 8e10fa54..e1a0c0cb 100644 --- a/src/index.md +++ b/src/index.md @@ -35,7 +35,7 @@ introduction/index.md topics/index.md tutorials.md faq.md -LICENSE.md +LICENSE.rst ``` [repo]: https://github.com/common-workflow-language/user_guide/issues From 8efb720d8ee310a313510607bbeb5bc35195f9d2 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 11:12:07 +0100 Subject: [PATCH 42/49] also fix the Spanish translation --- locales/es/LC_MESSAGES/user_guide.po | 1289 +++++++++++++------------- 1 file changed, 650 insertions(+), 639 deletions(-) diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index 3fa6daab..523946d0 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 16:53+0100\n" +"POT-Creation-Date: 2023-01-25 17:03+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" "Language: es\n" @@ -23,21 +23,24 @@ msgstr "" #: ../../LICENSE.rst:2 dcdc2e8da0ec4d9e9453601fdd83bac5 msgid "Licenses" -msgstr "" -"Licencias" +msgstr "Licencias" #: ../../LICENSE.rst:5 3e165520ca56481b8f8d494a8d471de3 msgid "Instructional Material" -msgstr "" -"Material didáctico" +msgstr "Material didáctico" #: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the `Creative Commons " +"Attribution license `_. The following is a human-readable " +"summary of (and not a substitute for) the `full legal text of the CC BY " +"4.0 license `_." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " "cambios en la estructura también están disponibles bajo la `licencia " -"Creative Commons Attribution `_. Lo que sigue es un resumen " -"legible por humanos (y no un sustituto) del `texto legal completo de la " +"Creative Commons Attribution `_. Lo que sigue es un resumen" +" legible por humanos (y no un sustituto) del `texto legal completo de la " "licencia CC BY 4.0 `_." #: ../../LICENSE.rst:12 b7a7a0fb40344fe087c1cc3ec19308aa @@ -58,38 +61,38 @@ msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 +#: ../../LICENSE.rst:20 8bc6672f4a33428296226112a1be6fbe msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia." -#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 +#: ../../LICENSE.rst:23 be38276e7b374f57b9997391bf898a62 msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" "Atribución — Usted debe dar crédito de manera adecuada(mencionando que su" " trabajo se deriva de un trabajo que tiene «Copyright © The Common " "Workflow Language Project» y, cuando sea práctico, con un enlace a " "https://www.commonwl.org/ ), brindar un `enlace a la licencia `_, e indicar si se han realizado cambios. Puede hacerlo en cualquier" -" forma razonable, pero no de forma tal que sugiera que usted o su uso " -"tienen el apoyo de la licenciante." +"human_>`_, e indicar si se han realizado cambios. Puede hacerlo en " +"cualquier forma razonable, pero no de forma tal que sugiera que usted o " +"su uso tienen el apoyo de la licenciante." -#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 +#: ../../LICENSE.rst:31 f00d5c3846034c2ea116c2f74786d9fc msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" "**No hay restricciones adicionales**---No puede aplicar términos legales " "ni medidas tecnológicas que restrinjan legalmente a otras a hacer " "cualquier uso permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limit +#: ../../LICENSE.rst:35 1798d65c10104040923c2fea2199bab2 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c +#: ../../LICENSE.rst:38 c65198b804f8436ba783643d51bc72d9 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " @@ -102,20 +105,28 @@ msgid "Software" msgstr "Software" #: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" `OSI`_-approved `Apache 2.0 license `_." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la `licencia Apache 2.0 `_ aprobada " -"por la `OSI`_." +"disponibles bajo la `licencia Apache 2.0 `_ aprobada por la " +"`OSI`_." #: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT" +" WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the" +" License for the specific language governing permissions and limitations " +"under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 -#: dfc7702e073140c985cf47272a20214d +#: 271049c39d294b11b9bd94cb6be2857f 61af90891e2d4542b5f45fb3ec6480af +#: bf309fa01bed4355bf052ae4afbf9a67 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -124,30 +135,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 +#: 055f0e960450410585b59760ef3ad284 6294af2e32e04207a87399c7f0780011 msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c +#: ../../src/episodes.md:9 6428125fc43c43bba8518ece2f5d150f msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c +#: ../../src/faq.md:1 ce8fade1e88e4b03ac0d3fc71d16f844 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 +#: ../../src/faq.md:11 9e7483b53a984b689964c69afcaa7123 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef +#: ../../src/faq.md:41 8c5a89257ef248cd99cba303713e5082 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 +#: ../../src/faq.md:43 9e80d8eeefcf4a9d95fd5fe9d9fa124a msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -155,94 +166,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b +#: ../../src/faq.md:59 c2e5f62490f940aab19166403a840597 msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 +#: ../../src/faq.md:61 ffcffabdf25a4c398e8e53bc817ea769 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd +#: ../../src/faq.md:82 c8a6b85cfca542ccb042a0269294e5e3 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 +#: ../../src/faq.md:84 98f583e5e36941c1856d719a16e58e4a msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: ../../src/faq.md:86 fb9cac0954474b5284793330b7424949 msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 +#: ../../src/faq.md:89 cc45d609de1f423db86d58eea933e132 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e +#: ../../src/faq.md:95 27ee63895cb14321a1814f4372d3180f msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab +#: ../../src/faq.md:97 f1c841980f3d4364a2158a4eb2f0d257 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 +#: ../../src/faq.md:104 6d53d38ddcf244fb997db37eae7fcf90 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 +#: ../../src/faq.md:113 b6d60d66f3744ab3aea1b175ecb23d4a msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e +#: ../../src/faq.md:115 cf4fa3ae602841d393b4143e9f6f5e82 msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 +#: ../../src/faq.md:135 41a3c9aa55c5406f9b52af2243c79ccc msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 +#: ../../src/faq.md:138 3b8eb247425a4a708f51c08cf258e30a msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 +#: ../../src/faq.md:140 388a6e091a054dc48afc928f46dac7b7 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 +#: ../../src/faq.md:165 28c59d12156e44ea833822fd3ecaf824 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 +#: ../../src/faq.md:167 8267843ff5c940c590b10047455f2102 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 +#: ../../src/faq.md:188 6e6f55bc915e4cceb8e360544d6b4ae5 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a +#: ../../src/faq.md:190 1bc80953bd60405082a10a7798c1413d msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -250,22 +261,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab +#: ../../src/faq.md:194 a6cd4bf4dc314e66a951f7f1227c7bb7 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b +#: ../../src/faq.md:196 7ab2440a92aa44b09e8a324cd67ca728 msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 +#: ../../src/faq.md:199 152a529dfa2c42c1b6f0083589fa5aeb msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf +#: ../../src/faq.md:201 b278c137167d4b958c099c0509edb79c msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -274,25 +285,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 +#: ../../src/faq.md:229 f0b38723838f479d9db8eb5142d28a1e msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 +#: ../../src/faq.md:231 fc1e4a808e85422cbb4d128c5a1f4d0c msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef +#: ../../src/faq.md:247 d74964c9d19241848f4dd92a201e201f msgid "" msgstr "" -#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 +#: ../../src/faq.md:248 859b8e18e05a4c3285fb20bbb44c1ed4 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 +#: ../../src/faq.md:250 eb6e932924a54afd9114c629b2d0e93b msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -300,26 +311,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 +#: ../../src/faq.md:267 31d70b41ddf042f6aa530b7bd6daae73 msgid "" msgstr "" -#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 +#: ../../src/faq.md:268 9aa3ff8c957b42c8a30f37167a8177fd msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc +#: ../../src/faq.md:270 777ac7f6bde2470b981efc91feb01c81 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca +#: ../../src/faq.md:322 8647071efc0548a1807c03fe8a4ee54c msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 +#: ../../src/faq.md:324 4404233183124085990c44793a6b25f6 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -328,77 +339,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 +#: ../../src/faq.md:342 c5eecacfa07f47649f07ef9d888f4c5e msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 +#: ../../src/faq.md:344 1efef04061fd48f1ab39a99508b5bc0b msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 +#: ../../src/faq.md:349 57e8ace8e8d64e7a90510e1ccea69612 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 +#: ../../src/faq.md:351 138606e8d7be40bb960f278977f9107f msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 +#: ../../src/faq.md:359 d0f668dc78464469a9f2bfc61a90aa76 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 +#: ../../src/faq.md:361 f2a49a7663e1456cac6b2eac0c46c662 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 +#: ../../src/faq.md:363 eefe4adebdba4063af0cac3ab5d46442 msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 +#: ../../src/faq.md:371 526f2816123a43ecbcf09c46904b4b5f msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a +#: ../../src/faq.md:373 0ecf267c5f4d4557ad0d7ddef2f4b5e6 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 +#: ../../src/faq.md:375 935a253376854d12928f00c2870ed4c0 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce +#: ../../src/faq.md:384 bc6c0bf679ae48e7822add7ab2cda220 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f +#: ../../src/faq.md:396 a63643806a2a4eee8ebd3502fd6ce2b5 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 +#: ../../src/faq.md:410 fc54964adcd648948d7baff02f47598e msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 +#: ../../src/faq.md:423 aabc495306a149fdb15835ae1df93c42 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 +#: ../../src/faq.md:436 2930faead8be45a6b9adbf51dcdfef6e msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc +#: ../../src/faq.md:442 f885e4716a8d4de0b25d2d3356789672 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 +#: ../../src/faq.md:445 6487ff3c19c944eb8257b2cf60d0aac7 msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -407,11 +418,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 +#: ../../src/faq.md:450 4cbacce539ce4f6cb5bb8ccf1574640c msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 +#: ../../src/faq.md:452 27321576de714cd5b82c67f59b2e3e6f msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -422,22 +433,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 +#: ../../src/index.md:1 6afded7ba21247099c9bfcedf40c9171 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a +#: ../../src/index.md:3 17c386e7cd25496784207140f9876b90 msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 +#: ../../src/index.md:7 3bfd9bcf826a4400935dfad338612b12 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab +#: ../../src/index.md:9 4b38f1439da44ebb967b5b1e3df8f78a msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -446,11 +457,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 +#: ../../src/index.md:16 a4a60a8d010448b0b8ad1e05cbc78f2b msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 +#: ../../src/index.md:18 e23e00e89c81410ba8381fd81bc73b3c msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -458,7 +469,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 +#: ../../src/index.md:23 7274d92e678a440eb0d3ae3109f4157a msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -466,15 +477,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b +#: ../../src/index.md:28 6ad5f2d254a24ac1b3faf382d08b58aa msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee +#: ../../src/introduction/basic-concepts.md:1 7208cbccb84d45d58c7d5becec74b7d3 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 +#: ../../src/introduction/basic-concepts.md:3 8b9809abb49840b195a89943ba15f78a msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -485,18 +496,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e +#: ../../src/introduction/basic-concepts.md:10 9a934bf0848b438aaef7c4f00e0f2901 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed +#: ../../src/introduction/basic-concepts.md:21 5a299600dc304fd886b7153de1a706f7 msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 +#: ../../src/introduction/basic-concepts.md:25 55f7696f07d64277ad1b39d283175b37 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -506,18 +517,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc +#: ../../src/introduction/basic-concepts.md:33 b854ca0af98347d2b66e74754eb92a50 msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 +#: ../../src/introduction/basic-concepts.md:37 d9785269c51e4902bf3a70e917d33238 msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 +#: ../../src/introduction/basic-concepts.md:39 b57a31b8d26545d1823fcd1fa2c83316 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -526,24 +537,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 +#: ../../src/introduction/basic-concepts.md:44 4e264b1a40bd4935abb5bdeb75fa5c64 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e +#: ../../src/introduction/basic-concepts.md:51 791b02bb1ee6459d8d8332fc2dee353c msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 9bba7c4f783942e4a299603430601363 +#: 17300bbe695044e7b8917d23bd0aa597 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: e2140e0f0e7747ef8383887c20a7945a +#: 526614f195614818a614fc9a576e7cb5 msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -552,39 +563,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 15bf490724cd46dcbcfab44633c5a9a2 +#: 7b47991653054f2d9f49a91720754abf msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 51d52d051e654a8395239f88df7c9d8c +#: aa8838c0ee0a4b4285cb1b5dc6eb5d31 msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: eb496cc818524fa7bae5a22ddd00a19c +#: 457c73a37cb143d98005ebf6e67f5bf1 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c4a22d12e7f149ff901d27de32b9361d +#: c28057f3b7814f8395dbc3ad54d5f6f9 msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 7618de899a7043989d77baacf62eb7b2 +#: 83afed0785cd4b0bb86863c2841ce982 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: 6f1544a220664b79b04bf008058b5a91 +#: f332864bcc1e49d582a82f3d721ff3cf msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: fbd14ac9a2f541478a320ed4cbc69e13 +#: 3005c6d669de412ab7f8e30d00752a20 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -593,7 +604,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: da4dba50d25d4533b3dbb92f54d32a30 +#: 2e4041cb402e4054a53ea5890b938ac1 msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -602,7 +613,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: ce11c9f8d65c4268984d0384d95144cc +#: 972f9a1e64394a63be3258d3af0b1d79 msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -612,7 +623,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 3a201aa497e84f70855bb2251e7e3281 +#: a572f0789084402fb2d216ac845bbfdb msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -621,24 +632,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: b78f7fa2be1c4bb090f6da895457ad1e +#: c7c5c9a1e98e47c0a5a6dfa69e96f921 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: f7e95d264ffa4e2db0864faccd9e5a0e +#: 357d42768e794286bf5463ca5850a7ed msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 3f1e5b01e49a4dc1b1c99936a4589afc +#: 61966aab989744c1b9b93f7751f35ebc msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 03c3048f38ae4938a484cf02001877b3 +#: e14a2082d2c44f3690a07d3cee5b13d1 msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -648,7 +659,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: f9715b5ec65c405c849bb030c1927060 +#: c128a76992e04d20bcc3edae8b6c0bc0 msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -657,12 +668,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 442662f50e9e4620970ce32b1b127969 +#: 42953a3d591c48c6b4e80e9ea4b97bb3 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 2b34c786af3840e88f29d214e19dc837 +#: e3762a763ba24571a9627efafe172441 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -676,7 +687,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: dd6aadff8cf54ce78ea6b317afbaddb0 +#: be8e01a012ed45d6b7e4e6aab1afcc32 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -685,7 +696,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: cf31aca4294d486cb0e25c6436996d17 msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -694,71 +705,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: d10cf45b3c7f49dc98bc0e5d1246f224 +#: cc7adbdc66df4aeaad1429f7268c90c0 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 -#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b +#: ../../src/introduction/quick-start.md:94 71beb059c9e54a9ab5430f0dc44e07ea +#: 84679c5b03a3469294de849d9abe0a82 fd690fdd46344e0e8d9fc546f6d4013b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 8badec9987ba40609cf1f626172b2b2d +#: 89ddaddb64f64b0c86c7e89da0edfaae msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: c75a8b4bf0e24781bf6713cf6f013cd1 +#: e920a824207746ffae63242d33137ac7 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 51d619152aa44651889ff2006c8f5800 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 07cca9a33d8f4b77ac6ad35ca8b95655 +#: 88f3f5dd8aa6401793b89e8de3b8c7a7 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: 31db11c8ddf2423192a8b2063b3e91c2 +#: f1f9ee90d07c4381a8bb0851bdac231e msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: d81dd96143ea444aa78ff45cfa0584b3 +#: e3b710dabec2482d8ec1072d64d4e1f8 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db +#: ../../src/introduction/index.md:1 418699fcb6c241dcbeeed81d82e9f84f msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 +#: ../../src/introduction/index.md:3 28b6521a55aa4ab190ca998a59c52609 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 +#: ../../src/introduction/prerequisites.md:1 0e4969399eda48b98d883a3fc1540633 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 +#: ../../src/introduction/prerequisites.md:6 6d59f082157b494ebcfff2f649abc524 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -768,11 +779,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e +#: ../../src/introduction/prerequisites.md:12 2b83beccbc1b43969b705156b9c29482 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 +#: ../../src/introduction/prerequisites.md:14 594fe5e0aaf0499ebfa9218aaad4d08d msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -780,29 +791,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 +#: ../../src/introduction/prerequisites.md:19 f69c7c75a36048f5af0ed1b56df9320d msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a +#: ../../src/introduction/prerequisites.md:21 f28638ffb8394ccead4ac52f30adc627 msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d +#: ../../src/introduction/prerequisites.md:24 8993d7d5c8d24fc5a9c7005800c0a1f1 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: ../../src/introduction/prerequisites.md:25 2073109799e748d68304f5558c82b105 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 +#: ../../src/introduction/prerequisites.md:26 9fb2c31bd36d495786397c7a7d6b3417 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b +#: ../../src/introduction/prerequisites.md:29 43e1957537034c5886574118fc2533da msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -812,11 +823,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 +#: ../../src/introduction/prerequisites.md:35 e3a3d9b94b1e44c48f298dfcdcd27104 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d +#: ../../src/introduction/prerequisites.md:41 8a385803ed3945ff81d38a3543a69d94 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -824,7 +835,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 +#: ../../src/introduction/prerequisites.md:46 bf56727d93994d3995b0af0c68c2c583 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -832,26 +843,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed +#: ../../src/introduction/prerequisites.md:51 9a959bd914d543b78f9625f03df95765 msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 +#: ../../src/introduction/prerequisites.md:62 198ce7d893a04fcb806ec1671838d588 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e +#: ../../src/introduction/prerequisites.md:65 cc2be8feeab54a22a0b64a2a72991003 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c +#: ../../src/introduction/prerequisites.md:67 749c672e8c234c1c9a5eb2cc9b77c4e3 msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 +#: ../../src/introduction/prerequisites.md:73 29c64936318a4a2ba882e1eae8f03f57 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -862,23 +873,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 +#: ../../src/introduction/prerequisites.md:79 44106744147f45bab675eb66148531c7 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d +#: ../../src/introduction/prerequisites.md:84 6d84c6890f564b4baf7b34f6a52cbfc4 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 +#: ../../src/introduction/prerequisites.md:86 7eb67993e8ca48dc929e1a992f78cb39 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 +#: ../../src/introduction/prerequisites.md:91 52886c54c3c54b83896c52ebd7d53fad msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 +#: ../../src/introduction/prerequisites.md:93 097945c33f7542e2bae2e9f7ba1cf84d msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -889,32 +900,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 +#: ../../src/introduction/prerequisites.md:101 3853bfc6a85747019c615a50c7ca6b40 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 +#: ../../src/introduction/prerequisites.md:104 662230f538504f44941c6f4801f6251c msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a +#: ../../src/introduction/prerequisites.md:111 1c9eb9e2bb9e40a9985ada16c34eea2d msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f +#: ../../src/introduction/prerequisites.md:115 7f53ba159979461393c0f278fe97fb30 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 +#: ../../src/introduction/prerequisites.md:120 7e8077c2dd584eda89ead60ecc5eabf3 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c +#: ../../src/introduction/prerequisites.md:125 1787a3c749ee48218b87c8401f6255d7 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -922,30 +933,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d +#: ../../src/introduction/prerequisites.md:129 a52ca4ce9a184e938c3a5cac9cb882ca msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 +#: ../../src/introduction/prerequisites.md:135 41d3287a9a774a73aefd49bd709764bf msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 +#: ../../src/introduction/prerequisites.md:137 3b9d30094611400b85b55db163cb303e msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 +#: ../../src/introduction/prerequisites.md:144 b6ea77357b4f45528ed1379f8fe67cfd msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 +#: ../../src/introduction/prerequisites.md:148 8797ce327d7443fdb3d4617d3fc2cf7f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 +#: ../../src/introduction/prerequisites.md:154 896b6896b1e44d0cab5f35e7d0dd88e3 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -955,47 +966,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 +#: ../../src/introduction/prerequisites.md:161 4b839d23d72f4d3fbe4f1ce7e568b20b msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 +#: ../../src/introduction/prerequisites.md:163 a42b9ab315b5402493e4ce0067d0a18e msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 +#: ../../src/introduction/prerequisites.md:167 2f63483960634a7782f95e9e2feaa5a6 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c +#: ../../src/introduction/prerequisites.md:171 3471105073204d7998aaf790b73f785d msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 +#: ../../src/introduction/prerequisites.md:172 0b8b47511b5e4296b7438be0ad2604ed msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 +#: ../../src/introduction/prerequisites.md:174 3e3eec00f23f4f21873ddb005204a875 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a +#: ../../src/introduction/prerequisites.md:177 2ceb25f2668442839e3e9f4512772a03 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a +#: ../../src/introduction/prerequisites.md:181 20c753c5371b43ed834fa741b0ce7692 msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1003,7 +1014,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb +#: ../../src/introduction/prerequisites.md:185 a19c4fc9fa404912a0389337536d9c25 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1011,57 +1022,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 +#: ../../src/introduction/prerequisites.md:191 a0f38c1e28ca4850b3986617625acbf2 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb +#: ../../src/introduction/prerequisites.md:198 37e1162f30894a1ca7dada9870ffa3da msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad +#: ../../src/introduction/prerequisites.md:199 1c25a51edf6f47c5979c721b19cf11b5 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 +#: ../../src/introduction/quick-start.md:1 ace930cf878d45a99f12b71bf0987a87 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: ../../src/introduction/quick-start.md:3 46587a5e0d534af5867ae4f70a116bee msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb +#: ../../src/introduction/quick-start.md:7 a0774d4e779e46f7a983922425203066 msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 +#: ../../src/introduction/quick-start.md:12 1658ee6f3cac4d04afc732aa758b1f48 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e +#: ../../src/introduction/quick-start.md:16 d8e2bc671b894f3fa8a091261754c728 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 +#: ../../src/introduction/quick-start.md:22 683a469bf4824c64a8ea32e048d5df73 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 +#: ../../src/introduction/quick-start.md:27 b7c50413f7864a86815f3b581561cdb5 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1069,11 +1080,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 +#: ../../src/introduction/quick-start.md:32 d2ed66bdfcab4f7dad95b00c95d4a3d6 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 +#: ../../src/introduction/quick-start.md:34 4dcbe776a70645e5a6c7513348fa6bee msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1081,11 +1092,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 +#: ../../src/introduction/quick-start.md:39 bae5b03fb74541e6ad79277a576e0516 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed +#: ../../src/introduction/quick-start.md:47 8ff0d7a8d37b48488e4504ff8e3adcc5 msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1093,32 +1104,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f +#: ../../src/introduction/quick-start.md:51 6255b499b9b144128afaeed64fabe8e5 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d +#: ../../src/introduction/quick-start.md:53 e861db9c43ed4b8ba262af8e435a350a msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc +#: ../../src/introduction/quick-start.md:57 c6318f06bcd74cda8c1f0caef9452b51 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 +#: ../../src/introduction/quick-start.md:62 c862e745217244d28cd4c2f0842e203f msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 +#: ../../src/introduction/quick-start.md:65 eba007736b92434a9711f683e64bb153 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 +#: ../../src/introduction/quick-start.md:70 aebc2caf5d1b47f1b7cc0aa53e5a684e msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1126,21 +1137,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: ../../src/introduction/quick-start.md:74 1242171f8b854562bb7848b06d2d065d msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f +#: ../../src/introduction/quick-start.md:80 24e82ecf7926428386a89f18a34eb00c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 +#: ../../src/introduction/quick-start.md:82 00e75efe03554835bc33ebaed0652626 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b +#: ../../src/introduction/quick-start.md:88 4ba34ec455704844a9cfcbac3522ea0c msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1148,46 +1159,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 +#: ../../src/introduction/quick-start.md:96 c0e9673440db454bb51af04432aeddbb msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd +#: ../../src/introduction/quick-start.md:97 39a23a9d02ab4bccb36d6a714639509b msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: ../../src/introduction/quick-start.md:98 23a878e0166b40d78984a2263f63b760 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: ../../src/introduction/quick-start.md:99 5d9c435820674bf4b1c5d3fef5df736d msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 +#: ../../src/introduction/quick-start.md:100 e724ee53db1940b9b09a909f4db531a4 msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 +#: ../../src/introduction/quick-start.md:101 7820eb801a8145feb603145f153263b9 msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e +#: ../../src/introduction/quick-start.md:102 e8db3f10be294f13abe3a4418bbae4b6 msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 +#: ../../src/setup.md:9 95211ea6924148a6a1fa5ae8facc2c7b msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1195,19 +1206,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 32f86f911ebe4a4c94975f81742333f3 +#: b742a74d586e42e6b0480b7af3e49c9e msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: cd3da03d43044ec9843e476a54e704be msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: c53ceee943ad4acea779e072b9137889 +#: 0d48e2f07d784504a17cad0ae20262c2 msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1218,37 +1229,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 7dfe9dffbf5744299bf232599644c7f6 +#: 4d372b89f0ce451db2a505b1754b8356 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: ../../src/topics/staging-input-files.md:15 573e903ef3d34514ab7b20e79c446567 +#: cfb40fbe52174d3799a6bec175db60a5 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 1f3c23a4769043ca985b8ddfed19391d +#: 95841b1c75c84f01bd5fcb7cf3afe78d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: f81b43c7cb194a1cad8672129223c833 +#: c8bca3654ebb4b29bf3f028b4c65fa35 msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: a20073a8f5374eb1bc8531ff33e622b6 +#: 1432105e38014a6d9d0cf80007141007 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d08869beca3a4774baf1097b63e79474 +#: bcad473b34ec43f7906253123a1661fa msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1259,11 +1270,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f +#: ../../src/topics/best-practices.md:1 e1c8949e663b4debaf87735f1d62a2fc msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 +#: ../../src/topics/best-practices.md:3 dcc991b647d34ffc8ea3bf9c3a38258d msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1271,13 +1282,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e +#: ../../src/topics/best-practices.md:8 f26c222638e54187b8bb62fe30b66bc3 msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 +#: ../../src/topics/best-practices.md:11 23720e4ab3d1407597f1d1c2a4d4d90c msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1293,7 +1304,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 +#: ../../src/topics/best-practices.md:20 b3638183c59744c897246af7dab5d10e msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1303,43 +1314,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 +#: ../../src/topics/best-practices.md:26 2c0291133b964ad8b751f8a8ed2338fc msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 +#: ../../src/topics/best-practices.md:28 325c8c4058f045aa8fbd705238122798 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 +#: ../../src/topics/best-practices.md:37 05333866485b43479352f7ee9326c7fd msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 +#: ../../src/topics/best-practices.md:40 f8140ec6e9cc41ee88ec4bde61a44d47 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f +#: ../../src/topics/best-practices.md:44 1d68f50dafaf4cc1851e2d67b3e78603 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd +#: ../../src/topics/best-practices.md:47 b283942434c54456a3f29fbb0960b6c4 msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 +#: ../../src/topics/best-practices.md:50 0b4477c5b0184e59aa0c07161008a7bf msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1347,13 +1358,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a +#: ../../src/topics/best-practices.md:55 9741651d51f249ffba1820694ab78e92 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 +#: ../../src/topics/best-practices.md:58 5e76d4a9708244ff91f2587350d684a4 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1365,44 +1376,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 +#: ../../src/topics/best-practices.md:66 89e7028e55b54f968e87b9c1c3caeecf msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 +#: ../../src/topics/best-practices.md:69 88e2338fb2614ef29dc497d8c01a2f2f msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d +#: ../../src/topics/best-practices.md:73 0f3aad35924344659eb5a6719ab2b8f0 msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 +#: ../../src/topics/best-practices.md:76 877cbb1d537b46d3b6d05b2d8c025e70 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d +#: ../../src/topics/best-practices.md:78 5c0debbc1c1b428ebb32b589b99fe17d msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 +#: ../../src/topics/best-practices.md:82 1ff97183191240edb98f0cc365cc028b msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc +#: ../../src/topics/best-practices.md:85 22f7725deb07422fa0a7bc2e6f01e4d0 msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1410,31 +1421,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 +#: ../../src/topics/best-practices.md:90 982313839ccc4f5a8527fe9a854c78eb msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b +#: ../../src/topics/best-practices.md:93 267c9d10ab5e4b6c8a6104952deb1690 msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 +#: ../../src/topics/best-practices.md:97 2eff0eec58c94f4d8986a4cb91b14b8e msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 +#: ../../src/topics/command-line-tool.md:1 f38db701740b442c89ce58e937bd35c5 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 +#: ../../src/topics/command-line-tool.md:3 034aac9e186645e384c28bb2a739cfff msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1442,52 +1453,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 +#: ../../src/topics/command-line-tool.md:8 5f835cdfc0ae4f378d8dad6ae7ab1855 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 +#: ../../src/topics/command-line-tool.md:19 02900cb8ae4c4da89d264b76a984d6cd msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb +#: ../../src/topics/command-line-tool.md:50 753e48d6dfd54a88a12773b996f182d7 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d +#: ../../src/topics/command-line-tool.md:57 c7ed6d1654c54bf390e933ef0f847b99 msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 +#: ../../src/topics/command-line-tool.md:68 0a0f855ce34449a0a37c036105c65839 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 +#: ../../src/topics/command-line-tool.md:69 c4300454f49548f49e4bd186192515a1 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 +#: ../../src/topics/command-line-tool.md:83 f985d58070de4c0fb5f5a491fd4dc31c msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 12cf5f2264504c44a2173e858bb2c283 +#: 2f4e2c85677a4e56a35b6bef36d67334 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 7694f9cabfe04308bbddd2c88ae6d9b9 +#: 13c6d5600a30406c81ffa25ce42eb0c8 msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1496,17 +1507,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: b557dc4f8ef549b98f59412a918643de +#: 3bf773b8560e44a3a37c68b6fcdc6a23 msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 3011eb003c084285b30cfa56a8da45b6 +#: 68b8578d2f6442929941ed2522b218ad msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: 755149ed46c348c2b723b49c3b3152a8 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1514,7 +1525,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: ce78b2d147054da895beba66d0ecdab4 +#: 54b7ff590d52454eb87d9f23fca44501 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1524,7 +1535,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a973846ec5a946eeaff02c5b00997da9 +#: a7c74a4a74c9414e9f29fa20bab7e295 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1532,13 +1543,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d -#: ccec7f73b9d948e79a6cdf32bc124092 +#: 0cbf233379024800bcebb963e0a3eb6f ae3bc02e4f3b404c89f3c461a62c5bc4 +#: dc32a2bacf2d4c8cb841be6eb8b839ad msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 22948f19cb78485f8f86244686a35c09 +#: 34a56bc23af44353a003ee295fb2c609 msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1546,7 +1557,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 001d9579bfce438e865377fb9c2df776 +#: c7855ec1f09d4945afcb0aec22567b31 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1558,7 +1569,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: e62618db8995428bb3f260e03ac8f459 +#: 5c60492e27014735bb9a86307ee654d6 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1568,19 +1579,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 -#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 -#: e9801b2142cd45368a73ef9b121c1d08 +#: 80a9c04358e64ca28ef4879ad74ef733 a2b470f06ad94871970b7d95339fd369 +#: dc65b4b5e48e48a6ada03da0fac18a51 ea2360c5286b43ccabac202dfa97fbe7 +#: ee4ca94dadf64ab69a70b6cd4eaf451a msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba +#: ../../src/topics/custom-types.md:1 285d23ef9bbc46c9890ae7957d487c12 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d +#: ../../src/topics/custom-types.md:3 3edd322daad940d8957f88a2637876b5 msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1589,21 +1600,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 +#: ../../src/topics/custom-types.md:9 a1bd9b0dfa234e6caa6a684e981d89b5 msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac +#: ../../src/topics/custom-types.md:12 0aeacb6ac20f4ebca3600425ca32f5f4 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 +#: ../../src/topics/custom-types.md:18 1c813ebce2904f008b5b33656f673ebc msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b +#: ../../src/topics/custom-types.md:24 cc36359e94c841d3aa5cbb26a094e1d5 msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1612,13 +1623,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 +#: ../../src/topics/custom-types.md:30 dc79668b05e8439591a0beb4b57acc66 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 +#: ../../src/topics/custom-types.md:46 08aba4f77aa442d4a34aa1535f78c49e msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1629,15 +1640,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed +#: ../../src/topics/custom-types.md:53 63431a972f994bccacf55d5fac0d614e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: ../../src/topics/custom-types.md:55 55e7695aca4f4319b1cf7551105a8782 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 +#: ../../src/topics/custom-types.md:61 0c5ab34ebbf54ff6940b8ce3f080d744 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1645,7 +1656,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 +#: ../../src/topics/custom-types.md:76 f97e18d2d3b946468c4fac227920e011 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1655,26 +1666,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 +#: ../../src/topics/environment-variables.md:1 62644031403548898ff36addbc0b1f6f msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 +#: ../../src/topics/environment-variables.md:3 595630b0687c4467aa65bfed289281f4 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 +#: ../../src/topics/environment-variables.md:7 34e005c135864a89a00e817d79118e2e msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb +#: ../../src/topics/expression-tool.md:1 b624f9f99c294e6996f212c8b62f20b0 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 +#: ../../src/topics/expression-tool.md:3 14df63ab847e4efca820f712548cd076 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1682,32 +1693,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 +#: ../../src/topics/expression-tool.md:8 91d4224b41c6473f936c03bd0ab9d370 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b +#: ../../src/topics/expression-tool.md:17 519989399dab493ea41941ed85cb9670 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf +#: ../../src/topics/expression-tool.md:48 28dd1cf24309404eaf717d417272e094 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 +#: ../../src/topics/expression-tool.md:67 3f536ad8c86d442c8bbe61777dbb1a54 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 +#: ../../src/topics/expressions.md:1 b9e9894c6d024e60929d020dbaa553f0 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd +#: ../../src/topics/expressions.md:3 482debe1a40f490b90d4ece1b3f9d732 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1715,7 +1726,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c +#: ../../src/topics/expressions.md:9 708346038be745d097685970cc462f4a msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1724,67 +1735,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab +#: ../../src/topics/expressions.md:16 99347b6b2c404a4b9bbcc96e0b4bd925 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 +#: ../../src/topics/expressions.md:22 e6629f0914324c76a08fe179575b73d5 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 +#: ../../src/topics/expressions.md:25 2287002a87184fb9b95d775a368f0e46 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 +#: ../../src/topics/expressions.md:31 c23d4543d9f949a9a7015fdcbb40dcd0 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 +#: ../../src/topics/expressions.md:35 c04a9dcc84b84f37bcf32c3790672038 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 +#: ../../src/topics/expressions.md:37 9f27c79365db455d9d31053576ebe05e msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad +#: ../../src/topics/expressions.md:47 a2b3ad1e2c884e24948a915c3305aee1 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 +#: ../../src/topics/expressions.md:54 dd7665bbc5e9449588c9539e3c1910de msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe +#: ../../src/topics/expressions.md:62 0972c757f7c74ea9beabf6b9ef9dbf4c msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 +#: ../../src/topics/expressions.md:64 175de3b9854546568f60a20cc19887de msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 +#: ../../src/topics/expressions.md:66 0c286e5ba1714a059a95b566fe49be31 msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: ../../src/topics/parameter-references.md:64 3029c1dfe5424c2b812597b03ea76178 +#: a5503b6c524e4848aa308b0f4c26d774 msgid "`arguments`" msgstr "" @@ -1792,32 +1803,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 -#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 -#: e7f1993580f0425098a719e83a64cc7f +#: ../../src/topics/parameter-references.md:86 0e03befa46c74dc2b09420e1eb2a6fbd +#: 50f81e7ab73a4713bbc60f6f5609b906 718dc3def33c462786174fb42097981f +#: 9c2acd930553458eb105f96213b5d7b0 d4bf86a995d546c0a9159b3f29a84125 +#: e98424244f554c7399e9e7ad560849a6 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: ../../src/topics/parameter-references.md:66 2be930b5da674874a0b634eca3ad9346 +#: ce445ad0f00f403985eed1328103a500 msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a -#: 92697d3179ec48898eaea9aba3c24dcd +#: ../../src/topics/parameter-references.md:67 2fe48d6404864ea39ef0634169f67be1 +#: 43453d90db244c558a815ca872dc716c msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 -#: d6722e3093884ad7b62696fbb2f48fdc +#: ../../src/topics/parameter-references.md:68 78eaa318ba81407e9ca9c2c1702ead11 +#: f5da7058f7f146d584314a5bf4de5498 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 +#: ../../src/topics/expressions.md:72 7189f4415d204fb388c4a7e927e15b71 msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1828,11 +1839,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 -#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef -#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c +#: ../../src/topics/parameter-references.md:90 17a83cc91963434e89822a3e46df8401 +#: 194d3e48d38c476fa8f731e3bc2d8c7f 3a3000a6446b4ef4ac66a28acb13b136 +#: 5cc35210e95e4f2ba6a1a6f118926fdd 68b3d1481a4e4375b1b0c4fca8285374 +#: 94f2bc195bc0487da014bc3f4d2dc8fa b92b4eff2429437d9da911ca68cef954 +#: fc0a1353e87e479d8c8b6c973d547465 msgid "`format`" msgstr "" @@ -1841,51 +1852,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 -#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c -#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b -#: f71216a4b35e4157aece5ffa2602d8bf +#: ../../src/topics/parameter-references.md:91 5478cbeadc64412bbb32619fae9b9958 +#: 6950cbe52d334fe58bf4fa20e5f1f8ca 6b5bda581d0047819c6d92edd8ac9045 +#: 8248329fbe504b3a96bcd890908b070f 978c0fea8ed1481a9f06b6abb31ebd21 +#: a24ba514d66d49cea281fd4c9c7a2b8d b6e2c8e7abf74d64b2915063dda8479b +#: bc184adfad0e4642bc864d367b8779b7 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a +#: ../../src/topics/expressions.md:75 5bba2d465e0a4c5d9575406d1294a225 msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c +#: ../../src/topics/expressions.md:77 da385d3cde614749887e195ea6d95291 msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a +#: ../../src/topics/expressions.md:80 487c95417f8e48be8391163578ca9519 msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: ../../src/topics/parameter-references.md:78 48437402c00147d4b4ca8bd6b38a5823 +#: bdcb3920048f4e578a4005fc2e30233b msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: ../../src/topics/parameter-references.md:79 121556d49d584cc491a15ef8404ce462 +#: 183ba52666744f7ca5772939db2efd6c msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: ../../src/topics/parameter-references.md:80 08ad064936d8406f8c3852526f4f863d +#: 30c927925c6b483b80b583ca7c735437 msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd +#: ../../src/topics/expressions.md:84 32a26dd9c5f84e88995f093cda953ac9 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1894,32 +1905,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: ../../src/topics/parameter-references.md:84 05ee6df2f9b247629d148fd59c293660 +#: e7b7d782b6ac49b3aa0c8d8ce7ff04d1 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe +#: ../../src/topics/expressions.md:88 b0cccc07e5bb4effb60424623351499e msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: ../../src/topics/parameter-references.md:87 4e5281c8663c4b6e8851be10f50143f1 +#: b5c22c66397e4268b4b3d53b9a253a3a msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: ../../src/topics/parameter-references.md:88 98a28fec818e42af9e177e17fa12aa7a +#: c37d0b1fd75e44a28b3b6409f912e865 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 +#: ../../src/topics/expressions.md:92 dcc42c6c49964a4ca7bcf2124e26ebfd msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1927,61 +1938,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 +#: ../../src/topics/expressions.md:95 d2ba352ac5fe427ea7ceb0bde01458ba msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 -#: c9534670f5f04769aa3749c3778eb705 +#: ../../src/topics/parameter-references.md:93 235cfd6e9baf48698102447fcb83e0e1 +#: 8aad01df8d8d4ab7905a5da7ce7f6bbf msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: ../../src/topics/parameter-references.md:94 058ba8c9c2da4ebf8b2291600dafd611 +#: cea47d3e10f641a2b64f08ee100ea6bf msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: ../../src/topics/parameter-references.md:95 3b039de5ad144207ae337aa88b3b1a1f +#: e0ecfe44b34e45dea513459b6b3e44a6 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 -#: fe3b9fb45e01490498c5a35c012b3de8 +#: ../../src/topics/parameter-references.md:96 1cfc6cb0be4e4ddd90f546adb796b805 +#: b62f6eaa7c394792929dda83a187c632 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: ../../src/topics/parameter-references.md:97 8b13b0e4071444179b26401929de8a10 +#: 8ffb471129c04fc6bb52b782fbd09f9b msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: ../../src/topics/parameter-references.md:98 331f58b998cd4d309940ebfcc60a44f8 +#: 5041700e6ccc48989e395a6dcb1be3c4 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 -#: fec70bb106ad4d95a2d55ebdcf711afc +#: ../../src/topics/parameter-references.md:99 14402b41c64548f8a9691c3b7ccaf3ac +#: cb4837a2b25343d2880a07143f85f40e msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 +#: 1d1c2894600544b686a8ec3c36cdf767 eaa30e987ec543ef8d6f7171de5525f0 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 +#: ../../src/topics/expressions.md:104 065c97a553904db6ba61c20cf9d9939c msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -1989,33 +2000,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 +#: 36be05289972455ea4a60aa1f0b9cbdf 49e1ab5bc5734debb83060759d5c3236 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 +#: ../../src/topics/expressions.md:106 f8e37cd35aea4bbb92d28e8d7e803ebb msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 +#: de816d1dc9f24c0cbef86fd6a09eff6b e265df9d1cfe439bb798ab6cd32485af msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 +#: 0363e32e12604eb896f4bdf6bbefd550 8b5289393b7f477699d007ded45a4df1 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 +#: 2c704cae43d64ecbbed33d18eb3f66f3 89acc8f8387d4643a844ac3efb186000 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b +#: ../../src/topics/expressions.md:110 0597c6c214924e75ba2f212cd6b0c9f2 msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2023,22 +2034,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c +#: 1eb1c2432dd943f6a27a1f8b92e3981b 5b9ba9380f10425b809c6157a1f0b052 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a +#: ../../src/topics/expressions.md:116 b4cc7cc55cf04449b291a27514fc99ae msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 +#: ../../src/topics/expressions.md:118 cdb48eff43e7459fbf3ed21eb7791d66 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 +#: ../../src/topics/expressions.md:122 67a4dc675c0e444585d579954b99614e msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2046,7 +2057,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 +#: ../../src/topics/expressions.md:128 ea3238db48494ab7b044bab9f96590af msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2056,54 +2067,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 +#: ../../src/topics/expressions.md:135 baf2f6ac8d514705a1f7bf7ea8c71d2e msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 +#: ../../src/topics/expressions.md:139 ef45f4e14fb943cd9fbf179f5d3680e5 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 +#: ../../src/topics/expressions.md:146 030261615c38485d83ed986c9c98ce15 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb +#: ../../src/topics/expressions.md:149 1728e2370cbb49ab97bee4c2f74fff2d msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 +#: ../../src/topics/expressions.md:155 4514fc0c99ac4688a37bf30bffe139e8 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ../../src/topics/expressions.md:158 33804649720143e5a70e890af9ad9119 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c +#: ../../src/topics/expressions.md:164 c114496be4c243d6834776e17bf15010 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 +#: ../../src/topics/expressions.md:171 c784e86f14f54e4982db206741fbd96e msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa +#: ../../src/topics/expressions.md:175 f9de69aad9b44afabded71221c84adc2 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 +#: ../../src/topics/expressions.md:181 b853c964611e45c2b37a8ac3c34a4133 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2112,15 +2123,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 +#: ../../src/topics/expressions.md:186 a10d143210b94f83857f62e972d69134 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 +#: ../../src/topics/expressions.md:193 b07734b172664040aff04f83bd4395a5 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b +#: ../../src/topics/expressions.md:200 1f9a5377a1f04ee3b8a9ae22390e0cae msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2129,11 +2140,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 +#: ../../src/topics/file-formats.md:1 359bb6448aa140f8b940baf769c13db6 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 +#: ../../src/topics/file-formats.md:3 c4aba730bee14931b051d6aead7c2dae msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2141,7 +2152,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 +#: ../../src/topics/file-formats.md:8 c4dfcff573424bccb97580fdd1ef27a1 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2150,34 +2161,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 +#: ../../src/topics/file-formats.md:14 1457fa489c894f1bae8a3949ef200527 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b +#: ../../src/topics/file-formats.md:17 cc4fa87d57b344ed8961c31bc4397e71 msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 +#: ../../src/topics/file-formats.md:20 091815ab1d824787a1460ce11ffb834d msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 +#: 414b68dac4654163b3dc13e140ffdbf8 96fad38b4aea461493bf0827476163bd msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 +#: ../../src/topics/file-formats.md:32 4f71de1140974e73ab033fe7dd9dc165 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 +#: ../../src/topics/file-formats.md:34 b84e3294c8f648aab634e59b6f58441e msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2185,11 +2196,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 +#: ../../src/topics/file-formats.md:39 6d9ae44900d64532906532432881d29d msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 +#: ../../src/topics/file-formats.md:45 5b99384b3a854832bcca2fb02bdfc1b6 msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2198,80 +2209,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 +#: ../../src/topics/index.md:1 3141fc6828024c3e8201e88ca10e19ee msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c +#: ../../src/topics/inputs.md:1 5f8c8ea68d7f46fead000315226ec164 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d +#: ../../src/topics/inputs.md:3 86c18e5105b1400d86d413e28ad72f48 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 +#: ../../src/topics/inputs.md:5 fa15037f9b0b4a2c9a1f4cff9b8fde43 msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 +#: ../../src/topics/inputs.md:9 fba6d2b7843e466abee33183103cf47d msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 +#: ../../src/topics/inputs.md:13 09f5a55611d14e39b2266245b79ed763 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c +#: ../../src/topics/inputs.md:16 bdfb39c2656040858616afe731111d1a msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 +#: ../../src/topics/inputs.md:18 c306335ff07e4c03955fe87cad16efd1 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc +#: ../../src/topics/inputs.md:24 50bd3db6bfb348eea13ba4714ecb2a20 msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 +#: ../../src/topics/inputs.md:26 5d32cfb6f6ed4dd8b11ed316830edba8 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 +#: ../../src/topics/inputs.md:33 b90fb1b2d38b42c1bad2d9667aaa22fd msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a +#: ../../src/topics/inputs.md:40 6029a96abf9c4d7295eb86d435a1f58d msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c +#: ../../src/topics/inputs.md:44 902e9df74f78431ca9cf1421a26e097a msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db +#: ../../src/topics/inputs.md:47 9760d15bad144e70a86dc0a8da72363a msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 +#: ../../src/topics/inputs.md:53 75bf3fae131049308441bc496f543f6e msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2279,7 +2290,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e +#: ../../src/topics/inputs.md:64 38d8a9c157404bb496bc49f1e427bf99 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2287,7 +2298,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 +#: ../../src/topics/inputs.md:70 502994ee84234f048e545633bb04cd3c msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2295,14 +2306,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 +#: ../../src/topics/inputs.md:83 551b06b8a3064bcd8d0f1693a4c0ee94 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 +#: ../../src/topics/inputs.md:95 1838e7438be5449c91c6406a7e40d8cb msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2310,7 +2321,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa +#: ../../src/topics/inputs.md:109 098bb02c941a4bf2a8d4dd9ab3bf052e msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2318,7 +2329,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 +#: ../../src/topics/inputs.md:124 b43194d2b3ef4fc6a8c4b58741317b29 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2328,13 +2339,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 +#: ../../src/topics/inputs.md:131 e17c55c9ed034dd68f4d24272a61d2f1 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 +#: ../../src/topics/inputs.md:134 c97a6945e4bc49888d280bbc43c3c069 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2345,17 +2356,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c +#: ../../src/topics/inputs.md:142 503666cda07b4d7397c65561714d8034 msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 +#: ../../src/topics/inputs.md:146 e5463be0a00d42e386aa6fd3dfacaeaf msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 +#: ../../src/topics/inputs.md:148 14b98bd0ef4a4065a24e66443458d607 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2365,23 +2376,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 +#: ../../src/topics/inputs.md:154 98fa5dab117e41d4a42da8d78c533c64 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 +#: ../../src/topics/inputs.md:160 116c212444da4488b32abdbd725db98a msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 -#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 +#: ../../src/topics/outputs.md:105 065e556e01b34c35b6be4b54b7cc0203 +#: 4745f370dcbd4ee8bbf4b3a20ac5b9fe d11761f2d576464f8a2c63bdec02d410 msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: ../../src/topics/inputs.md:178 b3bf1d7e95704682b1bae17472eaa4bc msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2391,7 +2402,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 +#: ../../src/topics/inputs.md:185 04bc655130234786b06b2d5b9e693635 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2402,11 +2413,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd +#: ../../src/topics/inputs.md:191 e2c18a43b2794448b45c489dd2fa951e msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 +#: ../../src/topics/inputs.md:193 38968ed627514ef38e43b3d1e4a5e25f msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2414,46 +2425,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 +#: ../../src/topics/inputs.md:198 06aab84eceeb41d087b7e295ffa21586 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce +#: ../../src/topics/inputs.md:204 a0317edb8b964cd2a36c59eaa6df302a msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb +#: ../../src/topics/inputs.md:215 5a3d1b82c79c4ccdb7d06381f4d0acda msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db +#: ../../src/topics/inputs.md:217 e1fc6c3a324a46ee84b0eb59f8396552 msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc +#: ../../src/topics/inputs.md:233 f22e7d9e23b541ef88f3254095147519 msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 +#: ../../src/topics/inputs.md:236 d473d2fa11f64e8fa86554b5777c98e4 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 +#: ../../src/topics/inputs.md:252 290461c321d14d23b39003b93008a7cb msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 +#: ../../src/topics/inputs.md:255 add43f7531bb4c6988053ae799c366f0 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 +#: ../../src/topics/inputs.md:257 b12b6f5e34c14dbc9b40458d92e6797f msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2461,18 +2472,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 +#: ../../src/topics/inputs.md:262 4d8f38679952486095a77692387db2d3 msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 +#: ../../src/topics/inputs.md:265 47ec49759e274e59834192b794ec2d9b msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d +#: ../../src/topics/inputs.md:271 0657044c742348fe9e63f662692570a1 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2480,7 +2491,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc +#: ../../src/topics/inputs.md:280 30c21cafda144f848bfe79d8e232296e msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2488,7 +2499,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f +#: ../../src/topics/inputs.md:289 1cc8ea6abb684470b7790808acea2be1 msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2498,12 +2509,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 71628ebe908b4cd28dd1fa17e3d2e2fb +#: c3b84742343449f9b3866285d98b53bb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: f123ca244c23413c91405a4b84887525 +#: 0a1b08fe707c41089ad3d4895960ba17 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2518,7 +2529,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 23299ae1bec94b00a32a8af7eeac350f +#: 5bc4ef6584c74b948ffd5c0bddf8e569 msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2526,17 +2537,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 2495a9f2032a47c188338cb81ba429eb +#: 47ee25d60a4a4faa80476797954ec7a9 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 3fd2f3cf7bdf44089df2ce3122534801 +#: 195d4a8d5aad41159beffafd198d4640 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: d5a5b8b490b640439db92da949266e4e +#: b0c5946fbf79415aa74c8e72fa88cf85 msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2546,15 +2557,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 5935ed94331d4b2f8ce597f31edea843 +#: a98236fc1be745a69271855e1b5eecdb msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe +#: ../../src/topics/operations.md:1 5f0da8d7e06a47fda38053dbadcbec18 msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 +#: ../../src/topics/operations.md:3 23d41792b0524742878a6ab8f3ff0fe1 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2562,56 +2573,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 +#: ../../src/topics/operations.md:7 c0f723242f11464392dfc32f67a3b67b msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa +#: ../../src/topics/operations.md:10 c9f3a48a3a064cb3b1759effe724301d msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 +#: ../../src/topics/operations.md:16 fbad0b0144984ae78b84307ea68d0a03 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 +#: ../../src/topics/operations.md:24 59e9ff3276454ff19eb351ff33737f12 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 +#: ../../src/topics/operations.md:55 ba74f2ab7f6d4c178f3c4c43c461afbd msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 +#: ../../src/topics/operations.md:58 93c8b61a12134991ae9bb78223e2017e msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 +#: ../../src/topics/operations.md:66 cbbdba36dc3841f2b1d820f369a8c680 msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc +#: ../../src/topics/outputs.md:1 4649c8d743f448ab94ee589a1b3a342a msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a +#: ../../src/topics/outputs.md:3 1a9d6e2e33244d01b820cf11fe2beaff msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d +#: ../../src/topics/outputs.md:5 233c8865faac4d6c8ec7704e9a997719 msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2619,7 +2630,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 +#: ../../src/topics/outputs.md:10 5aab1c0db3d5449cbb4a0f0dad615d87 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2628,17 +2639,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 +#: ../../src/topics/outputs.md:16 46b4eeb3ce8946dca0f8a94c399b4c96 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 +#: ../../src/topics/outputs.md:19 8d322609948a4d6e87d7962b3d29df2f msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 +#: ../../src/topics/outputs.md:21 9fdcb55e965444ee8b5d74a2a9870d27 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2646,71 +2657,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 +#: ../../src/topics/outputs.md:26 e4c490f599a0469a821aa8e74f4ef0ef msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e +#: ../../src/topics/outputs.md:32 b8ed6ebe6928455cb094ea430e21e5d4 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b +#: ../../src/topics/outputs.md:38 3e65c52d218946fc83b8c3e6adcb21fe msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 +#: ../../src/topics/outputs.md:45 03751b45cdf647b689a3a69156989db5 msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 +#: ../../src/topics/outputs.md:51 1b6f59623f5d4cd984426da21b8438bf msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a +#: ../../src/topics/outputs.md:62 095902cca30944d19a0d5f17f582e3b0 msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f +#: ../../src/topics/outputs.md:65 6d95fbfa321144a9932f26ab5f9ddc74 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 +#: ../../src/topics/outputs.md:67 8be7ef160e8b421a89124a639dc7fd84 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff +#: ../../src/topics/outputs.md:71 fcf4490c351d4cd6a208345308168ef7 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 +#: ../../src/topics/outputs.md:89 00f1bb92a38b4f3a8c0065ac75530689 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a +#: ../../src/topics/outputs.md:91 1477d0fc5c4c4f82bcc1c8e6ba8eed4d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 +#: ../../src/topics/outputs.md:93 dee904cb678d4eb49dc829d6590b267a msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f +#: ../../src/topics/outputs.md:99 a21c1fd3194a49ae992a743023653dc5 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 +#: ../../src/topics/outputs.md:112 e72c526da47a455da4b10e33938d1600 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2719,11 +2730,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 +#: ../../src/topics/parameter-references.md:1 6447f4b8bb5f4f93bd8ec2c7b1fb09cb msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 +#: ../../src/topics/parameter-references.md:3 1faea30495a440a68dbd1647dacc404c msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2736,40 +2747,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 +#: ../../src/topics/parameter-references.md:13 0c0a3f58a93f492dbfca14523809aacc msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 +#: ../../src/topics/parameter-references.md:19 460842f202db493dbb901be73a02797f msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 +#: ../../src/topics/parameter-references.md:25 2591c2cf9e5f402281031ea8dd41a251 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b +#: ../../src/topics/parameter-references.md:36 b093abbff3614b2ba0141f07376a5220 msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee +#: ../../src/topics/parameter-references.md:47 fda3718113354215bd2ac212553fb2d4 msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b +#: ../../src/topics/parameter-references.md:51 271e78089c274154a0233289d705e628 msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb +#: ../../src/topics/parameter-references.md:54 29ab4fa0876b4c11a0c7482cca56ed80 msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2777,45 +2788,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 +#: ../../src/topics/parameter-references.md:59 78e1857c5bd54af1b7ca4728879e6219 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 +#: ../../src/topics/parameter-references.md:61 dae7873015254aa7874379164c90a8d0 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 +#: ../../src/topics/parameter-references.md:63 7a45deb4682b49fd86d62fae41831db8 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e +#: ../../src/topics/parameter-references.md:69 442f77a69b314cba8e8857470263c706 msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 +#: ../../src/topics/parameter-references.md:72 d4455241f14549b791e59fc1f942c8cb msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 +#: ../../src/topics/parameter-references.md:74 ff4b1c05c5804ec7846043ae8814ad21 msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad +#: ../../src/topics/parameter-references.md:77 119e026b595f49c090d62aa7b7c77de4 msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: ../../src/topics/parameter-references.md:81 5449d9c5687544a3bfbf8b2b25640a83 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2823,13 +2834,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 +#: ../../src/topics/parameter-references.md:85 b3191a7bd03d4ff18802ae0f5d419676 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 +#: ../../src/topics/parameter-references.md:89 ea9cfbbd4cbd4f26ba4b0cb50d58635b msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2837,43 +2848,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 +#: ../../src/topics/parameter-references.md:92 7d39ed2a3a724dc1a75e6b2cdf87d91d msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 943ba46512ce48fe8c5b62327734c503 +#: a1306ee650344278ae39d6086b1ed7d9 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: bbcd43d5af7d44108aeb65075a6bd2be +#: 21d76d22f3044460b925fee68ac74454 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 834295755af841a78e466eea43864861 +#: 6b8a5c59217c4928874710ead1456622 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a6b626489bfa468e8f059ab3aa669201 +#: a9f6d09055c24029a5f85c3a663c4202 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: e1dbea105aa845c38cb1f90b43847271 +#: d3948618f9274ad0a333722567efeea5 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: e9640f47d40e45bca184eb30700df648 +#: 44623c81141345a0b0080e719e1418ab msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2883,14 +2894,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 0456efb3718b4356ad2b277ee16de967 +#: 6e80d82ed57b441b8292961ec3163213 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f7e97f926505407f8f8e9a427e055e43 +#: fc61f369e720463f8a5cd6c751d1d5e6 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2899,7 +2910,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: ec597ff8f6ee47bc815b069335869f1f +#: f20aadbfc13243498ad199376c314e72 msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2915,11 +2926,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: ../../src/topics/staging-input-files.md:1 e66956313b8f4f02bb96cfb256e2a7d4 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: ../../src/topics/staging-input-files.md:3 f18c5a8fcbe84135a6e06cbf8008cd63 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2929,26 +2940,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 +#: ../../src/topics/staging-input-files.md:9 87fe14c9a0594602aa56a7706e089458 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da +#: ../../src/topics/troubleshooting.md:1 6e10063f55b747e1b07d6109ab7b046b msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 +#: ../../src/topics/troubleshooting.md:3 e8831832b32449f4a8a3dde3c1b479cd msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 +#: ../../src/topics/troubleshooting.md:6 9c86467137864626a2079cb6cecb71c0 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 +#: ../../src/topics/troubleshooting.md:8 24b66a3e2e464ec6a85b5dfbaad1cbf4 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2957,7 +2968,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da +#: ../../src/topics/troubleshooting.md:14 6d28f1cd40c045f384313c4d74073ed2 msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2967,18 +2978,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 +#: ../../src/topics/troubleshooting.md:20 5235ff0c35c54396aceb799a65f6158e msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 +#: ../../src/topics/troubleshooting.md:27 fc49344510594559b4f888bc45093b51 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e +#: ../../src/topics/troubleshooting.md:35 6e62be8d7d1344e8917904278b508518 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2986,7 +2997,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 +#: ../../src/topics/troubleshooting.md:44 c91b3a2818b143f58bd37da63479c560 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -2994,7 +3005,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df +#: ../../src/topics/troubleshooting.md:48 86f283bc522c4be2adfac16256f01b0e msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3004,7 +3015,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: ../../src/topics/troubleshooting.md:59 5362aa1d28344968953ab9cb389ccd8e msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3014,15 +3025,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd +#: ../../src/topics/using-containers.md:1 4bb1aafde4f745a083d3a276497523dc msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c +#: ../../src/topics/using-containers.md:3 b00987baf6974ff9b7e3b8cdfd7abd9a msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 +#: ../../src/topics/using-containers.md:5 9ac51c5a2a0a45859e14d9e388edd5f0 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3035,35 +3046,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 +#: ../../src/topics/using-containers.md:15 5494ccdb1a354b2386c82bd9a6f0b6a9 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 +#: ../../src/topics/using-containers.md:18 4cfa8fc2bb224883946d5f63b372de82 msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 +#: ../../src/topics/using-containers.md:21 e16c1922527a46e28bb5d933614cdaf7 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa +#: ../../src/topics/using-containers.md:27 7498a71704be462abef71c42e6b83d1b msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd +#: ../../src/topics/using-containers.md:33 ac0689bff9db46ea8bff8cd35cde86f3 msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a +#: ../../src/topics/using-containers.md:44 c4b7da5575674ca3ae734424022ef090 msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3076,23 +3087,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 +#: ../../src/topics/using-containers.md:52 d24fcecc17d0461cbd8689067f770c0d msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 +#: ../../src/topics/using-containers.md:55 833d4d3b3f0e4c7cb8b1d35cb9a78a7e msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e +#: ../../src/topics/using-containers.md:69 50fc0573276e4dd4a47208ed81109991 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 +#: ../../src/topics/using-containers.md:72 f72e10e746604421904057ddf7078d3e msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3100,44 +3111,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 +#: ../../src/topics/workflows.md:1 ee126833f6014e378c7841c4048dae85 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 +#: ../../src/topics/workflows.md:3 0325bd610aa747b0b657afa0c978a1eb msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 +#: ../../src/topics/workflows.md:13 7c901105cf6949909d87be5681331368 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d +#: ../../src/topics/workflows.md:41 74138d0c2ded4311bf688df4a28387b5 msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d +#: ../../src/topics/workflows.md:51 1ec4773e7319414b997d746d1965ff56 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 +#: ../../src/topics/workflows.md:81 5f860dd70e3b435188c61a538e5de0ef msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: ../../src/topics/workflows.md:91 a9c56df6dca441dfabda7fa54fbe56c6 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 +#: ../../src/topics/workflows.md:150 586d561ddf724319b3da9ae857828648 msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3145,33 +3156,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 +#: ../../src/topics/workflows.md:160 f3e80b1903534065a30323611c267e9b msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a +#: ../../src/topics/workflows.md:165 6ed53c6f9fb94d4ab3d10532c605c46b msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 +#: ../../src/topics/workflows.md:167 3fcfdf43b0a049388634625c45e0b1bb msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb +#: ../../src/topics/workflows.md:170 49415efafae64f94b66cb46ca2bbd40a msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 +#: 4806a2ef982944e8b073fafd416d3d74 d45701eeaa6e42feb4ef79d2fc4af756 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 +#: ../../src/topics/workflows.md:180 155cd684ff304258ae374b2e13090e5f msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3184,34 +3195,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 +#: ../../src/topics/workflows.md:183 d8bdb44011274f94b606277799a6fa6f msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 +#: ../../src/topics/workflows.md:185 9e1d9bc2f83743ea9964ec418d225200 msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a +#: ../../src/topics/workflows.md:191 a1240eab3ef746cf82a2c5451042b888 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e +#: ../../src/topics/workflows.md:205 a73cdc43a8e44973808027c29903afa3 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf +#: ../../src/topics/workflows.md:212 4277837a9fd443378d5ca3d9252993c9 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 +#: ../../src/topics/workflows.md:221 09b714af60ee4ecc8ab1b95eac8284dd msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3219,7 +3230,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f +#: ../../src/topics/workflows.md:233 3e99a3be9265463daf74b00a21d89cff msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3228,7 +3239,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 +#: ../../src/topics/workflows.md:248 1c4a959d43b74686ab801a26ef412b3d msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3239,7 +3250,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b +#: ../../src/topics/workflows.md:256 55daf180336d4045ac0cc4c14af98cfc msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3247,7 +3258,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae +#: ../../src/topics/workflows.md:261 5ae40eb04d5440d5ba882a74aa5b9708 msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3257,13 +3268,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 +#: ../../src/topics/workflows.md:267 f93e9b776a4544018877b7a13399609b msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 +#: ../../src/topics/workflows.md:278 0e587435e3884334bc51a4abf4b4d785 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3273,11 +3284,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 +#: ../../src/topics/workflows.md:285 81b98764289245c79f18fcff478f4a9b msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 +#: ../../src/topics/workflows.md:287 9baddec4015f40ad82ea2dee30305654 msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3285,17 +3296,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 +#: ../../src/topics/workflows.md:297 986c3dd9460b42b3b20e2d01ba1fbe51 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 +#: ../../src/topics/workflows.md:300 4558f174fea445fd97b80d963fc74f43 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a +#: ../../src/topics/workflows.md:309 532823a13154401090e9fee3e018fda9 msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3303,7 +3314,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 +#: ../../src/topics/workflows.md:314 7b6f46b70bac4f848a956ea160243621 msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 +#: ../../src/topics/workflows.md:322 3861b4a31f71471b97bf9dc18cc80594 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3325,7 +3336,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 +#: ../../src/topics/workflows.md:336 a10c37f65ac14ef2a5971872bc9b8f9a msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3334,7 +3345,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 +#: ../../src/topics/workflows.md:341 34175f932716406f836840732618caee msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3344,7 +3355,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb +#: ../../src/topics/workflows.md:347 0d132dc39cdf4818bc8e20132073f669 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3352,14 +3363,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 +#: ../../src/topics/workflows.md:366 9f8c45f077974cf79612ee83df3d152b msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d +#: ../../src/topics/workflows.md:383 435f80d0599b4d93ae1339e8c7bc020a msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3368,7 +3379,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 +#: ../../src/topics/workflows.md:389 d39b024a1a8d4eae8d7fd3c929a782e9 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3377,7 +3388,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 +#: ../../src/topics/workflows.md:394 3cbbe074843d4306b762d2fbc6fe9850 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3385,11 +3396,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 +#: ../../src/topics/workflows.md:398 7118b6e09b9f44129c7d98d90570f2c2 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 +#: ../../src/topics/workflows.md:400 70f3e73ee3714f22ad6ee43dd5ece703 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3400,7 +3411,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 +#: ../../src/topics/workflows.md:411 279495257ead4a4fa725c7d68c504162 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3408,23 +3419,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 +#: ../../src/topics/workflows.md:415 86d1d742bb5c4a9898aa573ce648f0ec msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f +#: ../../src/topics/workflows.md:421 f4987847f46e4a2db54127ec7ebcadf7 msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae +#: ../../src/topics/workflows.md:429 80e7c22dfe4d40749f2e9c3bf02bf8bc msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a +#: ../../src/topics/workflows.md:441 e930bb5d430a41d9b5bf49e473dd2ed1 msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3432,7 +3443,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 +#: ../../src/topics/workflows.md:445 4076e9eb67ed4bd5942f089e394bad26 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3440,59 +3451,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 +#: ../../src/topics/workflows.md:450 1b44092e87b840de8f1d022676d0990d msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 +#: ../../src/topics/workflows.md:452 a8afac626f5d4240a57267085b9bef26 msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 +#: ../../src/topics/workflows.md:458 0896efc674bc402495c6e73c6c352523 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 +#: ../../src/topics/workflows.md:466 91a53d918d4b47bdbe0b0a6d4adfc0dc msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 +#: ../../src/topics/workflows.md:469 8325682d51d8421b9ea507f424f71e73 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f +#: ../../src/topics/workflows.md:472 503d068602d8477a820b91d835fa3f28 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb +#: ../../src/topics/workflows.md:480 4e768b91eb274a5cb157f1e3fe2f85cd msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 +#: ../../src/topics/workflows.md:483 18ec5231b7bf4c9ea59361b325fcdd01 msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed +#: ../../src/topics/workflows.md:489 87fd118dc2774cf08db0a3ba56520da5 msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 +#: ../../src/topics/workflows.md:491 8168ffcb23124b3f839a9862a7ec0958 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c +#: ../../src/topics/workflows.md:497 37c222ea14904fd4a8fa93a1e0103239 msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3510,7 +3521,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 +#: ../../src/topics/workflows.md:509 d392813fc6d14851a294a391426d41f6 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3518,38 +3529,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef +#: ../../src/topics/workflows.md:513 652155460eaa42b6856c16cffdb845c0 msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 +#: ../../src/topics/workflows.md:519 6313cb377dc249e0b2262a3fe732fe32 msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 +#: ../../src/topics/workflows.md:522 11f73cf24fb044e3a3afb3adb6137708 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce +#: ../../src/topics/workflows.md:524 def9e62bf73f49eebce09677954e2a92 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 +#: ../../src/topics/workflows.md:527 200dfe47d09d4b0b9e4acf29b7e038da msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a +#: ../../src/topics/workflows.md:566 858bda7fb6524e9dbfb35596ce6a6d07 msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 +#: ../../src/topics/workflows.md:573 28897819504247a3a6cf9a9d9476b63b msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3558,7 +3569,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 +#: ../../src/topics/workflows.md:587 4f8fd11e29b048e1851299002c3a48c4 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3566,62 +3577,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 +#: ../../src/topics/workflows.md:607 ed33196347d949eda752a081c7af4657 msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 +#: ../../src/topics/workflows.md:627 738c67568dbb4f2bbb5756fc5e727c01 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c +#: ../../src/topics/yaml-guide.md:1 19b016a1fec14056a9812c1c195c7c90 msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 +#: ../../src/topics/yaml-guide.md:6 a513367d60a74f559339c05d8ef10eb7 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 +#: ../../src/topics/yaml-guide.md:13 5e30680941164047a47f98417e916188 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 +#: ../../src/topics/yaml-guide.md:16 ca02f2bf1d754d5190f296674245b936 msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 +#: ../../src/topics/yaml-guide.md:18 466615194bb541fdbe2e6515b50531b3 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe +#: ../../src/topics/yaml-guide.md:19 33e664d59a30407891336db290a8a5b2 msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 +#: ../../src/topics/yaml-guide.md:20 3e52ab079dcf4fc6a3f052a517f4d31b msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 +#: ../../src/topics/yaml-guide.md:21 abcad6b7d37a4342a90c2d5952ea1232 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 +#: ../../src/topics/yaml-guide.md:22 500a489e4fae4d1abaa8883f632d1a24 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb +#: ../../src/topics/yaml-guide.md:24 546c1ef51a63487c91c98059dd46b0cb msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf +#: ../../src/topics/yaml-guide.md:26 72b4262833054edd9efe6078381de654 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3631,7 +3642,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f +#: ../../src/topics/yaml-guide.md:42 7b7e8242660744b791ba3868e4ed7e37 msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3640,7 +3651,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 +#: ../../src/topics/yaml-guide.md:51 492d994a541c4c948fb5da9041153bcf msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3651,28 +3662,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd +#: ../../src/topics/yaml-guide.md:61 e2209269db394f3988f18b147a57677c msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a +#: ../../src/topics/yaml-guide.md:63 e15c39c65aca47f690264d8008463bec msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 +#: ../../src/topics/yaml-guide.md:76 afa546fcb7fb447d939d4a167f206f79 msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 +#: ../../src/topics/yaml-guide.md:79 7dd375e0fd964413af4957396d2a0474 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b +#: ../../src/topics/yaml-guide.md:81 af8ef039a64a4c0783d7229dbdac65ef msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3683,7 +3694,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 +#: ../../src/topics/yaml-guide.md:104 3ce968cb39a443059f6a828b3c8c2f33 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3696,11 +3707,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e +#: ../../src/topics/yaml-guide.md:127 3c2f48a8e616400b9a8ffb4b6f7efc9b msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 +#: ../../src/topics/yaml-guide.md:129 c432b1656e0e49ef87aa3d6e42acad84 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3711,26 +3722,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 +#: ../../src/topics/yaml-guide.md:146 cac5e52767f74ce98693e2a19ee1eb0d msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 +#: ../../src/topics/yaml-guide.md:167 101666907f8b4fb994e25ceffcf04a13 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f +#: ../../src/topics/yaml-guide.md:169 5461960a469042a487b89e440f856aea msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 +#: ../../src/topics/yaml-guide.md:177 e31349c164c84a9da46e2fb1861793df msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 +#: ../../src/topics/yaml-guide.md:184 49a0b3dfdc9e4d58b6bc966db979ace8 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3740,52 +3751,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e +#: ../../src/topics/yaml-guide.md:194 e08ec8c473e847f98e8a18b9ca0f2670 msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee +#: ../../src/topics/yaml-guide.md:196 6ee7bfb4a9e04dd19b5180bca5b02705 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf +#: ../../src/tutorials.md:1 42614ab7ba1546f89abeb8f48991271c msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 +#: ../../src/tutorials.md:5 b8df5b8393ed4d869c066640fe83ec7b msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 +#: ../../src/tutorials.md:7 5b9aee5af41f438b9f4208294bf97f4a msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e +#: ../../src/tutorials.md:9 a71d3022dcfc44979cca4655ea51ad42 msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d +#: ../../src/tutorials.md:11 42b5a982e86f46dfbfcd7bfcc99d72a5 msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 +#: ../../src/tutorials.md:13 12dc402d053044b78d69927dd391fe9d msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 +#: ../../src/tutorials.md:15 687c20e2e4bc4f869c7ee9390e61476a msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e +#: ../../src/tutorials.md:17 a975fbb3ea7d467881ce0245de538295 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" From 354dbb22e2481aa41a1c14c47fbeec7da3440722 Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Thu, 26 Jan 2023 23:37:13 +0100 Subject: [PATCH 43/49] Patch MyST to keep the context needed to translate Markdown files --- src/conf.py | 82 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) diff --git a/src/conf.py b/src/conf.py index 921ced1e..bcfe20a8 100644 --- a/src/conf.py +++ b/src/conf.py @@ -238,3 +238,85 @@ gettext_uuid = True gettext_compact = "user_guide" locale_dirs = ['../locales/'] + + +# Patched MyST parser +# from __future__ import annotations + +from docutils import nodes +from docutils.parsers.rst import Parser as RstParser +from sphinx.parsers import Parser as SphinxParser +from sphinx.util import logging + +from myst_parser.config.main import ( + MdParserConfig, + TopmatterReadError, + merge_file_level, + read_topmatter, +) +from myst_parser.mdit_to_docutils.sphinx_ import SphinxRenderer, create_warning +from myst_parser.parsers.mdit import create_md_parser + +SPHINX_LOGGER = logging.getLogger(__name__) + +class MystParser(SphinxParser): + """Sphinx parser for Markedly Structured Text (MyST).""" + + supported: tuple[str, ...] = ("md", "markdown", "myst") + """Aliases this parser supports.""" + + settings_spec = RstParser.settings_spec + """Runtime settings specification. + Defines runtime settings and associated command-line options, as used by + `docutils.frontend.OptionParser`. This is a concatenation of tuples of: + - Option group title (string or `None` which implies no group, just a list + of single options). + - Description (string or `None`). + - A sequence of option tuples + """ + + config_section = "myst parser" + config_section_dependencies = ("parsers",) + translate_section_name = None + + def parse(self, inputstring: str, document: nodes.document) -> None: + """Parse source text. + :param inputstring: The source string to parse + :param document: The root docutils node to add AST elements to + """ + # get the global config + config: MdParserConfig = document.settings.env.myst_config + + # update the global config with the file-level config + try: + topmatter = read_topmatter(inputstring) + except TopmatterReadError: + pass # this will be reported during the render + else: + if topmatter: + warning = lambda wtype, msg: create_warning( # noqa: E731 + document, msg, line=1, append_to=document, subtype=wtype + ) + config = merge_file_level(config, topmatter, warning) + + parser = create_md_parser(config, SphinxRenderer) + # TODO: In the first pass, the call above will use MarkdownIt over the whole document, + # populating the ``.md_env`` correctly. Over the next passes, from transforms as + # ``sphinx.transforms.i18n.Locale`` it will create a blank new document, as well + # as a new MarkdownIT parser but using just the Docutils document that is being + # translated. As a result of this, the translation has no reference-links, and it + # gives you the translation without resolving the links. Here we just re-use the + # ``md_env`` dictionary that contains the ``.references`` populated in the first + # pass, fixing i18n with MyST Parser. + env = {} if not hasattr(document.settings, 'md_env') else document.settings.md_env + parser.options["document"] = document + parser.render(inputstring, env) + document.settings.md_env = parser.renderer.md_env + + +def setup(app): + """Sphinx setup callback.""" + + # TODO: Here we replace the MySTParser (that replaces the Sphinx default parser...), + # with our patched version above. + app.add_source_parser(MystParser, override=True) From 43a5611de823f4160cf8bad6d02d045d5ab9a4b9 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 11:19:15 +0100 Subject: [PATCH 44/49] Revert "also fix the Spanish translation" This reverts commit 8efb720d8ee310a313510607bbeb5bc35195f9d2. --- locales/es/LC_MESSAGES/user_guide.po | 1289 +++++++++++++------------- 1 file changed, 639 insertions(+), 650 deletions(-) diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index 523946d0..3fa6daab 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 17:03+0100\n" +"POT-Creation-Date: 2023-01-25 16:53+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" "Language: es\n" @@ -23,24 +23,21 @@ msgstr "" #: ../../LICENSE.rst:2 dcdc2e8da0ec4d9e9453601fdd83bac5 msgid "Licenses" -msgstr "Licencias" +msgstr "" +"Licencias" #: ../../LICENSE.rst:5 3e165520ca56481b8f8d494a8d471de3 msgid "Instructional Material" -msgstr "Material didáctico" +msgstr "" +"Material didáctico" #: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the `Creative Commons " -"Attribution license `_. The following is a human-readable " -"summary of (and not a substitute for) the `full legal text of the CC BY " -"4.0 license `_." +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " "cambios en la estructura también están disponibles bajo la `licencia " -"Creative Commons Attribution `_. Lo que sigue es un resumen" -" legible por humanos (y no un sustituto) del `texto legal completo de la " +"Creative Commons Attribution `_. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del `texto legal completo de la " "licencia CC BY 4.0 `_." #: ../../LICENSE.rst:12 b7a7a0fb40344fe087c1cc3ec19308aa @@ -61,38 +58,38 @@ msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.rst:20 8bc6672f4a33428296226112a1be6fbe +#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia." -#: ../../LICENSE.rst:23 be38276e7b374f57b9997391bf898a62 +#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" "Atribución — Usted debe dar crédito de manera adecuada(mencionando que su" " trabajo se deriva de un trabajo que tiene «Copyright © The Common " "Workflow Language Project» y, cuando sea práctico, con un enlace a " "https://www.commonwl.org/ ), brindar un `enlace a la licencia `_, e indicar si se han realizado cambios. Puede hacerlo en " -"cualquier forma razonable, pero no de forma tal que sugiera que usted o " -"su uso tienen el apoyo de la licenciante." +"human_>`_, e indicar si se han realizado cambios. Puede hacerlo en cualquier" +" forma razonable, pero no de forma tal que sugiera que usted o su uso " +"tienen el apoyo de la licenciante." -#: ../../LICENSE.rst:31 f00d5c3846034c2ea116c2f74786d9fc +#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" "**No hay restricciones adicionales**---No puede aplicar términos legales " "ni medidas tecnológicas que restrinjan legalmente a otras a hacer " "cualquier uso permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.rst:35 1798d65c10104040923c2fea2199bab2 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limit msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.rst:38 c65198b804f8436ba783643d51bc72d9 +#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " @@ -105,28 +102,20 @@ msgid "Software" msgstr "Software" #: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" `OSI`_-approved `Apache 2.0 license `_." +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la `licencia Apache 2.0 `_ aprobada por la " -"`OSI`_." +"disponibles bajo la `licencia Apache 2.0 `_ aprobada " +"por la `OSI`_." #: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT" -" WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the" -" License for the specific language governing permissions and limitations " -"under the License." +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 271049c39d294b11b9bd94cb6be2857f 61af90891e2d4542b5f45fb3ec6480af -#: bf309fa01bed4355bf052ae4afbf9a67 +#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 +#: dfc7702e073140c985cf47272a20214d msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -135,30 +124,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 055f0e960450410585b59760ef3ad284 6294af2e32e04207a87399c7f0780011 +#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 6428125fc43c43bba8518ece2f5d150f +#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 ce8fade1e88e4b03ac0d3fc71d16f844 +#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 9e7483b53a984b689964c69afcaa7123 +#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 8c5a89257ef248cd99cba303713e5082 +#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 9e80d8eeefcf4a9d95fd5fe9d9fa124a +#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -166,94 +155,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 c2e5f62490f940aab19166403a840597 +#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 ffcffabdf25a4c398e8e53bc817ea769 +#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 c8a6b85cfca542ccb042a0269294e5e3 +#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 98f583e5e36941c1856d719a16e58e4a +#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 fb9cac0954474b5284793330b7424949 +#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 cc45d609de1f423db86d58eea933e132 +#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 27ee63895cb14321a1814f4372d3180f +#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 f1c841980f3d4364a2158a4eb2f0d257 +#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 6d53d38ddcf244fb997db37eae7fcf90 +#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 b6d60d66f3744ab3aea1b175ecb23d4a +#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 cf4fa3ae602841d393b4143e9f6f5e82 +#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 41a3c9aa55c5406f9b52af2243c79ccc +#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 3b8eb247425a4a708f51c08cf258e30a +#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 388a6e091a054dc48afc928f46dac7b7 +#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 28c59d12156e44ea833822fd3ecaf824 +#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 8267843ff5c940c590b10047455f2102 +#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 6e6f55bc915e4cceb8e360544d6b4ae5 +#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 1bc80953bd60405082a10a7798c1413d +#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -261,22 +250,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 a6cd4bf4dc314e66a951f7f1227c7bb7 +#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 7ab2440a92aa44b09e8a324cd67ca728 +#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 152a529dfa2c42c1b6f0083589fa5aeb +#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 b278c137167d4b958c099c0509edb79c +#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -285,25 +274,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 f0b38723838f479d9db8eb5142d28a1e +#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 fc1e4a808e85422cbb4d128c5a1f4d0c +#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 d74964c9d19241848f4dd92a201e201f +#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef msgid "" msgstr "" -#: ../../src/faq.md:248 859b8e18e05a4c3285fb20bbb44c1ed4 +#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 eb6e932924a54afd9114c629b2d0e93b +#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -311,26 +300,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 31d70b41ddf042f6aa530b7bd6daae73 +#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 msgid "" msgstr "" -#: ../../src/faq.md:268 9aa3ff8c957b42c8a30f37167a8177fd +#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 777ac7f6bde2470b981efc91feb01c81 +#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 8647071efc0548a1807c03fe8a4ee54c +#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 4404233183124085990c44793a6b25f6 +#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -339,77 +328,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 c5eecacfa07f47649f07ef9d888f4c5e +#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 1efef04061fd48f1ab39a99508b5bc0b +#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 57e8ace8e8d64e7a90510e1ccea69612 +#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 138606e8d7be40bb960f278977f9107f +#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 d0f668dc78464469a9f2bfc61a90aa76 +#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 f2a49a7663e1456cac6b2eac0c46c662 +#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 eefe4adebdba4063af0cac3ab5d46442 +#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 526f2816123a43ecbcf09c46904b4b5f +#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 0ecf267c5f4d4557ad0d7ddef2f4b5e6 +#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 935a253376854d12928f00c2870ed4c0 +#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 bc6c0bf679ae48e7822add7ab2cda220 +#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 a63643806a2a4eee8ebd3502fd6ce2b5 +#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 fc54964adcd648948d7baff02f47598e +#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 aabc495306a149fdb15835ae1df93c42 +#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 2930faead8be45a6b9adbf51dcdfef6e +#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 f885e4716a8d4de0b25d2d3356789672 +#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 6487ff3c19c944eb8257b2cf60d0aac7 +#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -418,11 +407,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 4cbacce539ce4f6cb5bb8ccf1574640c +#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 27321576de714cd5b82c67f59b2e3e6f +#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -433,22 +422,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 6afded7ba21247099c9bfcedf40c9171 +#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 17c386e7cd25496784207140f9876b90 +#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 3bfd9bcf826a4400935dfad338612b12 +#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 4b38f1439da44ebb967b5b1e3df8f78a +#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -457,11 +446,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 a4a60a8d010448b0b8ad1e05cbc78f2b +#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 e23e00e89c81410ba8381fd81bc73b3c +#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -469,7 +458,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 7274d92e678a440eb0d3ae3109f4157a +#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -477,15 +466,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 6ad5f2d254a24ac1b3faf382d08b58aa +#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 7208cbccb84d45d58c7d5becec74b7d3 +#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 8b9809abb49840b195a89943ba15f78a +#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -496,18 +485,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 9a934bf0848b438aaef7c4f00e0f2901 +#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 5a299600dc304fd886b7153de1a706f7 +#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 55f7696f07d64277ad1b39d283175b37 +#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -517,18 +506,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b854ca0af98347d2b66e74754eb92a50 +#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 d9785269c51e4902bf3a70e917d33238 +#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 b57a31b8d26545d1823fcd1fa2c83316 +#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -537,24 +526,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 4e264b1a40bd4935abb5bdeb75fa5c64 +#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 791b02bb1ee6459d8d8332fc2dee353c +#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 17300bbe695044e7b8917d23bd0aa597 +#: 9bba7c4f783942e4a299603430601363 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 526614f195614818a614fc9a576e7cb5 +#: e2140e0f0e7747ef8383887c20a7945a msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -563,39 +552,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 7b47991653054f2d9f49a91720754abf +#: 15bf490724cd46dcbcfab44633c5a9a2 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: aa8838c0ee0a4b4285cb1b5dc6eb5d31 +#: 51d52d051e654a8395239f88df7c9d8c msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: 457c73a37cb143d98005ebf6e67f5bf1 +#: eb496cc818524fa7bae5a22ddd00a19c msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c28057f3b7814f8395dbc3ad54d5f6f9 +#: c4a22d12e7f149ff901d27de32b9361d msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 83afed0785cd4b0bb86863c2841ce982 +#: 7618de899a7043989d77baacf62eb7b2 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: f332864bcc1e49d582a82f3d721ff3cf +#: 6f1544a220664b79b04bf008058b5a91 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 3005c6d669de412ab7f8e30d00752a20 +#: fbd14ac9a2f541478a320ed4cbc69e13 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -604,7 +593,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: 2e4041cb402e4054a53ea5890b938ac1 +#: da4dba50d25d4533b3dbb92f54d32a30 msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -613,7 +602,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 972f9a1e64394a63be3258d3af0b1d79 +#: ce11c9f8d65c4268984d0384d95144cc msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -623,7 +612,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: a572f0789084402fb2d216ac845bbfdb +#: 3a201aa497e84f70855bb2251e7e3281 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -632,24 +621,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: c7c5c9a1e98e47c0a5a6dfa69e96f921 +#: b78f7fa2be1c4bb090f6da895457ad1e msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 357d42768e794286bf5463ca5850a7ed +#: f7e95d264ffa4e2db0864faccd9e5a0e msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 61966aab989744c1b9b93f7751f35ebc +#: 3f1e5b01e49a4dc1b1c99936a4589afc msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: e14a2082d2c44f3690a07d3cee5b13d1 +#: 03c3048f38ae4938a484cf02001877b3 msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -659,7 +648,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: c128a76992e04d20bcc3edae8b6c0bc0 +#: f9715b5ec65c405c849bb030c1927060 msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -668,12 +657,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 42953a3d591c48c6b4e80e9ea4b97bb3 +#: 442662f50e9e4620970ce32b1b127969 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: e3762a763ba24571a9627efafe172441 +#: 2b34c786af3840e88f29d214e19dc837 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -687,7 +676,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: be8e01a012ed45d6b7e4e6aab1afcc32 +#: dd6aadff8cf54ce78ea6b317afbaddb0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -696,7 +685,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: cf31aca4294d486cb0e25c6436996d17 +#: fe7f1f0b28434f8aaf0f6ac6589a83f0 msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -705,71 +694,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: cc7adbdc66df4aeaad1429f7268c90c0 +#: d10cf45b3c7f49dc98bc0e5d1246f224 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 71beb059c9e54a9ab5430f0dc44e07ea -#: 84679c5b03a3469294de849d9abe0a82 fd690fdd46344e0e8d9fc546f6d4013b +#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 +#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 89ddaddb64f64b0c86c7e89da0edfaae +#: 8badec9987ba40609cf1f626172b2b2d msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: e920a824207746ffae63242d33137ac7 +#: c75a8b4bf0e24781bf6713cf6f013cd1 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 51d619152aa44651889ff2006c8f5800 +#: 79b146ffe6d74e1b8f6019251dc4b7c2 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 88f3f5dd8aa6401793b89e8de3b8c7a7 +#: 07cca9a33d8f4b77ac6ad35ca8b95655 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: f1f9ee90d07c4381a8bb0851bdac231e +#: 31db11c8ddf2423192a8b2063b3e91c2 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: e3b710dabec2482d8ec1072d64d4e1f8 +#: d81dd96143ea444aa78ff45cfa0584b3 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 418699fcb6c241dcbeeed81d82e9f84f +#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 28b6521a55aa4ab190ca998a59c52609 +#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 0e4969399eda48b98d883a3fc1540633 +#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 6d59f082157b494ebcfff2f649abc524 +#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -779,11 +768,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 2b83beccbc1b43969b705156b9c29482 +#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 594fe5e0aaf0499ebfa9218aaad4d08d +#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -791,29 +780,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 f69c7c75a36048f5af0ed1b56df9320d +#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 f28638ffb8394ccead4ac52f30adc627 +#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 8993d7d5c8d24fc5a9c7005800c0a1f1 +#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 2073109799e748d68304f5558c82b105 +#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 9fb2c31bd36d495786397c7a7d6b3417 +#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 43e1957537034c5886574118fc2533da +#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -823,11 +812,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 e3a3d9b94b1e44c48f298dfcdcd27104 +#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 8a385803ed3945ff81d38a3543a69d94 +#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -835,7 +824,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 bf56727d93994d3995b0af0c68c2c583 +#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -843,26 +832,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 9a959bd914d543b78f9625f03df95765 +#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 198ce7d893a04fcb806ec1671838d588 +#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 cc2be8feeab54a22a0b64a2a72991003 +#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 749c672e8c234c1c9a5eb2cc9b77c4e3 +#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 29c64936318a4a2ba882e1eae8f03f57 +#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -873,23 +862,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 44106744147f45bab675eb66148531c7 +#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 6d84c6890f564b4baf7b34f6a52cbfc4 +#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 7eb67993e8ca48dc929e1a992f78cb39 +#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 52886c54c3c54b83896c52ebd7d53fad +#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 097945c33f7542e2bae2e9f7ba1cf84d +#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -900,32 +889,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 3853bfc6a85747019c615a50c7ca6b40 +#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 662230f538504f44941c6f4801f6251c +#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 1c9eb9e2bb9e40a9985ada16c34eea2d +#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 7f53ba159979461393c0f278fe97fb30 +#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 7e8077c2dd584eda89ead60ecc5eabf3 +#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 1787a3c749ee48218b87c8401f6255d7 +#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -933,30 +922,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 a52ca4ce9a184e938c3a5cac9cb882ca +#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 41d3287a9a774a73aefd49bd709764bf +#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 3b9d30094611400b85b55db163cb303e +#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 b6ea77357b4f45528ed1379f8fe67cfd +#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 8797ce327d7443fdb3d4617d3fc2cf7f +#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 896b6896b1e44d0cab5f35e7d0dd88e3 +#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -966,47 +955,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 4b839d23d72f4d3fbe4f1ce7e568b20b +#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 a42b9ab315b5402493e4ce0067d0a18e +#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2f63483960634a7782f95e9e2feaa5a6 +#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 3471105073204d7998aaf790b73f785d +#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 0b8b47511b5e4296b7438be0ad2604ed +#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3e3eec00f23f4f21873ddb005204a875 +#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 2ceb25f2668442839e3e9f4512772a03 +#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 20c753c5371b43ed834fa741b0ce7692 +#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1014,7 +1003,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 a19c4fc9fa404912a0389337536d9c25 +#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1022,57 +1011,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 a0f38c1e28ca4850b3986617625acbf2 +#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 37e1162f30894a1ca7dada9870ffa3da +#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 1c25a51edf6f47c5979c721b19cf11b5 +#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 ace930cf878d45a99f12b71bf0987a87 +#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 46587a5e0d534af5867ae4f70a116bee +#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 a0774d4e779e46f7a983922425203066 +#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 1658ee6f3cac4d04afc732aa758b1f48 +#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 d8e2bc671b894f3fa8a091261754c728 +#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 683a469bf4824c64a8ea32e048d5df73 +#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 b7c50413f7864a86815f3b581561cdb5 +#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1080,11 +1069,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 d2ed66bdfcab4f7dad95b00c95d4a3d6 +#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 4dcbe776a70645e5a6c7513348fa6bee +#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1092,11 +1081,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 bae5b03fb74541e6ad79277a576e0516 +#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 8ff0d7a8d37b48488e4504ff8e3adcc5 +#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1104,32 +1093,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 6255b499b9b144128afaeed64fabe8e5 +#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 e861db9c43ed4b8ba262af8e435a350a +#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 c6318f06bcd74cda8c1f0caef9452b51 +#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 c862e745217244d28cd4c2f0842e203f +#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 eba007736b92434a9711f683e64bb153 +#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 aebc2caf5d1b47f1b7cc0aa53e5a684e +#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1137,21 +1126,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1242171f8b854562bb7848b06d2d065d +#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 24e82ecf7926428386a89f18a34eb00c +#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 00e75efe03554835bc33ebaed0652626 +#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 4ba34ec455704844a9cfcbac3522ea0c +#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1159,46 +1148,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 c0e9673440db454bb51af04432aeddbb +#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 39a23a9d02ab4bccb36d6a714639509b +#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 23a878e0166b40d78984a2263f63b760 +#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 5d9c435820674bf4b1c5d3fef5df736d +#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 e724ee53db1940b9b09a909f4db531a4 +#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 7820eb801a8145feb603145f153263b9 +#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 e8db3f10be294f13abe3a4418bbae4b6 +#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 95211ea6924148a6a1fa5ae8facc2c7b +#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1206,19 +1195,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: b742a74d586e42e6b0480b7af3e49c9e +#: 32f86f911ebe4a4c94975f81742333f3 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: cd3da03d43044ec9843e476a54e704be +#: d5f1ad2b95ad46d48f8f2ca5e357bb5d msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 0d48e2f07d784504a17cad0ae20262c2 +#: c53ceee943ad4acea779e072b9137889 msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1229,37 +1218,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 4d372b89f0ce451db2a505b1754b8356 +#: 7dfe9dffbf5744299bf232599644c7f6 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 573e903ef3d34514ab7b20e79c446567 -#: cfb40fbe52174d3799a6bec175db60a5 +#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed +#: 991172e201ec4796992a349dee44f090 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 95841b1c75c84f01bd5fcb7cf3afe78d +#: 1f3c23a4769043ca985b8ddfed19391d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: c8bca3654ebb4b29bf3f028b4c65fa35 +#: f81b43c7cb194a1cad8672129223c833 msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 1432105e38014a6d9d0cf80007141007 +#: a20073a8f5374eb1bc8531ff33e622b6 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: bcad473b34ec43f7906253123a1661fa +#: d08869beca3a4774baf1097b63e79474 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1270,11 +1259,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 e1c8949e663b4debaf87735f1d62a2fc +#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 dcc991b647d34ffc8ea3bf9c3a38258d +#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1282,13 +1271,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 f26c222638e54187b8bb62fe30b66bc3 +#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 23720e4ab3d1407597f1d1c2a4d4d90c +#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1304,7 +1293,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 b3638183c59744c897246af7dab5d10e +#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1314,43 +1303,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 2c0291133b964ad8b751f8a8ed2338fc +#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 325c8c4058f045aa8fbd705238122798 +#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 05333866485b43479352f7ee9326c7fd +#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 f8140ec6e9cc41ee88ec4bde61a44d47 +#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 1d68f50dafaf4cc1851e2d67b3e78603 +#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 b283942434c54456a3f29fbb0960b6c4 +#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 0b4477c5b0184e59aa0c07161008a7bf +#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1358,13 +1347,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 9741651d51f249ffba1820694ab78e92 +#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 5e76d4a9708244ff91f2587350d684a4 +#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1376,44 +1365,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 89e7028e55b54f968e87b9c1c3caeecf +#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 88e2338fb2614ef29dc497d8c01a2f2f +#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 0f3aad35924344659eb5a6719ab2b8f0 +#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 877cbb1d537b46d3b6d05b2d8c025e70 +#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 5c0debbc1c1b428ebb32b589b99fe17d +#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 1ff97183191240edb98f0cc365cc028b +#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 22f7725deb07422fa0a7bc2e6f01e4d0 +#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1421,31 +1410,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 982313839ccc4f5a8527fe9a854c78eb +#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 267c9d10ab5e4b6c8a6104952deb1690 +#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 2eff0eec58c94f4d8986a4cb91b14b8e +#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 f38db701740b442c89ce58e937bd35c5 +#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 034aac9e186645e384c28bb2a739cfff +#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1453,52 +1442,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 5f835cdfc0ae4f378d8dad6ae7ab1855 +#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 02900cb8ae4c4da89d264b76a984d6cd +#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 753e48d6dfd54a88a12773b996f182d7 +#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 c7ed6d1654c54bf390e933ef0f847b99 +#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 0a0f855ce34449a0a37c036105c65839 +#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 c4300454f49548f49e4bd186192515a1 +#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 f985d58070de4c0fb5f5a491fd4dc31c +#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 2f4e2c85677a4e56a35b6bef36d67334 +#: 12cf5f2264504c44a2173e858bb2c283 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 13c6d5600a30406c81ffa25ce42eb0c8 +#: 7694f9cabfe04308bbddd2c88ae6d9b9 msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1507,17 +1496,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 3bf773b8560e44a3a37c68b6fcdc6a23 +#: b557dc4f8ef549b98f59412a918643de msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 68b8578d2f6442929941ed2522b218ad +#: 3011eb003c084285b30cfa56a8da45b6 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 755149ed46c348c2b723b49c3b3152a8 +#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1525,7 +1514,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 54b7ff590d52454eb87d9f23fca44501 +#: ce78b2d147054da895beba66d0ecdab4 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1535,7 +1524,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a7c74a4a74c9414e9f29fa20bab7e295 +#: a973846ec5a946eeaff02c5b00997da9 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1543,13 +1532,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 0cbf233379024800bcebb963e0a3eb6f ae3bc02e4f3b404c89f3c461a62c5bc4 -#: dc32a2bacf2d4c8cb841be6eb8b839ad +#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d +#: ccec7f73b9d948e79a6cdf32bc124092 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 34a56bc23af44353a003ee295fb2c609 +#: 22948f19cb78485f8f86244686a35c09 msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1557,7 +1546,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: c7855ec1f09d4945afcb0aec22567b31 +#: 001d9579bfce438e865377fb9c2df776 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1569,7 +1558,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 5c60492e27014735bb9a86307ee654d6 +#: e62618db8995428bb3f260e03ac8f459 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1579,19 +1568,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 80a9c04358e64ca28ef4879ad74ef733 a2b470f06ad94871970b7d95339fd369 -#: dc65b4b5e48e48a6ada03da0fac18a51 ea2360c5286b43ccabac202dfa97fbe7 -#: ee4ca94dadf64ab69a70b6cd4eaf451a +#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 +#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 +#: e9801b2142cd45368a73ef9b121c1d08 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 285d23ef9bbc46c9890ae7957d487c12 +#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 3edd322daad940d8957f88a2637876b5 +#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1600,21 +1589,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 a1bd9b0dfa234e6caa6a684e981d89b5 +#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 0aeacb6ac20f4ebca3600425ca32f5f4 +#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 1c813ebce2904f008b5b33656f673ebc +#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 cc36359e94c841d3aa5cbb26a094e1d5 +#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1623,13 +1612,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 dc79668b05e8439591a0beb4b57acc66 +#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 08aba4f77aa442d4a34aa1535f78c49e +#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1640,15 +1629,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 63431a972f994bccacf55d5fac0d614e +#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 55e7695aca4f4319b1cf7551105a8782 +#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 0c5ab34ebbf54ff6940b8ce3f080d744 +#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1656,7 +1645,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 f97e18d2d3b946468c4fac227920e011 +#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1666,26 +1655,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 62644031403548898ff36addbc0b1f6f +#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 595630b0687c4467aa65bfed289281f4 +#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 34e005c135864a89a00e817d79118e2e +#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 b624f9f99c294e6996f212c8b62f20b0 +#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 14df63ab847e4efca820f712548cd076 +#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1693,32 +1682,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 91d4224b41c6473f936c03bd0ab9d370 +#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 519989399dab493ea41941ed85cb9670 +#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 28dd1cf24309404eaf717d417272e094 +#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 3f536ad8c86d442c8bbe61777dbb1a54 +#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 b9e9894c6d024e60929d020dbaa553f0 +#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 482debe1a40f490b90d4ece1b3f9d732 +#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1726,7 +1715,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 708346038be745d097685970cc462f4a +#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1735,67 +1724,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 99347b6b2c404a4b9bbcc96e0b4bd925 +#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 e6629f0914324c76a08fe179575b73d5 +#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 2287002a87184fb9b95d775a368f0e46 +#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 c23d4543d9f949a9a7015fdcbb40dcd0 +#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 c04a9dcc84b84f37bcf32c3790672038 +#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 9f27c79365db455d9d31053576ebe05e +#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 a2b3ad1e2c884e24948a915c3305aee1 +#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 dd7665bbc5e9449588c9539e3c1910de +#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 0972c757f7c74ea9beabf6b9ef9dbf4c +#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 175de3b9854546568f60a20cc19887de +#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 0c286e5ba1714a059a95b566fe49be31 +#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 3029c1dfe5424c2b812597b03ea76178 -#: a5503b6c524e4848aa308b0f4c26d774 +#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 +#: c12625211cc542b68cb51365a63eef00 msgid "`arguments`" msgstr "" @@ -1803,32 +1792,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 0e03befa46c74dc2b09420e1eb2a6fbd -#: 50f81e7ab73a4713bbc60f6f5609b906 718dc3def33c462786174fb42097981f -#: 9c2acd930553458eb105f96213b5d7b0 d4bf86a995d546c0a9159b3f29a84125 -#: e98424244f554c7399e9e7ad560849a6 +#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 +#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe +#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: e7f1993580f0425098a719e83a64cc7f msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2be930b5da674874a0b634eca3ad9346 -#: ce445ad0f00f403985eed1328103a500 +#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff +#: c158e9ee5fbf4e868b152a0a5880092f msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 2fe48d6404864ea39ef0634169f67be1 -#: 43453d90db244c558a815ca872dc716c +#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a +#: 92697d3179ec48898eaea9aba3c24dcd msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 78eaa318ba81407e9ca9c2c1702ead11 -#: f5da7058f7f146d584314a5bf4de5498 +#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 +#: d6722e3093884ad7b62696fbb2f48fdc msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 7189f4415d204fb388c4a7e927e15b71 +#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1839,11 +1828,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 17a83cc91963434e89822a3e46df8401 -#: 194d3e48d38c476fa8f731e3bc2d8c7f 3a3000a6446b4ef4ac66a28acb13b136 -#: 5cc35210e95e4f2ba6a1a6f118926fdd 68b3d1481a4e4375b1b0c4fca8285374 -#: 94f2bc195bc0487da014bc3f4d2dc8fa b92b4eff2429437d9da911ca68cef954 -#: fc0a1353e87e479d8c8b6c973d547465 +#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 +#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 +#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef +#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 +#: c610220d06484d589313dc29faf8222c msgid "`format`" msgstr "" @@ -1852,51 +1841,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 5478cbeadc64412bbb32619fae9b9958 -#: 6950cbe52d334fe58bf4fa20e5f1f8ca 6b5bda581d0047819c6d92edd8ac9045 -#: 8248329fbe504b3a96bcd890908b070f 978c0fea8ed1481a9f06b6abb31ebd21 -#: a24ba514d66d49cea281fd4c9c7a2b8d b6e2c8e7abf74d64b2915063dda8479b -#: bc184adfad0e4642bc864d367b8779b7 +#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 +#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da +#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c +#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b +#: f71216a4b35e4157aece5ffa2602d8bf msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 5bba2d465e0a4c5d9575406d1294a225 +#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 da385d3cde614749887e195ea6d95291 +#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 487c95417f8e48be8391163578ca9519 +#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 48437402c00147d4b4ca8bd6b38a5823 -#: bdcb3920048f4e578a4005fc2e30233b +#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b +#: ba1fff3ebb274dfba845b3ee20ebd71f msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 121556d49d584cc491a15ef8404ce462 -#: 183ba52666744f7ca5772939db2efd6c +#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f +#: 722d3bd7184841639b9f9a38914002da msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 08ad064936d8406f8c3852526f4f863d -#: 30c927925c6b483b80b583ca7c735437 +#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 +#: 7b46d408e7e7481b91a950b2d4010c9a msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 32a26dd9c5f84e88995f093cda953ac9 +#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1905,32 +1894,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 05ee6df2f9b247629d148fd59c293660 -#: e7b7d782b6ac49b3aa0c8d8ce7ff04d1 +#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 +#: e9fc5f7fa4474dfc95039b94167fe894 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 b0cccc07e5bb4effb60424623351499e +#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 4e5281c8663c4b6e8851be10f50143f1 -#: b5c22c66397e4268b4b3d53b9a253a3a +#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 +#: 61744122b7d7494890cbe6b2fb72b9f7 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 98a28fec818e42af9e177e17fa12aa7a -#: c37d0b1fd75e44a28b3b6409f912e865 +#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 +#: e0c7ccc8f8664cf794cbb7330355f3fe msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 dcc42c6c49964a4ca7bcf2124e26ebfd +#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1938,61 +1927,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 d2ba352ac5fe427ea7ceb0bde01458ba +#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 235cfd6e9baf48698102447fcb83e0e1 -#: 8aad01df8d8d4ab7905a5da7ce7f6bbf +#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 +#: c9534670f5f04769aa3749c3778eb705 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 058ba8c9c2da4ebf8b2291600dafd611 -#: cea47d3e10f641a2b64f08ee100ea6bf +#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 +#: 7b0887a8caed41b2acccf7021bb323d3 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 3b039de5ad144207ae337aa88b3b1a1f -#: e0ecfe44b34e45dea513459b6b3e44a6 +#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd +#: e5e8b8c75f0f43cbb6e160e5bf810c6e msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 1cfc6cb0be4e4ddd90f546adb796b805 -#: b62f6eaa7c394792929dda83a187c632 +#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 +#: fe3b9fb45e01490498c5a35c012b3de8 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 8b13b0e4071444179b26401929de8a10 -#: 8ffb471129c04fc6bb52b782fbd09f9b +#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 +#: ddf82b12b12d416fb65f3ce3f51bbdf0 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 331f58b998cd4d309940ebfcc60a44f8 -#: 5041700e6ccc48989e395a6dcb1be3c4 +#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 +#: af14fda3cca645fbb2f3c5825fe0788e msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 14402b41c64548f8a9691c3b7ccaf3ac -#: cb4837a2b25343d2880a07143f85f40e +#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 +#: fec70bb106ad4d95a2d55ebdcf711afc msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1d1c2894600544b686a8ec3c36cdf767 eaa30e987ec543ef8d6f7171de5525f0 +#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 065c97a553904db6ba61c20cf9d9939c +#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -2000,33 +1989,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 36be05289972455ea4a60aa1f0b9cbdf 49e1ab5bc5734debb83060759d5c3236 +#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 f8e37cd35aea4bbb92d28e8d7e803ebb +#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: de816d1dc9f24c0cbef86fd6a09eff6b e265df9d1cfe439bb798ab6cd32485af +#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: 0363e32e12604eb896f4bdf6bbefd550 8b5289393b7f477699d007ded45a4df1 +#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2c704cae43d64ecbbed33d18eb3f66f3 89acc8f8387d4643a844ac3efb186000 +#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0597c6c214924e75ba2f212cd6b0c9f2 +#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2034,22 +2023,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 1eb1c2432dd943f6a27a1f8b92e3981b 5b9ba9380f10425b809c6157a1f0b052 +#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 b4cc7cc55cf04449b291a27514fc99ae +#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 cdb48eff43e7459fbf3ed21eb7791d66 +#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 67a4dc675c0e444585d579954b99614e +#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2057,7 +2046,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 ea3238db48494ab7b044bab9f96590af +#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2067,54 +2056,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 baf2f6ac8d514705a1f7bf7ea8c71d2e +#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 ef45f4e14fb943cd9fbf179f5d3680e5 +#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 030261615c38485d83ed986c9c98ce15 +#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 1728e2370cbb49ab97bee4c2f74fff2d +#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 4514fc0c99ac4688a37bf30bffe139e8 +#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 33804649720143e5a70e890af9ad9119 +#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 c114496be4c243d6834776e17bf15010 +#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 c784e86f14f54e4982db206741fbd96e +#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 f9de69aad9b44afabded71221c84adc2 +#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 b853c964611e45c2b37a8ac3c34a4133 +#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2123,15 +2112,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 a10d143210b94f83857f62e972d69134 +#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 b07734b172664040aff04f83bd4395a5 +#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 1f9a5377a1f04ee3b8a9ae22390e0cae +#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2140,11 +2129,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 359bb6448aa140f8b940baf769c13db6 +#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 c4aba730bee14931b051d6aead7c2dae +#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2152,7 +2141,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 c4dfcff573424bccb97580fdd1ef27a1 +#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2161,34 +2150,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 1457fa489c894f1bae8a3949ef200527 +#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 cc4fa87d57b344ed8961c31bc4397e71 +#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 091815ab1d824787a1460ce11ffb834d +#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 414b68dac4654163b3dc13e140ffdbf8 96fad38b4aea461493bf0827476163bd +#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 4f71de1140974e73ab033fe7dd9dc165 +#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 b84e3294c8f648aab634e59b6f58441e +#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2196,11 +2185,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 6d9ae44900d64532906532432881d29d +#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 5b99384b3a854832bcca2fb02bdfc1b6 +#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2209,80 +2198,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 3141fc6828024c3e8201e88ca10e19ee +#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5f8c8ea68d7f46fead000315226ec164 +#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 86c18e5105b1400d86d413e28ad72f48 +#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 fa15037f9b0b4a2c9a1f4cff9b8fde43 +#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 fba6d2b7843e466abee33183103cf47d +#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 09f5a55611d14e39b2266245b79ed763 +#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 bdfb39c2656040858616afe731111d1a +#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 c306335ff07e4c03955fe87cad16efd1 +#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 50bd3db6bfb348eea13ba4714ecb2a20 +#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 5d32cfb6f6ed4dd8b11ed316830edba8 +#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 b90fb1b2d38b42c1bad2d9667aaa22fd +#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 6029a96abf9c4d7295eb86d435a1f58d +#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 902e9df74f78431ca9cf1421a26e097a +#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 9760d15bad144e70a86dc0a8da72363a +#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 75bf3fae131049308441bc496f543f6e +#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2290,7 +2279,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 38d8a9c157404bb496bc49f1e427bf99 +#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2298,7 +2287,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 502994ee84234f048e545633bb04cd3c +#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2306,14 +2295,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 551b06b8a3064bcd8d0f1693a4c0ee94 +#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 1838e7438be5449c91c6406a7e40d8cb +#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2321,7 +2310,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 098bb02c941a4bf2a8d4dd9ab3bf052e +#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2329,7 +2318,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 b43194d2b3ef4fc6a8c4b58741317b29 +#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2339,13 +2328,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 e17c55c9ed034dd68f4d24272a61d2f1 +#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 c97a6945e4bc49888d280bbc43c3c069 +#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2356,17 +2345,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 503666cda07b4d7397c65561714d8034 +#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 e5463be0a00d42e386aa6fd3dfacaeaf +#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 14b98bd0ef4a4065a24e66443458d607 +#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2376,23 +2365,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 98fa5dab117e41d4a42da8d78c533c64 +#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 116c212444da4488b32abdbd725db98a +#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 065e556e01b34c35b6be4b54b7cc0203 -#: 4745f370dcbd4ee8bbf4b3a20ac5b9fe d11761f2d576464f8a2c63bdec02d410 +#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 +#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 b3bf1d7e95704682b1bae17472eaa4bc +#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2402,7 +2391,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 04bc655130234786b06b2d5b9e693635 +#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2413,11 +2402,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 e2c18a43b2794448b45c489dd2fa951e +#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 38968ed627514ef38e43b3d1e4a5e25f +#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2425,46 +2414,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 06aab84eceeb41d087b7e295ffa21586 +#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 a0317edb8b964cd2a36c59eaa6df302a +#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 5a3d1b82c79c4ccdb7d06381f4d0acda +#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 e1fc6c3a324a46ee84b0eb59f8396552 +#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 f22e7d9e23b541ef88f3254095147519 +#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 d473d2fa11f64e8fa86554b5777c98e4 +#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 290461c321d14d23b39003b93008a7cb +#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 add43f7531bb4c6988053ae799c366f0 +#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 b12b6f5e34c14dbc9b40458d92e6797f +#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2472,18 +2461,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 4d8f38679952486095a77692387db2d3 +#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 47ec49759e274e59834192b794ec2d9b +#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 0657044c742348fe9e63f662692570a1 +#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2491,7 +2480,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 30c21cafda144f848bfe79d8e232296e +#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2499,7 +2488,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 1cc8ea6abb684470b7790808acea2be1 +#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2509,12 +2498,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: c3b84742343449f9b3866285d98b53bb +#: 71628ebe908b4cd28dd1fa17e3d2e2fb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: 0a1b08fe707c41089ad3d4895960ba17 +#: f123ca244c23413c91405a4b84887525 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2529,7 +2518,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 5bc4ef6584c74b948ffd5c0bddf8e569 +#: 23299ae1bec94b00a32a8af7eeac350f msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2537,17 +2526,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 47ee25d60a4a4faa80476797954ec7a9 +#: 2495a9f2032a47c188338cb81ba429eb msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 195d4a8d5aad41159beffafd198d4640 +#: 3fd2f3cf7bdf44089df2ce3122534801 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: b0c5946fbf79415aa74c8e72fa88cf85 +#: d5a5b8b490b640439db92da949266e4e msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2557,15 +2546,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: a98236fc1be745a69271855e1b5eecdb +#: 5935ed94331d4b2f8ce597f31edea843 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 5f0da8d7e06a47fda38053dbadcbec18 +#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 23d41792b0524742878a6ab8f3ff0fe1 +#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2573,56 +2562,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 c0f723242f11464392dfc32f67a3b67b +#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 c9f3a48a3a064cb3b1759effe724301d +#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 fbad0b0144984ae78b84307ea68d0a03 +#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 59e9ff3276454ff19eb351ff33737f12 +#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 ba74f2ab7f6d4c178f3c4c43c461afbd +#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 93c8b61a12134991ae9bb78223e2017e +#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 cbbdba36dc3841f2b1d820f369a8c680 +#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 4649c8d743f448ab94ee589a1b3a342a +#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1a9d6e2e33244d01b820cf11fe2beaff +#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 233c8865faac4d6c8ec7704e9a997719 +#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2630,7 +2619,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 5aab1c0db3d5449cbb4a0f0dad615d87 +#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2639,17 +2628,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 46b4eeb3ce8946dca0f8a94c399b4c96 +#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 8d322609948a4d6e87d7962b3d29df2f +#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 9fdcb55e965444ee8b5d74a2a9870d27 +#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2657,71 +2646,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 e4c490f599a0469a821aa8e74f4ef0ef +#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 b8ed6ebe6928455cb094ea430e21e5d4 +#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 3e65c52d218946fc83b8c3e6adcb21fe +#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 03751b45cdf647b689a3a69156989db5 +#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 1b6f59623f5d4cd984426da21b8438bf +#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 095902cca30944d19a0d5f17f582e3b0 +#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 6d95fbfa321144a9932f26ab5f9ddc74 +#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 8be7ef160e8b421a89124a639dc7fd84 +#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 fcf4490c351d4cd6a208345308168ef7 +#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 00f1bb92a38b4f3a8c0065ac75530689 +#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 1477d0fc5c4c4f82bcc1c8e6ba8eed4d +#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 dee904cb678d4eb49dc829d6590b267a +#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 a21c1fd3194a49ae992a743023653dc5 +#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 e72c526da47a455da4b10e33938d1600 +#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2730,11 +2719,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 6447f4b8bb5f4f93bd8ec2c7b1fb09cb +#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 1faea30495a440a68dbd1647dacc404c +#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2747,40 +2736,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 0c0a3f58a93f492dbfca14523809aacc +#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 460842f202db493dbb901be73a02797f +#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 2591c2cf9e5f402281031ea8dd41a251 +#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 b093abbff3614b2ba0141f07376a5220 +#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 fda3718113354215bd2ac212553fb2d4 +#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 271e78089c274154a0233289d705e628 +#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 29ab4fa0876b4c11a0c7482cca56ed80 +#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2788,45 +2777,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 78e1857c5bd54af1b7ca4728879e6219 +#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 dae7873015254aa7874379164c90a8d0 +#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7a45deb4682b49fd86d62fae41831db8 +#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 442f77a69b314cba8e8857470263c706 +#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 d4455241f14549b791e59fc1f942c8cb +#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 ff4b1c05c5804ec7846043ae8814ad21 +#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 119e026b595f49c090d62aa7b7c77de4 +#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 5449d9c5687544a3bfbf8b2b25640a83 +#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2834,13 +2823,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b3191a7bd03d4ff18802ae0f5d419676 +#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 ea9cfbbd4cbd4f26ba4b0cb50d58635b +#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2848,43 +2837,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 7d39ed2a3a724dc1a75e6b2cdf87d91d +#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: a1306ee650344278ae39d6086b1ed7d9 +#: 943ba46512ce48fe8c5b62327734c503 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 21d76d22f3044460b925fee68ac74454 +#: bbcd43d5af7d44108aeb65075a6bd2be msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 6b8a5c59217c4928874710ead1456622 +#: 834295755af841a78e466eea43864861 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a9f6d09055c24029a5f85c3a663c4202 +#: a6b626489bfa468e8f059ab3aa669201 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: d3948618f9274ad0a333722567efeea5 +#: e1dbea105aa845c38cb1f90b43847271 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 44623c81141345a0b0080e719e1418ab +#: e9640f47d40e45bca184eb30700df648 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2894,14 +2883,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 6e80d82ed57b441b8292961ec3163213 +#: 0456efb3718b4356ad2b277ee16de967 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: fc61f369e720463f8a5cd6c751d1d5e6 +#: f7e97f926505407f8f8e9a427e055e43 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2910,7 +2899,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: f20aadbfc13243498ad199376c314e72 +#: ec597ff8f6ee47bc815b069335869f1f msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2926,11 +2915,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 e66956313b8f4f02bb96cfb256e2a7d4 +#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 f18c5a8fcbe84135a6e06cbf8008cd63 +#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2940,26 +2929,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 87fe14c9a0594602aa56a7706e089458 +#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 6e10063f55b747e1b07d6109ab7b046b +#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 e8831832b32449f4a8a3dde3c1b479cd +#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 9c86467137864626a2079cb6cecb71c0 +#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 24b66a3e2e464ec6a85b5dfbaad1cbf4 +#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2968,7 +2957,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 6d28f1cd40c045f384313c4d74073ed2 +#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2978,18 +2967,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 5235ff0c35c54396aceb799a65f6158e +#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 fc49344510594559b4f888bc45093b51 +#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 6e62be8d7d1344e8917904278b508518 +#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2997,7 +2986,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c91b3a2818b143f58bd37da63479c560 +#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -3005,7 +2994,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 86f283bc522c4be2adfac16256f01b0e +#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3015,7 +3004,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 5362aa1d28344968953ab9cb389ccd8e +#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3025,15 +3014,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 4bb1aafde4f745a083d3a276497523dc +#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 b00987baf6974ff9b7e3b8cdfd7abd9a +#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 9ac51c5a2a0a45859e14d9e388edd5f0 +#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3046,35 +3035,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 5494ccdb1a354b2386c82bd9a6f0b6a9 +#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 4cfa8fc2bb224883946d5f63b372de82 +#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 e16c1922527a46e28bb5d933614cdaf7 +#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 7498a71704be462abef71c42e6b83d1b +#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 ac0689bff9db46ea8bff8cd35cde86f3 +#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 c4b7da5575674ca3ae734424022ef090 +#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3087,23 +3076,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 d24fcecc17d0461cbd8689067f770c0d +#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 833d4d3b3f0e4c7cb8b1d35cb9a78a7e +#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 50fc0573276e4dd4a47208ed81109991 +#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 f72e10e746604421904057ddf7078d3e +#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3111,44 +3100,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 ee126833f6014e378c7841c4048dae85 +#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 0325bd610aa747b0b657afa0c978a1eb +#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 7c901105cf6949909d87be5681331368 +#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 74138d0c2ded4311bf688df4a28387b5 +#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 1ec4773e7319414b997d746d1965ff56 +#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 5f860dd70e3b435188c61a538e5de0ef +#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 a9c56df6dca441dfabda7fa54fbe56c6 +#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 586d561ddf724319b3da9ae857828648 +#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3156,33 +3145,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 f3e80b1903534065a30323611c267e9b +#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 6ed53c6f9fb94d4ab3d10532c605c46b +#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 3fcfdf43b0a049388634625c45e0b1bb +#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 49415efafae64f94b66cb46ca2bbd40a +#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 4806a2ef982944e8b073fafd416d3d74 d45701eeaa6e42feb4ef79d2fc4af756 +#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 155cd684ff304258ae374b2e13090e5f +#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3195,34 +3184,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 d8bdb44011274f94b606277799a6fa6f +#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 9e1d9bc2f83743ea9964ec418d225200 +#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 a1240eab3ef746cf82a2c5451042b888 +#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 a73cdc43a8e44973808027c29903afa3 +#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 4277837a9fd443378d5ca3d9252993c9 +#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 09b714af60ee4ecc8ab1b95eac8284dd +#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3230,7 +3219,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 3e99a3be9265463daf74b00a21d89cff +#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3239,7 +3228,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 1c4a959d43b74686ab801a26ef412b3d +#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3250,7 +3239,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 55daf180336d4045ac0cc4c14af98cfc +#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3258,7 +3247,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 5ae40eb04d5440d5ba882a74aa5b9708 +#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3268,13 +3257,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 f93e9b776a4544018877b7a13399609b +#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 0e587435e3884334bc51a4abf4b4d785 +#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3284,11 +3273,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 81b98764289245c79f18fcff478f4a9b +#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 9baddec4015f40ad82ea2dee30305654 +#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3296,17 +3285,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 986c3dd9460b42b3b20e2d01ba1fbe51 +#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 4558f174fea445fd97b80d963fc74f43 +#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 532823a13154401090e9fee3e018fda9 +#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3314,7 +3303,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 7b6f46b70bac4f848a956ea160243621 +#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 3861b4a31f71471b97bf9dc18cc80594 +#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3336,7 +3325,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 a10c37f65ac14ef2a5971872bc9b8f9a +#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3345,7 +3334,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 34175f932716406f836840732618caee +#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3355,7 +3344,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 0d132dc39cdf4818bc8e20132073f669 +#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3363,14 +3352,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 9f8c45f077974cf79612ee83df3d152b +#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 435f80d0599b4d93ae1339e8c7bc020a +#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3379,7 +3368,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 d39b024a1a8d4eae8d7fd3c929a782e9 +#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3388,7 +3377,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 3cbbe074843d4306b762d2fbc6fe9850 +#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3396,11 +3385,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 7118b6e09b9f44129c7d98d90570f2c2 +#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 70f3e73ee3714f22ad6ee43dd5ece703 +#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3411,7 +3400,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 279495257ead4a4fa725c7d68c504162 +#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3419,23 +3408,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 86d1d742bb5c4a9898aa573ce648f0ec +#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 f4987847f46e4a2db54127ec7ebcadf7 +#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 80e7c22dfe4d40749f2e9c3bf02bf8bc +#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 e930bb5d430a41d9b5bf49e473dd2ed1 +#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3443,7 +3432,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 4076e9eb67ed4bd5942f089e394bad26 +#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3451,59 +3440,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 1b44092e87b840de8f1d022676d0990d +#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 a8afac626f5d4240a57267085b9bef26 +#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 0896efc674bc402495c6e73c6c352523 +#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 91a53d918d4b47bdbe0b0a6d4adfc0dc +#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 8325682d51d8421b9ea507f424f71e73 +#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 503d068602d8477a820b91d835fa3f28 +#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4e768b91eb274a5cb157f1e3fe2f85cd +#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 18ec5231b7bf4c9ea59361b325fcdd01 +#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 87fd118dc2774cf08db0a3ba56520da5 +#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 8168ffcb23124b3f839a9862a7ec0958 +#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 37c222ea14904fd4a8fa93a1e0103239 +#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3521,7 +3510,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 d392813fc6d14851a294a391426d41f6 +#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3529,38 +3518,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 652155460eaa42b6856c16cffdb845c0 +#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 6313cb377dc249e0b2262a3fe732fe32 +#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 11f73cf24fb044e3a3afb3adb6137708 +#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 def9e62bf73f49eebce09677954e2a92 +#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 200dfe47d09d4b0b9e4acf29b7e038da +#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 858bda7fb6524e9dbfb35596ce6a6d07 +#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 28897819504247a3a6cf9a9d9476b63b +#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3569,7 +3558,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 4f8fd11e29b048e1851299002c3a48c4 +#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3577,62 +3566,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 ed33196347d949eda752a081c7af4657 +#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 738c67568dbb4f2bbb5756fc5e727c01 +#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 19b016a1fec14056a9812c1c195c7c90 +#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 a513367d60a74f559339c05d8ef10eb7 +#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 5e30680941164047a47f98417e916188 +#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 ca02f2bf1d754d5190f296674245b936 +#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 466615194bb541fdbe2e6515b50531b3 +#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 33e664d59a30407891336db290a8a5b2 +#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 3e52ab079dcf4fc6a3f052a517f4d31b +#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 abcad6b7d37a4342a90c2d5952ea1232 +#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 500a489e4fae4d1abaa8883f632d1a24 +#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 546c1ef51a63487c91c98059dd46b0cb +#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 72b4262833054edd9efe6078381de654 +#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3642,7 +3631,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 7b7e8242660744b791ba3868e4ed7e37 +#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3651,7 +3640,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 492d994a541c4c948fb5da9041153bcf +#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3662,28 +3651,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 e2209269db394f3988f18b147a57677c +#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 e15c39c65aca47f690264d8008463bec +#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 afa546fcb7fb447d939d4a167f206f79 +#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 7dd375e0fd964413af4957396d2a0474 +#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 af8ef039a64a4c0783d7229dbdac65ef +#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3694,7 +3683,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 3ce968cb39a443059f6a828b3c8c2f33 +#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3707,11 +3696,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 3c2f48a8e616400b9a8ffb4b6f7efc9b +#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 c432b1656e0e49ef87aa3d6e42acad84 +#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3722,26 +3711,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 cac5e52767f74ce98693e2a19ee1eb0d +#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 101666907f8b4fb994e25ceffcf04a13 +#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 5461960a469042a487b89e440f856aea +#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 e31349c164c84a9da46e2fb1861793df +#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 49a0b3dfdc9e4d58b6bc966db979ace8 +#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3751,52 +3740,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 e08ec8c473e847f98e8a18b9ca0f2670 +#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 6ee7bfb4a9e04dd19b5180bca5b02705 +#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 42614ab7ba1546f89abeb8f48991271c +#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 b8df5b8393ed4d869c066640fe83ec7b +#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 5b9aee5af41f438b9f4208294bf97f4a +#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 a71d3022dcfc44979cca4655ea51ad42 +#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 42b5a982e86f46dfbfcd7bfcc99d72a5 +#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 12dc402d053044b78d69927dd391fe9d +#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 687c20e2e4bc4f869c7ee9390e61476a +#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a975fbb3ea7d467881ce0245de538295 +#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" From eab42db5f89e05fd13496aa0600c3ff13008703c Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 11:19:56 +0100 Subject: [PATCH 45/49] Revert "convert license to RST to restore indirect links (#366)" This reverts commit a8098340780f4db905c755358391ddc75417727a. --- LICENSE.md | 63 ++ LICENSE.rst | 59 -- locales/es/LC_MESSAGES/user_guide.po | 1380 ++++++++++++------------- locales/pt/LC_MESSAGES/user_guide.po | 1385 +++++++++++++------------- locales/user_guide.pot | 1358 ++++++++++++------------- src/LICENSE.md | 2 + src/LICENSE.rst | 1 - src/index.md | 2 +- 8 files changed, 2153 insertions(+), 2097 deletions(-) create mode 100644 LICENSE.md delete mode 100644 LICENSE.rst create mode 100644 src/LICENSE.md delete mode 100644 src/LICENSE.rst diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 00000000..75596a51 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,63 @@ +# Licenses + +## Instructional Material + +All Common Workflow Language project instructional material and changes +to the structure are also made available under the [Creative Commons Attribution +license][cc-by-human]. The following is a human-readable summary of +(and not a substitute for) the [full legal text of the CC BY 4.0 +license][cc-by-legal]. + +You are free: + +* to **Share**---copy and redistribute the material in any medium or format +* to **Adapt**---remix, transform, and build upon the material + +for any purpose, even commercially. + +The licensor cannot revoke these freedoms as long as you follow the +license terms: + + + +* **Attribution**---You must give appropriate credit (mentioning that + your work is derived from work that is Copyright © the Common Workflow + Language project, and, where practical, linking to + https://www.commonwl.org/ ), provide a [link to the + license][cc-by-human], and indicate if changes were made. You may do + so in any reasonable manner, but not in any way that suggests the + licensor endorses you or your use. + +* **No additional restrictions**---You may not apply legal terms or +technological measures that legally restrict others from doing +anything the license permits. With the understanding that: + + * You do not have to comply with the license for elements of the + material in the public domain or where your use is permitted by an + applicable exception or limitation. + * No warranties are given. The license may not give you all of the + permissions necessary for your intended use. For example, other + rights such as publicity, privacy, or moral rights may limit how you + use the material. + +## Software + +Except where otherwise noted, the example programs and other software +provided by Common Workflow Language project are made available under the +[OSI][osi]-approved +[Apache 2.0 license][apache-2.0-license]. + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + + + + +[cc-by-human]: https://creativecommons.org/licenses/by/4.0/ +[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode +[apache-2.0-license]: https://opensource.org/licenses/Apache-2.0 +[mit-license]: https://opensource.org/licenses/mit-license.html +[osi]: https://opensource.org diff --git a/LICENSE.rst b/LICENSE.rst deleted file mode 100644 index cc6a19b0..00000000 --- a/LICENSE.rst +++ /dev/null @@ -1,59 +0,0 @@ -Licenses -======== - -Instructional Material ----------------------- - -All Common Workflow Language project instructional material and changes -to the structure are also made available under the `Creative Commons -Attribution license `_. The following is a human-readable summary of (and -not a substitute for) the `full legal text of the CC BY 4.0 license `_. - -You are free: - -- to **Share**—copy and redistribute the material in any medium or - format -- to **Adapt**—remix, transform, and build upon the material - -for any purpose, even commercially. - -The licensor cannot revoke these freedoms as long as you follow the -license terms: - -- **Attribution**—You must give appropriate credit (mentioning that - your work is derived from work that is Copyright © the Common - Workflow Language project, and, where practical, linking to - https://www.commonwl.org/ ), provide a `link to the license `_, and - indicate if changes were made. You may do so in any reasonable - manner, but not in any way that suggests the licensor endorses you or - your use. - -- **No additional restrictions**—You may not apply legal terms or - technological measures that legally restrict others from doing - anything the license permits. With the understanding that: - - - You do not have to comply with the license for elements of the - material in the public domain or where your use is permitted by an - applicable exception or limitation. - - No warranties are given. The license may not give you all of the - permissions necessary for your intended use. For example, other - rights such as publicity, privacy, or moral rights may limit how - you use the material. - -Software --------- - -Except where otherwise noted, the example programs and other software -provided by Common Workflow Language project are made available under -the `OSI`_-approved `Apache 2.0 license `_. - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an “AS IS” BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -.. _cc-by-human: https://creativecommons.org/licenses/by/4.0/ -.. _cc-by-legal: https://creativecommons.org/licenses/by/4.0/legalcode -.. _OSI: https://opensource.org -.. _Apache-2.0: https://opensource.org/licenses/Apache-2.0 diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index 3fa6daab..ba080ed4 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,113 +9,149 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 16:53+0100\n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" +"Language-Team: Spanish \n" "Language: es\n" -"Language-Team: Spanish \n" -"Plural-Forms: nplurals=2; plural=n != 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.rst:2 dcdc2e8da0ec4d9e9453601fdd83bac5 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" -msgstr "" -"Licencias" +msgstr "Licencias" -#: ../../LICENSE.rst:5 3e165520ca56481b8f8d494a8d471de3 +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" -msgstr "" -"Material didáctico" +msgstr "Material didáctico" -#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " -"cambios en la estructura también están disponibles bajo la `licencia " -"Creative Commons Attribution `_. Lo que sigue es un resumen " -"legible por humanos (y no un sustituto) del `texto legal completo de la " -"licencia CC BY 4.0 `_." +"cambios en la estructura también están disponibles bajo la [licencia " +"Creative Commons Attribution][cc-by-human]. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del [texto legal completo de la " +"licencia CC BY 4.0][cc-by-legal]." -#: ../../LICENSE.rst:12 b7a7a0fb40344fe087c1cc3ec19308aa +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "Usted es libre de:" -#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 -msgid "to **Share**—copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -"**Compartir**—copiar y redistribuir el material en cualquier medio o " +"**Compartir**---copiar y redistribuir el material en cualquier medio o " "formato" -#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 -msgid "to **Adapt**—remix, transform, and build upon the material" -msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" -#: ../../LICENSE.rst:18 430ff4de74924bc3a3b2c7e809ea4456 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia." -#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 -msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." msgstr "" -"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su" -" trabajo se deriva de un trabajo que tiene «Copyright © The Common " -"Workflow Language Project» y, cuando sea práctico, con un enlace a " -"https://www.commonwl.org/ ), brindar un `enlace a la licencia `_, e indicar si se han realizado cambios. Puede hacerlo en cualquier" -" forma razonable, pero no de forma tal que sugiera que usted o su uso " -"tienen el apoyo de la licenciante." +"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " +"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " +"Language Project» y, cuando sea práctico, con un enlace a https://www." +"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " +"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " +"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " +"licenciante." -#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 -msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -"**No hay restricciones adicionales**---No puede aplicar términos legales " -"ni medidas tecnológicas que restrinjan legalmente a otras a hacer " -"cualquier uso permitido por la licencia. Con el entendimiento de que:" +"**No hay restricciones adicionales**---No puede aplicar términos legales ni " +"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " +"permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limit +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " -"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como" -" publicidad, privacidad, o derechos morales pueden limitar la forma en " -"que utilice el material." +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " +"publicidad, privacidad, o derechos morales pueden limitar la forma en que " +"utilice el material." -#: ../../LICENSE.rst:44 3d7ca3f2cede4d5f998bf014bd970748 +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "Software" -#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la `licencia Apache 2.0 `_ aprobada " -"por la `OSI`_." +"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " +"la [OSI][Osi]." -#: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 -#: dfc7702e073140c985cf47272a20214d +#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 +#: eab02dc13915490bb3c9ba744d78b6a7 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -124,30 +160,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -155,94 +191,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -250,22 +286,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -274,25 +310,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" -#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -300,26 +336,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" -#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -328,77 +364,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -407,11 +443,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -422,22 +458,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -446,11 +482,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -458,7 +494,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -466,15 +502,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -485,18 +521,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -506,18 +542,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -526,24 +562,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 9bba7c4f783942e4a299603430601363 +#: a5ebc727fb3443f78e81d6b7ed5ac750 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: e2140e0f0e7747ef8383887c20a7945a +#: 86e6a06992dc4228bfda7add48e28ca3 msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -552,39 +588,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 15bf490724cd46dcbcfab44633c5a9a2 +#: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 51d52d051e654a8395239f88df7c9d8c +#: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: eb496cc818524fa7bae5a22ddd00a19c +#: b97ba368fd664caab0494e2392795697 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c4a22d12e7f149ff901d27de32b9361d +#: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 7618de899a7043989d77baacf62eb7b2 +#: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: 6f1544a220664b79b04bf008058b5a91 +#: cf2922f645904ac7955428ecddc37b8a msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: fbd14ac9a2f541478a320ed4cbc69e13 +#: 5f47aae608c041aeb4134d59dad314d2 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -593,7 +629,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: da4dba50d25d4533b3dbb92f54d32a30 +#: f6f589481d0c4891beaccb63160619ef msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -602,7 +638,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: ce11c9f8d65c4268984d0384d95144cc +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -612,7 +648,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 3a201aa497e84f70855bb2251e7e3281 +#: 4ace6b92f4e04a07aa202840ebe36417 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -621,24 +657,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: b78f7fa2be1c4bb090f6da895457ad1e +#: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: f7e95d264ffa4e2db0864faccd9e5a0e +#: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 3f1e5b01e49a4dc1b1c99936a4589afc +#: 907674a4ecff4826a2b880e28fc38f33 msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 03c3048f38ae4938a484cf02001877b3 +#: 037cd0e5ceda482eaeaca03d51745aee msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -648,7 +684,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: f9715b5ec65c405c849bb030c1927060 +#: e4643938445b48cc80eb8973ceeb126e msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -657,12 +693,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 442662f50e9e4620970ce32b1b127969 +#: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 2b34c786af3840e88f29d214e19dc837 +#: 3eb6a013a2a4478ca2ad134661f65c58 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -676,7 +712,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: dd6aadff8cf54ce78ea6b317afbaddb0 +#: 074af9633627470485e5225326d5f20a msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -685,7 +721,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: 847951c055b94a83b1e081594cef22ee msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -694,71 +730,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: d10cf45b3c7f49dc98bc0e5d1246f224 +#: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 -#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b +#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 +#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 8badec9987ba40609cf1f626172b2b2d +#: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: c75a8b4bf0e24781bf6713cf6f013cd1 +#: 36eb4b3b966640af90faa55db3789cb6 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 2ccb956baa6b4376a04ad9fcc4654631 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 07cca9a33d8f4b77ac6ad35ca8b95655 +#: 72889b830c514afe9a7cb1e64b5666a0 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: 31db11c8ddf2423192a8b2063b3e91c2 +#: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: d81dd96143ea444aa78ff45cfa0584b3 +#: c377a7f5dbe645cebbb6c7eccf831a0b msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -768,11 +804,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -780,29 +816,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -812,11 +848,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -824,7 +860,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -832,26 +868,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -862,23 +898,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -889,32 +925,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -922,30 +958,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -955,47 +991,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1003,7 +1039,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1011,57 +1047,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1069,11 +1105,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1081,11 +1117,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1093,32 +1129,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1126,21 +1162,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1148,46 +1184,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1195,19 +1231,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 32f86f911ebe4a4c94975f81742333f3 +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: c53ceee943ad4acea779e072b9137889 +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1218,37 +1254,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 7dfe9dffbf5744299bf232599644c7f6 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 1f3c23a4769043ca985b8ddfed19391d +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: f81b43c7cb194a1cad8672129223c833 +#: 9643449da1da46d7861866dce490cbcb msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: a20073a8f5374eb1bc8531ff33e622b6 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d08869beca3a4774baf1097b63e79474 +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1259,11 +1295,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1271,13 +1307,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1293,7 +1329,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1303,43 +1339,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1347,13 +1383,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1365,44 +1401,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1410,31 +1446,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1442,52 +1478,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 12cf5f2264504c44a2173e858bb2c283 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 7694f9cabfe04308bbddd2c88ae6d9b9 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1496,17 +1532,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: b557dc4f8ef549b98f59412a918643de +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 3011eb003c084285b30cfa56a8da45b6 +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1514,7 +1550,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: ce78b2d147054da895beba66d0ecdab4 +#: 9454a330b9324744b89448f2694b1b03 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1524,7 +1560,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a973846ec5a946eeaff02c5b00997da9 +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1532,13 +1568,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d -#: ccec7f73b9d948e79a6cdf32bc124092 +#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 22948f19cb78485f8f86244686a35c09 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1546,7 +1582,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 001d9579bfce438e865377fb9c2df776 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1558,7 +1594,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: e62618db8995428bb3f260e03ac8f459 +#: 1741804e33aa43ce88b4320c11ae5973 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1568,19 +1604,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 -#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 -#: e9801b2142cd45368a73ef9b121c1d08 +#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f +#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 +#: f924d65fed0c4cb5b0a019b084a8b535 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1589,21 +1625,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1612,13 +1648,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1629,15 +1665,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1645,7 +1681,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1655,26 +1691,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1682,32 +1718,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1715,7 +1751,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1724,67 +1760,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 +#: 1acb064f7a4a482aa0174bdc847c6382 msgid "`arguments`" msgstr "" @@ -1792,32 +1828,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 -#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 -#: e7f1993580f0425098a719e83a64cc7f +#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e +#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 +#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a -#: 92697d3179ec48898eaea9aba3c24dcd +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 -#: d6722e3093884ad7b62696fbb2f48fdc +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1828,11 +1864,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 -#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef -#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c +#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc +#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd +#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 +#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -1841,51 +1877,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 -#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c -#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b -#: f71216a4b35e4157aece5ffa2602d8bf +#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 +#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d +#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f +#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c +#: f760465a49d64d4c8468ad9c4fea62b1 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b +#: d555a3d991e344a5a8e1289168d7c6d1 msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c +#: e9fa9430535c424fa3e8be5d460d2ba4 msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1894,32 +1930,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c +#: b0290d1a477b48119e17cf1fed9d6dff msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 +#: e1cde4aa32c041238ed2596173c6d824 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf +#: c2a92d3eca7f4ee39cec649170eeea53 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1927,61 +1963,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 -#: c9534670f5f04769aa3749c3778eb705 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 +#: 718ceee9973240ec9c100977bbcc8921 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 +#: c07ab08eb75d4528949c56a3d7c12b28 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 -#: fe3b9fb45e01490498c5a35c012b3de8 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 -#: fec70bb106ad4d95a2d55ebdcf711afc +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -1989,33 +2025,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 +#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2023,22 +2059,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2046,7 +2082,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2056,54 +2092,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2112,15 +2148,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2129,11 +2165,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2141,7 +2177,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2150,34 +2186,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2185,11 +2221,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2198,80 +2234,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2279,7 +2315,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2287,7 +2323,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2295,14 +2331,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2310,7 +2346,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2318,7 +2354,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2328,13 +2364,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2345,17 +2381,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2365,23 +2401,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 -#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 +#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 +#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2391,7 +2427,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2402,11 +2438,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2414,46 +2450,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2461,18 +2497,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2480,7 +2516,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2488,7 +2524,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2498,12 +2534,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 71628ebe908b4cd28dd1fa17e3d2e2fb +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: f123ca244c23413c91405a4b84887525 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2518,7 +2554,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 23299ae1bec94b00a32a8af7eeac350f +#: 80af387fe3ff4e2da999903385bd602b msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2526,17 +2562,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 2495a9f2032a47c188338cb81ba429eb +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 3fd2f3cf7bdf44089df2ce3122534801 +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: d5a5b8b490b640439db92da949266e4e +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2546,15 +2582,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 5935ed94331d4b2f8ce597f31edea843 +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2562,56 +2598,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2619,7 +2655,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2628,17 +2664,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2646,71 +2682,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2719,11 +2755,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2736,40 +2772,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2777,45 +2813,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2823,13 +2859,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2837,43 +2873,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 943ba46512ce48fe8c5b62327734c503 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: bbcd43d5af7d44108aeb65075a6bd2be +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 834295755af841a78e466eea43864861 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a6b626489bfa468e8f059ab3aa669201 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: e1dbea105aa845c38cb1f90b43847271 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: e9640f47d40e45bca184eb30700df648 +#: 574d93d1d592458a985f259519c036cb msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2883,14 +2919,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 0456efb3718b4356ad2b277ee16de967 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f7e97f926505407f8f8e9a427e055e43 +#: 02e40154eac74ecc98d0447d03475b44 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2899,7 +2935,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: ec597ff8f6ee47bc815b069335869f1f +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2915,11 +2951,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2929,26 +2965,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2957,7 +2993,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2967,18 +3003,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2986,7 +3022,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -2994,7 +3030,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3004,7 +3040,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3014,15 +3050,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3035,35 +3071,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3076,23 +3112,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3100,44 +3136,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3145,33 +3181,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3184,34 +3220,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3219,7 +3255,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3228,7 +3264,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3239,7 +3275,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3247,7 +3283,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3257,13 +3293,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3273,11 +3309,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3285,17 +3321,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3303,7 +3339,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3325,7 +3361,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3334,7 +3370,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3344,7 +3380,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3352,14 +3388,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3368,7 +3404,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3377,7 +3413,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3385,11 +3421,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3400,7 +3436,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3408,23 +3444,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3432,7 +3468,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3440,59 +3476,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3510,7 +3546,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3518,38 +3554,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3558,7 +3594,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3566,62 +3602,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3631,7 +3667,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3640,7 +3676,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3651,28 +3687,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3683,7 +3719,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3696,11 +3732,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3711,26 +3747,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3740,52 +3776,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index 3ed0733d..3584ce39 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -9,115 +9,142 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 16:53+0100\n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" +"Language-Team: Portuguese \n" "Language: pt\n" -"Language-Team: Portuguese \n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" +"Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" -#: ../../LICENSE.rst:2 75de2be8809847b8bf1ccd42aa694a24 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.rst:5 2edd71801f6245ef821887a74f21b94c +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" msgstr "" -#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" "Todo o material instrucional do projeto Common Workflow Language e " -"alterações na estrutura também são disponibilizados sob a `licença " -"Creative Commons Attribution `_. O seguinte é um resumo " -"legível por humanos de (e não um substituto para) o `texto legal completo" -" da licença CC BY 4.0 `_." +"alterações na estrutura também são disponibilizados sob a [licença Creative " +"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o [texto legal completo da licença CC " +"BY 4.0][cc-by-legal]." -#: ../../LICENSE.rst:12 90cc755d172e4c82b882b4ee620fe652 +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "Você tem o direito de:" -#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 -msgid "to **Share**—copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -"**Compartilhar**—copiar e redistribuir o material em qualquer suporte " -"ou formato" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " +"formato" -#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 -msgid "to **Adapt**—remix, transform, and build upon the material" -msgstr "**Adaptar**—remixar, transformar, e criar a partir do material" +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.rst:18 430ff4de74924bc3a3b2c7e809ea4456 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " "termos da licença." -#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 -msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." msgstr "" "Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " "trabalho deriva de um trabalho que é «Copyright © The Common Workflow " -"Language project», e, quando prático, criar uma ligação para " -"https://www.commonwl.org/ ), fornecer um `link para a licença `_, e indicar se foram feitas alterações. Você pode fazê-lo de " -"qualquer forma razoável, mas não de uma forma que sugira que o " -"licenciante o apoia ou aprova o seu uso." +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " +"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " +"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " +"uso." -#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 -msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -"**Sem restrições adicionais**—Você não pode aplicar termos jurídicos ou" -" medidas de caráter tecnológico que restrinjam legalmente outros de " -"fazerem algo que a licença permita. Com o entendimento de que:" +"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " +"algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" "Não tem de cumprir com os termos da licença relativamente a elementos do " -"material que estejam no domínio público ou cuja utilização seja permitida" -" por uma exceção ou limitação que seja aplicável." +"material que estejam no domínio público ou cuja utilização seja permitida " +"por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" "Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " "autorizações necessárias para o uso pretendido. Por exemplo, outros " -"direitos, tais como direitos de imagem, de privacidade ou direitos " -"morais, podem limitar o uso do material." +"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " +"podem limitar o uso do material." -#: ../../LICENSE.rst:44 3d7ca3f2cede4d5f998bf014bd970748 +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "Software" -#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob" -" a `licença Apache 2.0 `_ aprovada pela `OSI`_." +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" +"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." -#: ../../LICENSE.rst:50 9c4d58a1129a4d4eb4db1bfabbeddb6e +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT" -" WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the" -" License for the specific language governing permissions and limitations " -"under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 -#: dfc7702e073140c985cf47272a20214d +#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 +#: eab02dc13915490bb3c9ba744d78b6a7 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -126,30 +153,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -157,94 +184,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -252,22 +279,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -276,25 +303,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" -#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -302,26 +329,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" -#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -330,77 +357,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -409,11 +436,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -424,22 +451,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -448,11 +475,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -460,7 +487,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -468,15 +495,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -487,18 +514,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -508,18 +535,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -528,24 +555,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 9bba7c4f783942e4a299603430601363 +#: a5ebc727fb3443f78e81d6b7ed5ac750 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: e2140e0f0e7747ef8383887c20a7945a +#: 86e6a06992dc4228bfda7add48e28ca3 msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -554,39 +581,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 15bf490724cd46dcbcfab44633c5a9a2 +#: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 51d52d051e654a8395239f88df7c9d8c +#: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: eb496cc818524fa7bae5a22ddd00a19c +#: b97ba368fd664caab0494e2392795697 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c4a22d12e7f149ff901d27de32b9361d +#: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 7618de899a7043989d77baacf62eb7b2 +#: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: 6f1544a220664b79b04bf008058b5a91 +#: cf2922f645904ac7955428ecddc37b8a msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: fbd14ac9a2f541478a320ed4cbc69e13 +#: 5f47aae608c041aeb4134d59dad314d2 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -595,7 +622,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: da4dba50d25d4533b3dbb92f54d32a30 +#: f6f589481d0c4891beaccb63160619ef msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -604,7 +631,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: ce11c9f8d65c4268984d0384d95144cc +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -614,7 +641,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 3a201aa497e84f70855bb2251e7e3281 +#: 4ace6b92f4e04a07aa202840ebe36417 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -623,24 +650,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: b78f7fa2be1c4bb090f6da895457ad1e +#: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: f7e95d264ffa4e2db0864faccd9e5a0e +#: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 3f1e5b01e49a4dc1b1c99936a4589afc +#: 907674a4ecff4826a2b880e28fc38f33 msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 03c3048f38ae4938a484cf02001877b3 +#: 037cd0e5ceda482eaeaca03d51745aee msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -650,7 +677,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: f9715b5ec65c405c849bb030c1927060 +#: e4643938445b48cc80eb8973ceeb126e msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -659,12 +686,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 442662f50e9e4620970ce32b1b127969 +#: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 2b34c786af3840e88f29d214e19dc837 +#: 3eb6a013a2a4478ca2ad134661f65c58 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -678,7 +705,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: dd6aadff8cf54ce78ea6b317afbaddb0 +#: 074af9633627470485e5225326d5f20a msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -687,7 +714,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: 847951c055b94a83b1e081594cef22ee msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -696,71 +723,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: d10cf45b3c7f49dc98bc0e5d1246f224 +#: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 -#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b +#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 +#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 8badec9987ba40609cf1f626172b2b2d +#: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: c75a8b4bf0e24781bf6713cf6f013cd1 +#: 36eb4b3b966640af90faa55db3789cb6 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 2ccb956baa6b4376a04ad9fcc4654631 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 07cca9a33d8f4b77ac6ad35ca8b95655 +#: 72889b830c514afe9a7cb1e64b5666a0 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: 31db11c8ddf2423192a8b2063b3e91c2 +#: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: d81dd96143ea444aa78ff45cfa0584b3 +#: c377a7f5dbe645cebbb6c7eccf831a0b msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -770,11 +797,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -782,29 +809,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -814,11 +841,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -826,7 +853,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -834,26 +861,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -864,23 +891,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -891,32 +918,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -924,30 +951,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -957,47 +984,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1005,7 +1032,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1013,57 +1040,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1071,11 +1098,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1083,11 +1110,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1095,32 +1122,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1128,21 +1155,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1150,46 +1177,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1197,19 +1224,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 32f86f911ebe4a4c94975f81742333f3 +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: c53ceee943ad4acea779e072b9137889 +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1220,37 +1247,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 7dfe9dffbf5744299bf232599644c7f6 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 1f3c23a4769043ca985b8ddfed19391d +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: f81b43c7cb194a1cad8672129223c833 +#: 9643449da1da46d7861866dce490cbcb msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: a20073a8f5374eb1bc8531ff33e622b6 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d08869beca3a4774baf1097b63e79474 +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1261,11 +1288,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1273,13 +1300,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1295,7 +1322,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1305,43 +1332,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1349,13 +1376,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1367,44 +1394,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1412,31 +1439,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1444,52 +1471,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 12cf5f2264504c44a2173e858bb2c283 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 7694f9cabfe04308bbddd2c88ae6d9b9 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1498,17 +1525,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: b557dc4f8ef549b98f59412a918643de +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 3011eb003c084285b30cfa56a8da45b6 +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1516,7 +1543,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: ce78b2d147054da895beba66d0ecdab4 +#: 9454a330b9324744b89448f2694b1b03 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1526,7 +1553,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a973846ec5a946eeaff02c5b00997da9 +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1534,13 +1561,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d -#: ccec7f73b9d948e79a6cdf32bc124092 +#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 22948f19cb78485f8f86244686a35c09 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1548,7 +1575,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 001d9579bfce438e865377fb9c2df776 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1560,7 +1587,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: e62618db8995428bb3f260e03ac8f459 +#: 1741804e33aa43ce88b4320c11ae5973 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1570,19 +1597,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 -#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 -#: e9801b2142cd45368a73ef9b121c1d08 +#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f +#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 +#: f924d65fed0c4cb5b0a019b084a8b535 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1591,21 +1618,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1614,13 +1641,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1631,15 +1658,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1647,7 +1674,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1657,26 +1684,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1684,32 +1711,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1717,7 +1744,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1726,67 +1753,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 +#: 1acb064f7a4a482aa0174bdc847c6382 msgid "`arguments`" msgstr "" @@ -1794,32 +1821,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 -#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 -#: e7f1993580f0425098a719e83a64cc7f +#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e +#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 +#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a -#: 92697d3179ec48898eaea9aba3c24dcd +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 -#: d6722e3093884ad7b62696fbb2f48fdc +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1830,11 +1857,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 -#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef -#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c +#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc +#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd +#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 +#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -1843,51 +1870,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 -#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c -#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b -#: f71216a4b35e4157aece5ffa2602d8bf +#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 +#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d +#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f +#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c +#: f760465a49d64d4c8468ad9c4fea62b1 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b +#: d555a3d991e344a5a8e1289168d7c6d1 msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c +#: e9fa9430535c424fa3e8be5d460d2ba4 msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1896,32 +1923,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c +#: b0290d1a477b48119e17cf1fed9d6dff msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 +#: e1cde4aa32c041238ed2596173c6d824 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf +#: c2a92d3eca7f4ee39cec649170eeea53 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1929,61 +1956,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 -#: c9534670f5f04769aa3749c3778eb705 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 +#: 718ceee9973240ec9c100977bbcc8921 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 +#: c07ab08eb75d4528949c56a3d7c12b28 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 -#: fe3b9fb45e01490498c5a35c012b3de8 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 -#: fec70bb106ad4d95a2d55ebdcf711afc +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -1991,33 +2018,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 +#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2025,22 +2052,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2048,7 +2075,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2058,54 +2085,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2114,15 +2141,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2131,11 +2158,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2143,7 +2170,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2152,34 +2179,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2187,11 +2214,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2200,80 +2227,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2281,7 +2308,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2289,7 +2316,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2297,14 +2324,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2312,7 +2339,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2320,7 +2347,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2330,13 +2357,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2347,17 +2374,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2367,23 +2394,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 -#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 +#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 +#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2393,7 +2420,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2404,11 +2431,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2416,46 +2443,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2463,18 +2490,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2482,7 +2509,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2490,7 +2517,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2500,12 +2527,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 71628ebe908b4cd28dd1fa17e3d2e2fb +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: f123ca244c23413c91405a4b84887525 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2520,7 +2547,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 23299ae1bec94b00a32a8af7eeac350f +#: 80af387fe3ff4e2da999903385bd602b msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2528,17 +2555,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 2495a9f2032a47c188338cb81ba429eb +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 3fd2f3cf7bdf44089df2ce3122534801 +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: d5a5b8b490b640439db92da949266e4e +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2548,15 +2575,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 5935ed94331d4b2f8ce597f31edea843 +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2564,56 +2591,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2621,7 +2648,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2630,17 +2657,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2648,71 +2675,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2721,11 +2748,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2738,40 +2765,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2779,45 +2806,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2825,13 +2852,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2839,43 +2866,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 943ba46512ce48fe8c5b62327734c503 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: bbcd43d5af7d44108aeb65075a6bd2be +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 834295755af841a78e466eea43864861 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a6b626489bfa468e8f059ab3aa669201 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: e1dbea105aa845c38cb1f90b43847271 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: e9640f47d40e45bca184eb30700df648 +#: 574d93d1d592458a985f259519c036cb msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2885,14 +2912,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 0456efb3718b4356ad2b277ee16de967 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f7e97f926505407f8f8e9a427e055e43 +#: 02e40154eac74ecc98d0447d03475b44 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2901,7 +2928,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: ec597ff8f6ee47bc815b069335869f1f +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2917,11 +2944,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2931,26 +2958,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2959,7 +2986,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2969,18 +2996,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2988,7 +3015,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -2996,7 +3023,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3006,7 +3033,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3016,15 +3043,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3037,35 +3064,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3078,23 +3105,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3102,44 +3129,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3147,33 +3174,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3186,34 +3213,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3221,7 +3248,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3230,7 +3257,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3241,7 +3268,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3249,7 +3276,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3259,13 +3286,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3275,11 +3302,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3287,17 +3314,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3305,7 +3332,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3327,7 +3354,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3336,7 +3363,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3346,7 +3373,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3354,14 +3381,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3370,7 +3397,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3379,7 +3406,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3387,11 +3414,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3402,7 +3429,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3410,23 +3437,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3434,7 +3461,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3442,59 +3469,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3512,7 +3539,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3520,38 +3547,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3560,7 +3587,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3568,62 +3595,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3633,7 +3660,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3642,7 +3669,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3653,28 +3680,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3685,7 +3712,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3698,11 +3725,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3713,26 +3740,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3742,64 +3769,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" -#~ msgid "" -#~ "Unless required by applicable law or " -#~ "agreed to in writing, software " -#~ "distributed under the License is " -#~ "distributed on an \"AS IS\" BASIS, " -#~ "WITHOUT WARRANTIES OR CONDITIONS OF ANY" -#~ " KIND, either express or implied. See" -#~ " the License for the specific " -#~ "language governing permissions and limitations" -#~ " under the License." -#~ msgstr "" - diff --git a/locales/user_guide.pot b/locales/user_guide.pot index a806cea1..0a669946 100644 --- a/locales/user_guide.pot +++ b/locales/user_guide.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 16:53+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -16,1273 +16,1273 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" -#: ../../LICENSE.rst:2 -#: 75de2be8809847b8bf1ccd42aa694a24 +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 msgid "Licenses" msgstr "" -#: ../../LICENSE.rst:5 -#: 2edd71801f6245ef821887a74f21b94c +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" msgstr "" -#: ../../LICENSE.rst:7 -#: 3c0a9704ed8f4367893242a4f75d703f -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." msgstr "" -#: ../../LICENSE.rst:12 -#: 90cc755d172e4c82b882b4ee620fe652 +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "" -#: ../../LICENSE.rst:14 -#: e5246890525144bda8547106b6643382 -msgid "to **Share**—copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -#: ../../LICENSE.rst:16 -#: 4d96baa7ca7a4240b75be213696558ba -msgid "to **Adapt**—remix, transform, and build upon the material" +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" -#: ../../LICENSE.rst:18 -#: e19adbba09d14d069534251a7ef70993 +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "" -#: ../../LICENSE.rst:20 -#: 8bc6672f4a33428296226112a1be6fbe +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" -#: ../../LICENSE.rst:23 -#: be38276e7b374f57b9997391bf898a62 -msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" -#: ../../LICENSE.rst:31 -#: f00d5c3846034c2ea116c2f74786d9fc -msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" -#: ../../LICENSE.rst:35 -#: 1798d65c10104040923c2fea2199bab2 +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" -#: ../../LICENSE.rst:38 -#: c65198b804f8436ba783643d51bc72d9 +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" -#: ../../LICENSE.rst:44 -#: 4777f6a958394b138c5b68eee0367734 +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "" -#: ../../LICENSE.rst:46 -#: 7dec2236137f4de5ac7df7a8c8eaf98b -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" -#: ../../LICENSE.rst:50 -#: 9c4d58a1129a4d4eb4db1bfabbeddb6e -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 #: ../../src/_includes/what-is-cwl.md:2 -#: bdd540403a5746ff99edf2dcad0e3122 -#: 5ad4be9b62d54c95a913795b514676fd -#: dfc7702e073140c985cf47272a20214d +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." msgstr "" #: ../../src/episodes.md:5 #: ../../src/setup.md:5 -#: f1b89ae4325343f783bce8b7c9971047 -#: 810c4e8dd79247d6a6fd51a8f65d3975 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 -#: 3060770b3bef41d7bcfcdfb413d7689c +#: cc11f5d29206492d9f2f0922882b6159 msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." msgstr "" #: ../../src/faq.md:1 -#: 48bb9f628b344ba1a3b67ae1cb264e3c +#: e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "" #: ../../src/faq.md:11 -#: 7e3684e9672643738846756e1ebafd18 +#: 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 -#: 187ceabb7fd9480bb8cf0f2da47f65ef +#: d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 -#: b548b76bcc85420a9b30792386105139 +#: fc62427c0a004810b055dee90ec5e2d9 msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 -#: 9ce692b78ead47e4b0f8cdae8837d35b +#: 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 -#: 6df1201c159343da9e7515379980d6a0 +#: bc7ad10c929848a3a9a240a3c501d299 msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 -#: f9ab1d0dc1c842b6abb5385268c1d3bd +#: 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 -#: 9f6a84ab6a9343b6ad7db826f8964362 +#: 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 -#: fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: 450edf800a18423195bea4fe8793a2cb msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 -#: 3a871012fcfd4f3ebeca0cb86ec93435 +#: 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 -#: d954edfff2584288ac8c600733070d2e +#: a7d84f740a714ec588503ee084fbbc34 msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" msgstr "" #: ../../src/faq.md:97 -#: af6b1e37d6be4450a761854480ec9aab +#: 569d553abe85450c9d1c37456bf412f4 msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." msgstr "" #: ../../src/faq.md:104 -#: 31f4a2d43062493ca64c648f80afc8e9 +#: 95f5dbbd21084a318413b9528fb867be msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 -#: 41c54e71b6cd4f63b2a619a515240d34 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." msgstr "" #: ../../src/faq.md:115 -#: 8edc3541ad134ab5a1d23c724f1f0a4e +#: 8d86baa239364f799d4f9d5ea2b0e314 msgid "The second method involves including an input of `type: File` in the script itself:" msgstr "" #: ../../src/faq.md:135 -#: ac0ea81eba8842a18801ab03cbf80a57 +#: f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 -#: 52be1a5640234feabe958ff7ade33653 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 -#: c6db734d5aef4f4f99676bdebf9c83c9 +#: 2c38cc58cbb340bc935a5f00e96ba95c msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 -#: a9f7b47c0dd741739795da39bf114879 +#: ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 -#: e3fdd9228b924905a4a1f4b2b7ad7159 +#: d06cbf89028b4638ad54c2529bcbfa25 msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 -#: 3f7cda1437cc48f18745a827ebb74582 +#: d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 -#: 5aeaba2cae64442e816bbd458aee833a +#: d9e30e11533b4d53a144f5df7041268d msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 -#: 5af827a402834978addd82c70be6b5ab +#: 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 -#: 6d69e42bd8e443c4b19d80807c7efd6b +#: 937cb94a370640c788fbc3fe0b19f2e5 msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 -#: 404640397b6e40c2a2cd5cf85ab3b1c0 +#: a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 -#: 1682c2486e224770b62269709a8663cf +#: c8c235a9bf6240628f0b5493ffebf7e0 msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." msgstr "" #: ../../src/faq.md:229 -#: 9078fc009bc145808813c9cc2b734b58 +#: 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 -#: d4b5a54a400c409cb7984428f6a03ec8 +#: 89b90d3bf1ea4ebd88482d435241fac5 msgid "To make an input parameter optional, add a question mark to the type declaration." msgstr "" #: ../../src/faq.md:247 -#: 9e8dbee6e8f84d08b1a54fffa06394ef +#: a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" #: ../../src/faq.md:248 -#: 1d846bfb5f054d09a4afad1da8e4b642 +#: f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 -#: 2d0e95fec8084787b734388d60188574 +#: 10af80fa13af4158aec7060550485350 msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 -#: eccc4a364330470fa474dcaaa3433390 +#: ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" #: ../../src/faq.md:268 -#: e945f6a337af4e4686bed482a4fe6c39 +#: 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 -#: 8a3efaa0ad1548428bcfd6e01d135cdc +#: 52b8538177c64090af51f5f6a696c28c msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." msgstr "" #: ../../src/faq.md:322 -#: cdab644adc5643708870fb08c06cbfca +#: f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 -#: 089a5a0b076b44aeaab4d69ee3c79f97 +#: 7dc0540508084a3495ff3b2ac90fd323 msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." msgstr "" #: ../../src/faq.md:342 -#: 561172559c6f41a68819608fd9e58bb0 +#: b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 -#: c5ee4946d2e840abaa3dc796a62652c7 +#: cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 -#: 4f2069a2113c414db18eca95550e9e09 +#: 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 -#: 31f3390e6771414ba7bf57c044c4b0c4 +#: 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 -#: 3b77ce4930ae46d5be9f6965e8c54727 +#: 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 -#: 06f36bbe4d3840229b7374f27b86ae80 +#: 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 -#: 3cb2f70d00274a4dafd972ccd8c519c2 +#: fdaec25650ab4b0fb1c527610e24ae5a msgid "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 -#: 093a1529262043ef84a99675054938e0 +#: 182959fc9f4746d082994e07d05c8cde msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 -#: 45b6d9acbfaa47e5984184f7da554d0a +#: cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 -#: 5705c9bacca5405ca6f14315a5575db8 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 -#: 82bfc285b59a439ca97d3278997f0fce +#: 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 -#: 181d5130101d45ccb22aebae3d154c2f +#: ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" #: ../../src/faq.md:410 -#: e864390b5ddb423aaa10e9d33d257dc1 +#: e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 -#: fe637c32fb15427a9045679b5da42ec5 +#: f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 -#: 1f8004b9df8547029d82e57f9abdc979 +#: 190099a242a645c9b9f8bc3ce89d920d msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 -#: 70990dc5a0034099921ceb89c89e2dcc +#: 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 -#: f679e26f18d9455f945fd13361a9c906 +#: 1901c34201054a9cae199b0dbb8b945e msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 -#: fcd0273dbdd84e728cfd8fbe239f2a01 +#: 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 -#: 173ddbd1e7c64927a8dcb12a2a2140f8 +#: d7b044f5224a48eda09bc949cf645193 msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" #: ../../src/index.md:1 -#: 662fe273e2fb4042b688512955e450a1 +#: 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 -#: a15b52205f0145feaac298510e4d678a +#: f8d6e4cd54cb42c88182a43171d97bab msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" #: ../../src/index.md:7 -#: 512aa0c7166b429e8116f71eef007f79 +#: 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 -#: b1b19e17a18540939cb3bb7f8a700cab +#: 0f47157605a34ea58770ea898deebae4 msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 -#: d58b36ac43ac44139897be752fbb1f87 +#: 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 -#: 6726cf3585a646a8b4cbeb543cf84a38 +#: ed74c9a4b623464480e2c184668fcec0 msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" #: ../../src/index.md:23 -#: 2e504aa7c46a426fa959e7254e9a84a5 +#: cfa67cf5521b414da6f7d34cbed283f7 msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 -#: e7be0df0838b432d9c7f296d777f120b +#: ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" #: ../../src/introduction/basic-concepts.md:1 -#: 173e0816db20432c8d9dba1de5393dee +#: e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" #: ../../src/introduction/basic-concepts.md:3 -#: 30eacc583f6841719e2142d283811d97 +#: ac62d326a68145b695e46b714d4e8156 msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." msgstr "" #: ../../src/introduction/basic-concepts.md:10 -#: 791b8f38a14147bbaa174c7eb595f17e +#: 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" #: ../../src/introduction/basic-concepts.md:21 -#: 1a3989dcbb9844b39d84bf6df6b352ed +#: cbe1d761da5b403d9605fa1fb8e62fdf msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." msgstr "" #: ../../src/introduction/basic-concepts.md:25 -#: db1bbc6e980f404f9f3fcd08e92ee9a3 +#: 3a71b269bd3c49eb913cf69b60373c24 msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." msgstr "" #: ../../src/introduction/basic-concepts.md:33 -#: acc7887c65974114996f700a38a7eccc +#: b171b72c48d44050a3416a7a42c4021d msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." msgstr "" #: ../../src/introduction/basic-concepts.md:37 -#: d2476d9bcff44f21b8d84a3a0d87a246 +#: b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" #: ../../src/introduction/basic-concepts.md:39 -#: f86415e4d78e48c4a8a76ced81221b98 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." msgstr "" #: ../../src/introduction/basic-concepts.md:44 -#: c5524d73708c4c779980528864506fd4 +#: c3869b4ec5ff47d99e8da79770722e04 msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." msgstr "" #: ../../src/introduction/basic-concepts.md:51 -#: ac46a9f8850a434bac5bc2b41ee6294e +#: 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 9bba7c4f783942e4a299603430601363 +#: a5ebc727fb3443f78e81d6b7ed5ac750 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: e2140e0f0e7747ef8383887c20a7945a +#: 86e6a06992dc4228bfda7add48e28ca3 msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 15bf490724cd46dcbcfab44633c5a9a2 +#: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 51d52d051e654a8395239f88df7c9d8c +#: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: eb496cc818524fa7bae5a22ddd00a19c +#: b97ba368fd664caab0494e2392795697 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c4a22d12e7f149ff901d27de32b9361d +#: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 7618de899a7043989d77baacf62eb7b2 +#: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: 6f1544a220664b79b04bf008058b5a91 +#: cf2922f645904ac7955428ecddc37b8a msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: fbd14ac9a2f541478a320ed4cbc69e13 +#: 5f47aae608c041aeb4134d59dad314d2 msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: da4dba50d25d4533b3dbb92f54d32a30 +#: f6f589481d0c4891beaccb63160619ef msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: ce11c9f8d65c4268984d0384d95144cc +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 3a201aa497e84f70855bb2251e7e3281 +#: 4ace6b92f4e04a07aa202840ebe36417 msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: b78f7fa2be1c4bb090f6da895457ad1e +#: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: f7e95d264ffa4e2db0864faccd9e5a0e +#: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 3f1e5b01e49a4dc1b1c99936a4589afc +#: 907674a4ecff4826a2b880e28fc38f33 msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 03c3048f38ae4938a484cf02001877b3 +#: 037cd0e5ceda482eaeaca03d51745aee msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: f9715b5ec65c405c849bb030c1927060 +#: e4643938445b48cc80eb8973ceeb126e msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 442662f50e9e4620970ce32b1b127969 +#: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 2b34c786af3840e88f29d214e19dc837 +#: 3eb6a013a2a4478ca2ad134661f65c58 msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: dd6aadff8cf54ce78ea6b317afbaddb0 +#: 074af9633627470485e5225326d5f20a msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: 847951c055b94a83b1e081594cef22ee msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: d10cf45b3c7f49dc98bc0e5d1246f224 +#: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 #: ../../src/introduction/quick-start.md:94 -#: ebf339ed376a4d3b89b15b4d5afe593b -#: 332b6e8b831e4bc5aed3745938230a57 -#: ce7fc63b808d4499b9bf9828c2dafe35 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 8badec9987ba40609cf1f626172b2b2d +#: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: c75a8b4bf0e24781bf6713cf6f013cd1 +#: 36eb4b3b966640af90faa55db3789cb6 msgid "The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 2ccb956baa6b4376a04ad9fcc4654631 msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 07cca9a33d8f4b77ac6ad35ca8b95655 +#: 72889b830c514afe9a7cb1e64b5666a0 msgid "The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: 31db11c8ddf2423192a8b2063b3e91c2 +#: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: d81dd96143ea444aa78ff45cfa0584b3 +#: c377a7f5dbe645cebbb6c7eccf831a0b msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." msgstr "" #: ../../src/introduction/index.md:1 -#: c54984605872472190ae7771809a20db +#: 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" #: ../../src/introduction/index.md:3 -#: 01a237b8ec2f46c9acd31d142591ce75 +#: 950370f0a36048b38e1bde9b78f80816 msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." msgstr "" #: ../../src/introduction/prerequisites.md:1 -#: 3fb9888b666945eab1e3ff109646c574 +#: f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" #: ../../src/introduction/prerequisites.md:6 -#: 5fb0486762354f93853fff209f835c08 +#: 353b14f06ee845d0a06a829643e31534 msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." msgstr "" #: ../../src/introduction/prerequisites.md:12 -#: 5f1e7a608e0b455196d191c845a5c98e +#: b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" #: ../../src/introduction/prerequisites.md:14 -#: 7ba4b5c51be24f5392949d06ee42e018 +#: ff2bb4c6504b456bac7ca9c514414dbf msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." msgstr "" #: ../../src/introduction/prerequisites.md:19 -#: e2d3e6dd13b14d819a504c35da6fe8e7 +#: cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" #: ../../src/introduction/prerequisites.md:21 -#: 91251d1f0efb4d4cb083b4517ff3107a +#: 5089fdba8aed4113983fa86e698df98b msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" msgstr "" #: ../../src/introduction/prerequisites.md:24 -#: 6ad263e267514c5fb05794d3d76d418d +#: dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" #: ../../src/introduction/prerequisites.md:25 -#: 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" #: ../../src/introduction/prerequisites.md:26 -#: 5195706d9c6c4573aff135fd539759a2 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" #: ../../src/introduction/prerequisites.md:29 -#: 9c4506915e4c40599527bc1d2b18645b +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." msgstr "" #: ../../src/introduction/prerequisites.md:35 -#: 37d9eb784ec1425786158f98e3f63890 +#: 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" #: ../../src/introduction/prerequisites.md:41 -#: 572f493a985141a1b92dafbdba92790d +#: 0f2704bf1f7148be95e999e312899f11 msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." msgstr "" #: ../../src/introduction/prerequisites.md:46 -#: 9606d3c4849f4b17b2e55a298210f055 +#: 86264c9e56104ecea9146407c379aae2 msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" msgstr "" #: ../../src/introduction/prerequisites.md:51 -#: 754fc59967d94ffa935284676d55ffed +#: 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" #: ../../src/introduction/prerequisites.md:62 -#: 2905c6362d4146e8b35bc74744841972 +#: f7aaafeee230400da056464c853582c2 msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." msgstr "" #: ../../src/introduction/prerequisites.md:65 -#: 091278ece252483a9838fb771de3e04e +#: 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:67 -#: 0928a5c668c3414a945bc9eda147892c +#: 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:73 -#: 56f3c481762848298214a88e559fc0f9 +#: 6391e08e0bde49f4b21286d8fdb97433 msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" msgstr "" #: ../../src/introduction/prerequisites.md:79 -#: 710c266ab4a5477b84d6ea987420fa20 +#: cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:84 -#: cc353db5da2546bb88a77ce1a202ff9d +#: d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" #: ../../src/introduction/prerequisites.md:86 -#: b62df08ec96f4cdb887600079856dd76 +#: 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:91 -#: 97e02557293440d1a58ba659dad21113 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" #: ../../src/introduction/prerequisites.md:93 -#: 0935c3ff01634c75b5c91546dc36c7b9 +#: 096d0a50f69e48bd9915238d1b4264c1 msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." msgstr "" #: ../../src/introduction/prerequisites.md:101 -#: cfb37fd605164a8d9cc75bf892ce97c0 +#: f9df974a8e2645a6918e67466bd1fdc2 msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" #: ../../src/introduction/prerequisites.md:104 -#: 5f06a7a6aae343d989a5b30979c600f6 +#: 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" #: ../../src/introduction/prerequisites.md:111 -#: 5f956260f3874b6dbeaf3ad7ecc09c9a +#: 746c6fc9c29d466494458a08d4c96672 msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." msgstr "" #: ../../src/introduction/prerequisites.md:115 -#: d35e4effec554a638d6c3047ef3fd05f +#: b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:120 -#: 15a1f944a0d642729d3736ed1c907074 +#: 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:125 -#: fa34c808bb494ddfa3f3926bc42e650c +#: 705807fae182425dbf4244dbf2be1226 msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" #: ../../src/introduction/prerequisites.md:129 -#: 0c15f62eb7534e809f625f3fa213e92d +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:135 -#: d67719a6f0ce4ba1bb6152a10507b729 +#: 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" #: ../../src/introduction/prerequisites.md:137 -#: 1c96e75281844bfab0578bab2e816854 +#: bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" #: ../../src/introduction/prerequisites.md:144 -#: bece1fc3c3f842b0b30d8f1b7fbfc200 +#: 695184d1b45a42f393e2da99c3721773 msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." msgstr "" #: ../../src/introduction/prerequisites.md:148 -#: a7caa36b0f83448b91ef2e76e30abc51 +#: 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" #: ../../src/introduction/prerequisites.md:154 -#: 39321e93e9994fcca20b425aa45c2894 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," msgstr "" #: ../../src/introduction/prerequisites.md:161 -#: 601cf500d76c4e0287af4429a46b36d2 +#: eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" #: ../../src/introduction/prerequisites.md:163 -#: b286d5359e184ef58054c72df4014629 +#: f6b39b12bd5c495cb53e2795bf9200ed msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" #: ../../src/introduction/prerequisites.md:167 -#: e14423edd829401faed0950772123240 +#: 2fdb62a13f9447bc89183426260ce781 msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" msgstr "" #: ../../src/introduction/prerequisites.md:171 -#: 889c44360bd54a0e85e7f0e61aa6593c +#: 1f07135156254f74a6b043bf33d00cc3 msgid "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" #: ../../src/introduction/prerequisites.md:172 -#: 7b9bff73624947ac90a99c7880e2e911 +#: de344f356b1c466d9131cdbd4d7353a3 msgid "cwl-plugin for IntelliJ - " msgstr "" #: ../../src/introduction/prerequisites.md:174 -#: c5ff687c86ef4ccaae25d8bcfbd5f873 +#: 3f9324ede11441f58d93875867034cf0 msgid "The CWL community also maintains a list of editors and viewers: " msgstr "" #: ../../src/introduction/prerequisites.md:177 -#: 0a610a9632064deb824afd0719429d3a +#: 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" #: ../../src/introduction/prerequisites.md:181 -#: ec0c47438a5242cb99dffa7a4997e95a +#: 40cfd559d6a848d1aae354d3bdaa8e9c msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." msgstr "" #: ../../src/introduction/prerequisites.md:185 -#: aae94ac2114641f186eac0f4117223eb +#: 8a9a50b0ebe847ce90593881ffe0d69c msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." msgstr "" #: ../../src/introduction/prerequisites.md:191 -#: 209e072724ed4d27b37e9bff6d55d811 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." msgstr "" #: ../../src/introduction/prerequisites.md:198 -#: 3bf47876e3694e6cadb05123326459cb +#: 9390b03889de44638141d705e0ef8322 msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." msgstr "" #: ../../src/introduction/prerequisites.md:199 -#: 459a65b8e67c4a9aaa03138c1abe94ad +#: 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" #: ../../src/introduction/quick-start.md:1 -#: 898eb29ac7714c69840b795633953a05 +#: cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" #: ../../src/introduction/quick-start.md:3 -#: 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: c43d9675ed134b78b02acb5a102a764a msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." msgstr "" #: ../../src/introduction/quick-start.md:7 -#: 32dd2e28cf0f40b6930750f0162355eb +#: 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" #: ../../src/introduction/quick-start.md:12 -#: 471c47d311074ecfac071b6d52d9cfb6 +#: cb203354977d42a58112d09357f62565 msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" msgstr "" #: ../../src/introduction/quick-start.md:16 -#: 5078140028ea4d04973cb9cd20f0607e +#: 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" #: ../../src/introduction/quick-start.md:22 -#: ab127d4ba0a44526ab129587a8160923 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." msgstr "" #: ../../src/introduction/quick-start.md:27 -#: d5cc6b4295a74f3586f022b0227759b3 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." msgstr "" #: ../../src/introduction/quick-start.md:32 -#: 585a4fe583ce44e180a062742b3b0849 +#: 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" #: ../../src/introduction/quick-start.md:34 -#: 0d81b0c9ea58420789d1d71cca32ce88 +#: f3e56aedd56b4b93bdc3894273e8c144 msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" msgstr "" #: ../../src/introduction/quick-start.md:39 -#: ea4ab0782d8049d8b1b89cea4ae60048 +#: 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "" #: ../../src/introduction/quick-start.md:47 -#: f6f3b7453a254f828bd4c9e9fef92bed +#: a81342e756d24c40acc15835d0a768f2 msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." msgstr "" #: ../../src/introduction/quick-start.md:51 -#: 3bf9050175d4444ebbbabe219412574f +#: c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" #: ../../src/introduction/quick-start.md:53 -#: e03f72a14dcf4bf38ce8232598ca761d +#: 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" msgstr "" #: ../../src/introduction/quick-start.md:57 -#: 3dcfb2facd324dccb3084c02487625dc +#: ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:62 -#: b8531da183964b02bca19f818ec076d4 +#: 0d8a788402914ebd8f09a5ca80650011 msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" msgstr "" #: ../../src/introduction/quick-start.md:65 -#: 7ba1ddebeb2843179fe99fc410b193c6 +#: 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" #: ../../src/introduction/quick-start.md:70 -#: a6dc303e9d284b60bf1102212505ca27 +#: 2ea056ab04b6419a9faf350de22a17f2 msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" msgstr "" #: ../../src/introduction/quick-start.md:74 -#: 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" #: ../../src/introduction/quick-start.md:80 -#: 6d1d6f42ada2418ba0a1de1371825b9f +#: e76bfcc0c9f84bcdb3f6d5277869a88c msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" msgstr "" #: ../../src/introduction/quick-start.md:82 -#: 1cd924fe8ace4a82ad8701f37b5e7d84 +#: d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:88 -#: aa297c52cd964291a47bb91c0135156b +#: b6d59e4b9c854abab1b3f7a0fa26f504 msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." msgstr "" #: ../../src/introduction/quick-start.md:96 -#: 28b02c90397745bfbacc03c3b1034939 +#: 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" #: ../../src/introduction/quick-start.md:97 -#: ef2a4f39f01049b891868b84d968c0dd +#: 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" #: ../../src/introduction/quick-start.md:98 -#: 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: 7282abfa7155497ca47c30f9abfb6474 msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." msgstr "" #: ../../src/introduction/quick-start.md:99 -#: 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: 176d8d47830f4031bb95dc231ebf1303 msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" #: ../../src/introduction/quick-start.md:100 -#: 46f6f8d050ce4f8c897056167d9707a7 +#: 82a7ca3703bc4f0daa18942a1ac8943b msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" #: ../../src/introduction/quick-start.md:101 -#: 5ee00ee409b746dc951ca1d4c360e624 +#: d039a9d6461c44628d4660c00d9ce6ff msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." msgstr "" #: ../../src/introduction/quick-start.md:102 -#: d4af972281174b8999eab55ee0ab1a0e +#: fbc3383d9e1c4eaca7931c3cc4f1752b msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" #: ../../src/setup.md:9 -#: 80401cfffae042ab9ec4b3754af04b25 +#: 1330bd38c4b5495f890b98c669f81a9d msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 32f86f911ebe4a4c94975f81742333f3 +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: c53ceee943ad4acea779e072b9137889 +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 7dfe9dffbf5744299bf232599644c7f6 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 -#: 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 1f3c23a4769043ca985b8ddfed19391d +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: f81b43c7cb194a1cad8672129223c833 +#: 9643449da1da46d7861866dce490cbcb msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: a20073a8f5374eb1bc8531ff33e622b6 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d08869beca3a4774baf1097b63e79474 +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 -#: 109b773789024b2b9c063a6169c6169f +#: 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 -#: 959fa04f88e54d42b9b774cc95d85ee0 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 -#: 64674980c3f24c45bbfbf3f957dda55e +#: 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 -#: 90f2e4265919446a902e17627f4420e2 +#: 4dee8504a8e5496081dadc386ab45540 msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 -#: 6b5f91a749fd44b5acfd6071c9913342 +#: 674c238b25e240eda05e22e399f2f78f msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 -#: 5fe2962837b14f0e9989063be4a506c3 +#: b651f80f47b4442fbf29454a233697fc msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 -#: 4e1bdea962ed4618884cb9d1d59d7509 +#: 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 -#: 37eff4ca02e843259f6ffa38e4a87a04 +#: 3a87a0fb2a364e3da5aaa4017e430b19 msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 -#: ae47231c203d40a98c10045038ea9b65 +#: ecf2b9c0b1664afe9c4e180610610021 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 -#: 018a6d5dbf1044559b365c7b9017eb3f +#: e24cb13d98014e558b6a6946758359e0 msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 -#: e073d8f990c44b09a73d642cfe49bebd +#: f2b14a92374e449d9fb1e8c86ae0dd61 msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 -#: e04fae88d9b64493ac69eaee24585098 +#: 928e3df7ca3e479ca6474a8e72cf36eb msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" #: ../../src/topics/best-practices.md:55 -#: b26b9c9b1c4346a297a31c9721f0172a +#: d355f035676446c88b028f327aeb4829 msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 -#: b50500c3c3f54b16a535a16175a44653 +#: 339b852df24242189d6efcd2898a3396 msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 -#: 623f3a804199449bb85e23e00c8bb507 +#: 3ef57e6862f240bebcf193a52397af0a msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." msgstr "" #: ../../src/topics/best-practices.md:69 -#: effea0b1356447c0899ca0746667ea31 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 -#: 00e8ef87864c4ca2b2c1c0548b02b38d +#: 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "Custom types should be defined with one external YAML per type definition for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 -#: 6e6f48d70b894a6c959ca30fe6bad772 +#: c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 -#: 02fe08760a4a4ab49e96f4e51316a81d +#: fae385da16aa443da996fa23ac03d6ae msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." msgstr "" #: ../../src/topics/best-practices.md:82 -#: 172ed7915a654964ba63f860b2d65330 +#: 92430be71ecc40e18bbbb80d5576c613 msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." msgstr "" #: ../../src/topics/best-practices.md:85 -#: 4d0a2871a7484e21b3c39c4dbaaa63fc +#: 387d83db81024f65aa9a890c2d07874a msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 -#: 1eea9f1e284447718141f5417b6bb433 +#: d8e2280a75a74916a1630afaa2fe2ae3 msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 -#: 509411d353fe4314b087b81b09ea960b +#: f1c1340f9745458980e0fbd641738687 msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 -#: a54bc80bf08243bba67d98dd682ee134 +#: 5424e5472c3d466fa2a3d2022c6cb475 msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 -#: 69ecdaea24ef42eebef9d86e5d716b11 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 -#: 3cc5847468d1478bb5589dee68147189 +#: 12f57b2ba76b492abe1816e06bfb1417 msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 -#: 98c6bc409420485095ae65d6b0b9a3a0 +#: e1f657a46ce94a0d83671540e2cc2dab msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 -#: ebe23e5378514f888a9ec32a2adb1e98 +#: abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 -#: 387cfe85604f424f8d31c4a4c9c15edb +#: 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 -#: 7b1d65754e854693bb60289c97d3fb5d +#: a5eacdbc9aa142c890b177869da4143d msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 -#: f440cef729c8410281432307a4da8d55 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 -#: 4fbb8ceb1b59480583ac611142167049 +#: e3bdaceae8784ab0807b2cf356a98580 msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 -#: b87869204838415bbf694214e3680593 +#: ed521ac365db4a6ba5a1051fbaa2932e msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 12cf5f2264504c44a2173e858bb2c283 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 7694f9cabfe04308bbddd2c88ae6d9b9 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: b557dc4f8ef549b98f59412a918643de +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 3011eb003c084285b30cfa56a8da45b6 +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: ce78b2d147054da895beba66d0ecdab4 +#: 9454a330b9324744b89448f2694b1b03 msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a973846ec5a946eeaff02c5b00997da9 +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "To test the above CWL tool, use this job to provide the input value `message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 #: ../../src/topics/outputs.md:77 -#: ccec7f73b9d948e79a6cdf32bc124092 -#: 9e8eb1542db640ff9e300649ce50dc9d -#: 294fd83a97a64249bac38f7482159372 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 22948f19cb78485f8f86244686a35c09 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 001d9579bfce438e865377fb9c2df776 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: e62618db8995428bb3f260e03ac8f459 +#: 1741804e33aa43ce88b4320c11ae5973 msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." msgstr "" @@ -1291,193 +1291,193 @@ msgstr "" #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 #: ../../src/topics/workflows.md:198 -#: 98e0548845fa447fb05a29c9fc2f17b5 -#: e9801b2142cd45368a73ef9b121c1d08 -#: 457756c4e9544f068af897113358cc89 -#: de5e8aad4e3046bf9bfc2ad8ccba17d0 -#: 6d5ae75431424ea788c3440606f22940 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/custom-types.md:1 -#: ee2bca9bdbb74b60a706c3118d6a17ba +#: cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 -#: e63ae9694f40438d872d141ae824a42d +#: 67573252cc064b27ab13eebc468ac58a msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 -#: 750fdd4c270e46a09f79e867358f7414 +#: 73e68b3af9cf41338d843c0c40e50cdc msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 -#: b3f688cc82444ef7a7a0aa63dac39cac +#: ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 -#: 3638be18b4f64cf08053d512e590dda3 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 -#: 7d5b9c21739c48f18c13614ca6967f6b +#: a999b1acda2641598086648c64aa3831 msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 -#: 8fea29993f944d8d8d3181afa29bd0a6 +#: f8c12a58cb0b46a488823c6ae95f25ea msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 -#: 02d0b648d70f49d7892f690be06df585 +#: f25a63e0926d4932bbe64b2e4bdabf9e msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 -#: 0743bef42b9a42328849c8c2f9da9eed +#: b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 -#: 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 -#: be848f30769543eb9c0be55263e3f758 +#: d718630a296545f3a989c8c71e9ddc77 msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 -#: cbff44a64ba4432cb59a82f82c2f0103 +#: 9a97acd430064710bcdf76edbd9f711c msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 -#: 617f1c0084cf42d9be4c7a8fa5a48432 +#: 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 -#: cee79afa3c6f43c29ef05e06b7843d35 +#: 3c821c9c46d841ec89b8a5b1018f3af8 msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 -#: 225903b11efa417989df42de86ad2451 +#: bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 -#: 1a5f058290064c1cad05e63eb127fcbb +#: 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 -#: 74ad8d69cf294ae880dbbe28e25b3545 +#: 48deb71f361a43e48a56ed483075bca8 msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 -#: 5293e8ee9b3b4f59947cfc164ef111c4 +#: 716b56506ca7470299899c5d820a9ea2 msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 -#: ffa1955c759942c68e7589429e5ea86b +#: b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 -#: 038bc0ba5f6a405a8255a7be76979baf +#: 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 -#: fae1c63de02e48c0969a98e4c49b2e06 +#: e3ecac0a8e604f2b98a2a12b0579990a msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 -#: 7093a94695524851a5463193f0701b78 +#: c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 -#: dc8274ecb15948c29a31db89b12a58bd +#: 007a345b4bad49cf996c4301b8386473 msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 -#: cec8eef8a5aa49778ecedd4195ab9f2c +#: 2edbd398eadb458b8eacd5fa5496f0a2 msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 -#: df100967597043c78112bf43b520cfab +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 -#: 59ccf4daba39406581a6bc2d9bb1b7d2 +#: efb5fd14988c4e2a8f834ee5369d4102 msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 -#: 570cc75699dd4e0a987fc9aca9a01ee4 +#: e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 -#: 9e123723048546d495ed5110d7177708 +#: 276f688ba7cc471a842f085ca852b1d9 msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 -#: 26543894f6e04270b89ab702451bcc89 +#: ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 -#: f403c1d4e43a4aa0aef8488d2b5a6262 +#: 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 -#: 249dffb569a944c897ce5862e5f28fad +#: 8b70a1ad70514039b97164fa630c12e4 msgid "Note that requirements can be provided with the map syntax, as in the example above:" msgstr "" #: ../../src/topics/expressions.md:54 -#: 1641c96aca2f4923885fe8a509eb3a49 +#: 2f28ab412d2843ffa5f14acdc01fc732 msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 -#: bc63405a0d964df2bd9493996abc48fe +#: d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 -#: 5c191d1420db4e26aca31c1b1e34cb75 +#: cbec9277b5004e50af2728cbda0df740 msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 -#: d6a5c65e824a4bbc94578df9597d4716 +#: e259f55f8000479bbd8009e25cf0ca6c msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 -#: a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 msgid "`arguments`" msgstr "" @@ -1487,38 +1487,38 @@ msgstr "" #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 #: ../../src/topics/parameter-references.md:86 -#: 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba -#: 2a2286a9c8494e3b88db35bf63230f33 -#: e7f1993580f0425098a719e83a64cc7f -#: 05c34a5a2e404a14b9d284a9d0c73bd3 -#: e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 -#: 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 -#: 92697d3179ec48898eaea9aba3c24dcd -#: 3f29e4a3087847e9af6f19166a8def9a +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 -#: d6722e3093884ad7b62696fbb2f48fdc -#: c0eaef93bc3743279549bcfb8b014ca3 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 -#: 37c493fdc2f0410a9748f8faf09ce5b5 +#: 8210b36347a749889450529ecdf4ff0e msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" @@ -1530,14 +1530,14 @@ msgstr "" #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 #: ../../src/topics/parameter-references.md:90 -#: 9cfb6ca1255241aa9e5928ea981286e9 -#: 4ff7326e660f42d8b45c3353005554f8 -#: 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 -#: 6020618711d449a48618c11215453487 -#: c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c -#: 7b132c6e720f4256859757778f5c4fef +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -1549,1574 +1549,1574 @@ msgstr "" #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 #: ../../src/topics/parameter-references.md:91 -#: e193aebe7124444c90be1f6cad81482a -#: 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d -#: a44c278bde5849aeac122c981294332c -#: 6dfc264200a9496f9d2458fc759993d8 -#: f71216a4b35e4157aece5ffa2602d8bf -#: 662b36e3505f4ac3bb5070bb6e055217 -#: ee3d416cc68c4f11a79849bb67395f1b +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 -#: a3c775a0f04b4541a9b712bfe2e4e69a +#: 23088850ad02459696f6bbd385109aac msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 -#: ef16c4a9a7ea415fa399297b63b9710c +#: f02257a822ad46ac93c5981531cc85d5 msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 -#: 2592e429c74c4ff5b8ba68a36f060c1a +#: 989a1c4aaa1143be9f53b90cd8b6d500 msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 -#: 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 -#: 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 -#: 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 -#: f09e7371708b4c0685eef2a314791ccd +#: d289541e460147aa933f7878996f8649 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 -#: aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 -#: 6c37a1ff939748bf83a86c07c3d017fe +#: 81b4d1f23a3642bfa9bb395b94260cd1 msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 -#: 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 -#: 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 -#: 58a1773b1cf546d7890010fdebd47388 +#: f495da32f05a4a5ba9539be0a54c1a59 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 -#: 230f3227ed1144f7abe0f8c231bebbd5 +#: bdb4c68a175047ddbe141ca24960127f msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 -#: c9534670f5f04769aa3749c3778eb705 -#: 5c77dc9f8afe4dd88933943030e836f2 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 -#: 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 -#: aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 -#: fe3b9fb45e01490498c5a35c012b3de8 -#: 266dfb5fe6a842078baf66073cac9623 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 -#: 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 -#: 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 -#: fec70bb106ad4d95a2d55ebdcf711afc -#: 09120baec1464afb8aed4edd773bf509 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: c98db5b115ee4c4abb211481fe7214b0 -#: 2e128858cd06466680fc6bbfb577b818 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 -#: 1dc4148caef748428a7d13caff37b1b1 +#: 97b61352363f47cb890e8937c5613fa3 msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 8caf296626024598b4450311ade09e56 -#: 568406e34c8642578396177b40043014 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 -#: 947b1ca132a54ed39745cd12ebcd65e1 +#: 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3af8e4ce750048e6b9de12d26b9647a6 -#: f56fb5fa08994fe08cc8ae8c193828d9 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: c6dbe0a66b9f47e5b4b47c44d9f54519 -#: 063e2ae9a0eb404e8c277ef7090eb6bc +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 72acfeef964841e7b65937b62b5850f0 -#: 39c6edc2866542cfa7da9f842fd3edd0 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 -#: 5fa512d352d945e7a3e0d59b0987cd1b +#: 0bc424ef2ca346099f29b937379908a0 msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 79755be159fb45b0ad06cecce623ce2c -#: 520bf799546b4700a4f38f950ffd913b +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 -#: 81e91df082834d2cab7ef1f62d8ba57a +#: 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 -#: e6bfd1dc2e324992b6c3332c11ae3445 +#: 29b73e1dd72744f68377f0a38c10f062 msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 -#: acf10261df2944ec890d754fd56c6b28 +#: 38a2afaf4a6c4d04909af22c93f2808d msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 -#: bda6b8f398554b0c946c2c7d96308a42 +#: cd74f34b21af4de9be96fd897efc469b msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 -#: 454c02c3918647039c90ae387005dea6 +#: f12e371f3f1a4b0cb2cff9800352d48c msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 -#: e1fad28bf9cb4c4c85eb74dd520ba107 +#: 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 -#: 9835d0b399b84a0084fe5a4d9e7e6405 +#: 8f0e8f050e334ac08334e9215e1dcf61 msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 -#: 410ba7a5ac6349a98460c6337ee5c4fb +#: 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 -#: d2daf50d7f3d4de18331c8fd2c8a5786 +#: 7a6be0005a6441feb67f036d005d7885 msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 -#: 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 -#: f0ff919ffc12439d89d7b40f51ade84c +#: 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 -#: 307a17a893fc4dafaec2a63a95704644 +#: 06635145b441418aaae84dc804f3d6ac msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 -#: 7f393e86b114470f8dda47b2deec63aa +#: 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 -#: c3f459b87b96435583637b3f1573e658 +#: 04eaf1f7c630450db318dcd8b7626e15 msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 -#: 9f676022eb2744839ca2109920250cb6 +#: c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 -#: ede7285f77864fb0aee6cfecc2c97fa0 +#: 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 -#: c55fb184bc614ee2b6e5e64611e5df9b +#: fd4579a3c9844492b314b5c3c1775fc7 msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 -#: 66b522f46ce242149386e79f63b32cf8 +#: 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 -#: 64a20285785d48ca86227a0cf6353ad4 +#: e024bcb70e04412e90e1838426d1b69a msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 -#: 5f71bbe2c74e4260b79d4d9230d35397 +#: a3db21c0b3114802a8a5b610e252ef13 msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 -#: 63bfff437e3348428f7e33ece7ec55e7 +#: 0f5bc8520d6a4dafa37c65343da9702a msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 -#: 6ce83d9c06e4436881aa47d94ef41e0b +#: 5cb830da47464a8b9c3950983fa4d56f msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 -#: 55006c594abf4e70a38e979568fadcf4 +#: 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 12ba2083a9ae4c78bf502ab762a29c7d -#: 5c8f1709fe61423bba3ceaca2fc7cf09 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 -#: 1a1905ff2d624eca952c8a53b3bee678 +#: 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 -#: 368ff92476b14f5c8331260eafc5acb5 +#: a2ce43b391864e8bbde16328cc19b32b msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 -#: 5d530afa23f349a79f54d51d40724747 +#: aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 -#: 16f965f86712483aa7f95dfa3f944a17 +#: 56ee4dcfff6141d5bef80eb96559876d msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 -#: dc629e2c90ed458b96107a6994676434 +#: 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 -#: cf2f077cf8044079a7005e6e508dcd8c +#: 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 -#: 129e1d2a71894d28b009f4846754a75d +#: d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 -#: d6791bbe575042b9a7282c69407dd907 +#: 96671c56523c4ea9992fb5dfcfa6490e msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 -#: e8da87f8bb664334adf831995601f462 +#: bcc6246742cb46bfb185e415c4a3431a msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 -#: de6c322618304207b6d1364d1ec2dc13 +#: 86dce36de687449c88fb5eb9d64eb045 msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 -#: 43bdcf6dc1b14030bff27fa53289c02c +#: cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 -#: 056510b42ea64717996ab49c307bda86 +#: 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 -#: 6852f5dbd9094c99bb68f2a88f76c9bc +#: c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 -#: f33b6800367248b7927d97ad7b4be5b5 +#: dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 -#: 8ad812d7e88f4cbba83228ffb1711576 +#: 36ab1d9edafc4831bb1bca5f123b04b0 msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 -#: cc680bbf091a46f8b4b3dbe6324c040a +#: 7dc630ea86464b1dba3a4e5079260b3b msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." msgstr "" #: ../../src/topics/inputs.md:44 -#: 446ac81f078d46289a18f494748f482c +#: ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 -#: 3d6d958d111943f3a2139b4dbb7810db +#: 651e032007ea4a119d20c820bb61f86b msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." msgstr "" #: ../../src/topics/inputs.md:53 -#: ba0ec9157709430c822f4e91459288e2 +#: 0b056dde9e87428996e47870b12119da msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" msgstr "" #: ../../src/topics/inputs.md:64 -#: 2565f8fd4a15429e887aeb71eacdff1e +#: 628124a1670b4b058bb0fb6e495a099c msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" msgstr "" #: ../../src/topics/inputs.md:70 -#: 659ed5c64fb546399b741553a347b8e8 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 -#: 3d87e69d41374fbab23b26d36c1aee03 +#: ec2adb3912bc46e28891229e9e0d9a1c msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 -#: 07bc81683e2c4ac68b379462bae95207 +#: a519be60726a44af9941fdce04735353 msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." msgstr "" #: ../../src/topics/inputs.md:109 -#: 3e304da2150f448d9e39715ac5f5deaa +#: cb8fc8c4c79e467eac5fab4ca685201e msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 -#: fd8a98686e3c4c609f79ae427f1558d3 +#: a26cc105716f47cb807174c9003153b0 msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 -#: f1a2e1bbb1104a4fab5a7f04cac845c7 +#: cc159dd5fe5748caac838862f5b8c4d1 msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 -#: 6a7f0ccd227e4f90a8c8ca96744bda68 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." msgstr "" #: ../../src/topics/inputs.md:142 -#: 1f79d115d8a145189638c68c3095396c +#: 6812698e9ad84d3385de5e88e9dde0b3 msgid "The `baseCommand` field will always appear in the final command line before the parameters." msgstr "" #: ../../src/topics/inputs.md:146 -#: 6e1b3e2d90184e34925891099d2b5cc1 +#: 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 -#: 4f6df7f13e42448eb4a53f03bc477b56 +#: d1f02be278754267893dfce5a940997d msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 -#: dbc0b52627514ad0908969d0b4ddfdf4 +#: 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 -#: f173dd96ad124470a53573c86a8df203 +#: 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 #: ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 -#: e0098a77080d4349b05ceb7735a5fdf5 -#: af25945b530048b685891b1de4e35e72 -#: cb07caa4ff0149b3ae832be53f8d76f6 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/inputs.md:178 -#: 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: 75d59e395c66416cae9b352db5081516 msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 -#: 4459819ba75647d185986a3386939494 +#: 874c6f19abbf45d7ab7d30a378c4048d msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 -#: 8f163bd34ded4785b6e28c8e2147e0dd +#: 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 -#: 1799e11a7b9c4929a3d1379d7ea45d03 +#: dea0d4b681f94e73b13965dcfe75cf7d msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 -#: 9510c0b431a44b5e84e0b583de7c5446 +#: ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 -#: efb4eb6f5e994b50a52fa2c707dad1ce +#: d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 -#: 34599c6f10ce4104be2359a1b37f91cb +#: 750474486a84482292eeba45f118287f msgid "In the first example, you can't provide `itemA` without also providing `itemB`." msgstr "" #: ../../src/topics/inputs.md:217 -#: 0663ea7918994d3f9c45c652a3ed12db +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 -#: a98dda6ca4b14edba467de638bba28fc +#: 1eb0e39bb6d04b8cab300f44a79f3add msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 -#: 10d0e9f8df8c47788703073b17529bc8 +#: bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 -#: 9a0e1a130fba4d24a9168ca3e455cd23 +#: 4b2ab812f62c4f949dd25c8527f2411c msgid "In the third example, only `itemD` is provided, so it appears on the command line." msgstr "" #: ../../src/topics/inputs.md:255 -#: 992a8c801ceb4233acf56b6bff315188 +#: b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 -#: 9027d23fa7074b789c3b86ca5ea17fa4 +#: 2c3b884cb1c54521900cc90782e8a58d msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 -#: 68b47710a8ea4b978428b42c627944e9 +#: a1073b6306044dffb414319ae01f68bb msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." msgstr "" #: ../../src/topics/inputs.md:265 -#: d33e4cac65d14111a89c838c4d1759b9 +#: 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 -#: 24cea1cf7d774b6ab56959f289cab39d +#: 9a1d92334685449386dfa3b3a899ed48 msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 -#: b866867d6f8e4d3999b62a85e6884ebc +#: fb623af4c480411b8fde28d01c981411 msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 -#: 80c49ed168b14d25b2f09b3b0186b44f +#: e98e165f6bba40809c90473d72f9d592 msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 71628ebe908b4cd28dd1fa17e3d2e2fb +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: f123ca244c23413c91405a4b84887525 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 23299ae1bec94b00a32a8af7eeac350f +#: 80af387fe3ff4e2da999903385bd602b msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 2495a9f2032a47c188338cb81ba429eb +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 3fd2f3cf7bdf44089df2ce3122534801 +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: d5a5b8b490b640439db92da949266e4e +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 5935ed94331d4b2f8ce597f31edea843 +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 -#: 5feb559552194ba58da7206c601292fe +#: 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 -#: b7124ba4df9042baadc1641ee09545d6 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." msgstr "" #: ../../src/topics/operations.md:7 -#: d34b698c62114041a64e0abce25ca935 +#: 5565c1b2d8a349169a305a9b26b4574d msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 -#: cba2c31262bd450cbafc7ca77f4fb8fa +#: 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 -#: b01be5f632104096b5af6193aab34d90 +#: 88160cef4cfa4add9020aa89511a5749 msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 -#: 60a6a02c1367403db6df3ec10f75eb69 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 -#: 314ea7bc35154f41b2af5fa6683ca389 +#: 730ba1434a1445ae847ec6153b6a3b72 msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 -#: d81e679b13474f74bc5e1ce1e31c2bc6 +#: 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 -#: d7fb27131ee44bfc82f698ee44b2bae0 +#: a25d0b1e13324b40a6b8fcd227948c4f msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 -#: b8ef11eafd1d46e088f1277f4ac372bc +#: da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 -#: d2382ed1f644459594655d5b5b4d838a +#: 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 -#: 6651632d977b44479b721174fffeda2d +#: d661df070e3040869da412d07a71f716 msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/outputs.md:10 -#: bee5f532554241088764ac9e56abbe85 +#: a11585474d3849cca5467512ed964743 msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 -#: 0c7c506f38be421399073871f64e99b0 +#: 2682f9ca8e604a0c9986f7746fdec960 msgid "The following example demonstrates how to return a file that has been extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 -#: 8b60286e56cc42a8ab5f751a97adf771 +#: 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 -#: fa0ad674f15348339a1eee771a6ba9e2 +#: 22447a560f6f4317bf67bd7c4336126c msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" msgstr "" #: ../../src/topics/outputs.md:26 -#: 177b5f1b95a34fb9b2eb42f733d79ac8 +#: f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 -#: a08a6d8aca8e490482e127a8fd5e650e +#: ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 -#: c2c60f68b1e045f88844076e191fda9b +#: dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 -#: 6d939f62526e4e6d95acb57d72f60a84 +#: 52703d6b7f914097934bfad13663abeb msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/outputs.md:51 -#: c48edd9034364b81ad42540a98b51d91 +#: 5e1c79df657d4a6e84e055dd6b300a5d msgid "The field `outputBinding` describes how to set the value of each output parameter." msgstr "" #: ../../src/topics/outputs.md:62 -#: 9ebe0186a7124dfaa30e558e8f59653a +#: 329d2809dfae4f90bc638f5f03a47ee3 msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 -#: 9381b7d7c9904df0a5e16dac29c2e08f +#: 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 -#: 2aa9c6916e3546b7b92fa64bb83275d1 +#: c6bcf7c6a8774dd6be41cc775848c3b8 msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 -#: 63afb7a597fc4e459b6a7dbd40bbf6ff +#: 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 -#: 7418915470f041c9af5bd39ea652de36 +#: 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 -#: f82db001b58c4969b2d8bc1dcbd7cf8a +#: 9647019d8c37466886e7aab6f176634d msgid "You can also capture multiple output files into an array of files using `glob`." msgstr "" #: ../../src/topics/outputs.md:93 -#: 26d9f0b28d384617a8e490c1f8e26e52 +#: b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 -#: cf46c971b31b4e10bf0fefb4cd028c2f +#: cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 -#: a4347983fb9945a4a2773af88e426dc9 +#: cc067051f22f433bbece08f60933e002 msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 -#: c5489e0633114372b273098ee2c9ffd9 +#: a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 -#: 75de9fd63393429daf1ca10a85339aa7 +#: dbfe2c1123144316aa026374b0f353d3 msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 -#: 8b5d0ada32d645be9359f43a431f5f91 +#: 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 -#: 2ed93dc8778e44209194f41b9ad193d5 +#: 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 -#: a80dd6d9920540e9880514e04035af86 +#: 074cf5d912854d8c864607cc24b15302 msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 -#: 9de300f7b9da49f59d1c9fd96dec4a8b +#: 0290af3e3cbb4b32b0450c8771f3bf95 msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 -#: a61f52d3c1024c3692899e05fcea4bee +#: b54240bb94f746bba7511633aa969db0 msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 -#: dafc9ba578c14fd79d075160e6b7bd6b +#: 8b70a072aa87414c88e89a3e19af0a51 msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 -#: 28ca6cae42904559bcec98fb9d2b07cb +#: eea20f89c45f424a888178df53713b28 msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 -#: 616c9ff9fcae489285f0bbbc67f07d29 +#: cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 -#: ac17acd83ddb43dc9fb7a5e595ab1153 +#: 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 -#: 156573324cde41ee8b3c47deabf43db8 +#: 7647e0229a924f988cf02b7812a55c06 msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 -#: c9725be01e8a401fb3ad9ff01339f81e +#: 9d663249666045618a0d3acddb85a9a9 msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 -#: 6797335256e2412cbbe7636507931455 +#: 5fed4984f6784347b4cbe0630b1dd2c2 msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 -#: 05a5f0fcb7454cb697e3d810d55fac26 +#: dbf6153cd02542a6a01c172803122b7f msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 -#: 406e68280b5c4ee494632f94b635b7ad +#: b6250cf6fa8a4a0c94b33302e0decca5 msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 -#: 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: fa6ca3bbc6784380a03a950a6f49a180 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 -#: e71a974b29624210a107fc2d097d4196 +#: b92b516e537a4773ad67b4af586e7a25 msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 -#: b59df98754e24654bfef0b1fe1d91660 +#: 467a701228504d06b971b79a59c69064 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 -#: d2bccbff1ce646348fe38c776ad183e1 +#: 2634f989eb304009a8568d70ed42786c msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 943ba46512ce48fe8c5b62327734c503 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: bbcd43d5af7d44108aeb65075a6bd2be +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 834295755af841a78e466eea43864861 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a6b626489bfa468e8f059ab3aa669201 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: e1dbea105aa845c38cb1f90b43847271 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: e9640f47d40e45bca184eb30700df648 +#: 574d93d1d592458a985f259519c036cb msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 0456efb3718b4356ad2b277ee16de967 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "In this example, the software requirement being described is InterProScan version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f7e97f926505407f8f8e9a427e055e43 +#: 02e40154eac74ecc98d0447d03475b44 msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: ec597ff8f6ee47bc815b069335869f1f +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 -#: 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 -#: 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 -#: a03372581fa44f9b8e3e088a4099cdd9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 -#: 36e082be73464be0ad5d0b681cc510da +#: 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 -#: 4464455b51ad4873ac13c4a63ee5fb54 +#: fbe0c65b444441f785d0054176d036a6 msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 -#: ed7ff0753d1743a995f4cfedd6e5dcc2 +#: 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 -#: 4c2dd10dd66446058477a52fb8d2c602 +#: 9a710602e00c4934ae3a3b471aa68458 msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 -#: 978b6a5fd5fa425fa9a18d9f0e8788da +#: 21b5be7270a14f0987240c81d1ec879b msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 -#: 000c0d6ae8bf414d9293b9f13fd2e448 +#: 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 -#: 7e91b8811be14f8e80df39ac4c5bd316 +#: cfe9d8241fe84bd5b74042a5625d933f msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 -#: d42799cc5bd4484bb6beb309a61e103e +#: 764d933cc4da446abd8dd8f913f05dac msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 -#: 48bb0f6666ac48648c7d969608b3bd48 +#: c93efc6d4e004859981ee7f5fa28ed03 msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 -#: f8876044db184cbaaca56579d0c773df +#: 546601da44cb49bd9611b1c85807fd90 msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 -#: a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 -#: 4c240a18c4e6441189489011242c1efd +#: eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 -#: e37e76ef376a4ee695e600998906ec1c +#: 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 -#: 51a307b0ba7c4c1d89309ba8d2250471 +#: e07f33d01b804663a25ffb08aad74821 msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." msgstr "" #: ../../src/topics/using-containers.md:15 -#: 13cc38d72d34468fa4eb6d91f23ff105 +#: 7a644506619a4f08958ec7d4540cd557 msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 -#: 42a48398d3ef4b03bd7395120f2cfb42 +#: b5195b7d8eaa419fb2b90cb33a57783a msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 -#: d59387b433bc4ecfaf7e72026624db02 +#: 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 -#: d963418ccc0b4803bbc758d718ccb5aa +#: 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 -#: a224d1510c9e46aab23d8bdc03c349dd +#: 2713594c937d4c528fc8d04d9e9819ed msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 -#: 0a82f8a45b0546aaac4c976dcc98014a +#: cf94c1424fc2413c85647fd1ee73d951 msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 -#: bc418a2a535e49359c4cd44b373bbe02 +#: dc0452107c604e29bdf32bb289fe5db8 msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 -#: a799fba2322944cea00e413c08066536 +#: 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 -#: 35379c6b972940bd8451f10b74dd793e +#: 483181f498fc4d968b5fe6ef427709f7 msgid "Notice the CWL runner has constructed a Docker command line to run the script." msgstr "" #: ../../src/topics/using-containers.md:72 -#: 2d5265525ad544a0b64ad2cf07aacc26 +#: 7487485d6aa4458089a4b4bdf107ea64 msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 -#: e2521b89596d42f8a87a3207fd6c32f2 +#: 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 -#: 3676f23b63e142cb8e5715ae07216a47 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" #: ../../src/topics/workflows.md:13 -#: 00725aed13a440ca8b3c4f9155fbee99 +#: f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 -#: 2e38a4f9072b4ad9bbb74f943d22084d +#: 5870ac44e4c24b8daf5f06c49f95ce04 msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 -#: 2b9f4035ea864b6db50c861a1819289d +#: a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 -#: 28e9064780e7418a8e02a22f92e34404 +#: 93188ed43ee949cc98b3ea679ce14feb msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 -#: 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 -#: 8dc00528c3d2426c8a3492a8191f1d81 +#: 1cc17ad26e9c474b895ba5cd20c8b66a msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 -#: f9ef5e258f7c4971a8543d1dfed711a8 +#: 24aca0bea4d94e3593b844cf0586cffe msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 -#: 324bc51071d743ea80124c23880ddc0a +#: 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 -#: d8c13e01976b43a1af34c11a7bc36897 +#: 9c56528acd5f49deb139e034dfbfac7c msgid "This workflow extracts a java source file from a tar file and then compiles it." msgstr "" #: ../../src/topics/workflows.md:170 -#: 43910a8ab4484e529a17df418b1aedbb +#: 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 #: ../../src/topics/workflows.md:180 -#: eab3ac7490f24645bbf0babb20aa9df0 -#: 56917e39cfa34470a7a88b52b1f955d9 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 -#: 7ad12d67e815400c94080804b9285629 +#: a2dd833fdca4443181648e41051a5232 msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 -#: 457d5a31c79143acae2683d95d27f7a3 +#: 7e40cc9f9e1341c195e843c009575b94 msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" msgstr "" #: ../../src/topics/workflows.md:185 -#: a2a73901bf634547900d08b9a1ac8889 +#: 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 -#: f347d80e62384b14acf6423675e5359a +#: 6fcf8ad3d1bd49afa4a105622437bd59 msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 -#: 2a845a4f3f98428fb82f3ca7ce038a6e +#: 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 -#: e2007c74d5f449a882809d6b91c010bf +#: def35d6021394def80a53ae49a2cdbde msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 -#: 7f5e53ee7cf94be2bff45ef64db28a24 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 -#: a0d076b7b8b048478580c99ef0c8429f +#: c84d4450bc6a475dbf34e0b22cea9130 msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 -#: 7fd926c18ad548e98845e9b5134dd6f2 +#: cca9665f6daa44b49233baf34ab9fcc7 msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." msgstr "" #: ../../src/topics/workflows.md:256 -#: 789fbd47f8564cceb430ef3c0bc90e9b +#: 547edbf5fa424b8286cc21674ff159b0 msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 -#: 45c4d0492d6143ca9cebe81e9b2cf3ae +#: 7ca248888b9d484cb544cd76ba538662 msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 -#: 73bd3da2af8545928d5ea71d0f7454f6 +#: ae6b240718104380b08db5552d7355ea msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 -#: 15ce3d2700424f0fbb280d602ccebcf6 +#: e5a8b7f84be64020b191099f3fad30ed msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 -#: af4268f19202436eb0a7e8c6bed5e386 +#: f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 -#: 94a4eadca6b949d79de2990a0150eee8 +#: 12a06d8358534102b202965d4258c18e msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 -#: 09c1619e8cbd4febbb637f7e99ad5890 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" msgstr "" #: ../../src/topics/workflows.md:300 -#: 677ea7a27eb64568ab3689142d6efe70 +#: 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 -#: 097e6d47f9394e62b80110700492783a +#: b7f93705e5b8416696be01850072e8c0 msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 -#: e93affce8c104bf6977182047c1f1077 +#: e87045829b344089ab59dc27063ddd7a msgid "\"Visualization \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 -#: 06c9e04ba890473b851240a0fa9c3b12 +#: 42ef2f145b824d69b63abc1da175c216 msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 -#: 0380dc1fe3aa48e4b62283b7b2a611d8 +#: c61cedf543664d388183e04b3939cc39 msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." msgstr "" #: ../../src/topics/workflows.md:341 -#: 49b251f7a313492ea60504b00109e526 +#: 9e39e3f1501c4fcaab3e8962e090f6be msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 -#: 7ee55702d7dd4679a24ff052f6f0cbeb +#: 03e2f767c4da461982fc3c0f3ba94762 msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" #: ../../src/topics/workflows.md:366 -#: 85d7e2e270874aa6b9f477cec0f48154 +#: 3bea5822b8694e2aa32c446e1c54a045 msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 -#: 570e94513c984c09ad6aa255f534216d +#: 426023bd6e3a471cbb30dbda3d6f9e57 msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 -#: a107258662fb4bd4a9a3d8754e34d1e9 +#: 0d498cd4caf54c15891ca1afe58e2727 msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 -#: fc1a6502d831458ab8371a575cea47e2 +#: b2d75045e02741b4850f5ff1243f7858 msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." msgstr "" #: ../../src/topics/workflows.md:398 -#: 2d10806bf1ce4e26b92adda61efc0862 +#: cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 -#: 046c5e134de94b629cc22d416f3c9182 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 -#: 52fa22d3277940049fbb589a3ea73433 +#: 5fa79c62049a447c8328ebf9db54ebf4 msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 -#: 6043beb96c2c49648011ec556aa9e986 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 -#: 5ac4310515124e2986724425bed5651f +#: 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 -#: 7958e91d5c2f4046aa9d2070a900f9ae +#: f1cb55fc59824cc18a95fd6dcb32cf4c msgid "First of all, notice that the main workflow level input here requires an array of strings." msgstr "" #: ../../src/topics/workflows.md:441 -#: 2db234d776fe4fd38bab07245dcb783a +#: d947c54933d64aad90df392a1cedd63f msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 -#: 7cfb17230e284ee7b6e2a00efe8eeb74 +#: 651d35997332404186aa6d5711da4a3d msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 -#: 4311ac98544e4fb0b2f4b24985710a01 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 -#: 780f9c72e6c34c39918642c7e2477355 +#: 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 -#: cc4a7316db644b438cbaa181ad9ef2d3 +#: b662c1a5a4424c8d8350a806356acc61 msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 -#: dfc461a03fe8487794837904febb8b63 +#: 04d6babfd87343d7a5f13867ea02b65f msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 -#: 1e83485b00b64dfaba897bd8d772e0f0 +#: 2eaacf1a90204a2b9bd621344560f2a1 msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 -#: d0321d6805ec4d3abf3877d02a0a417f +#: 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 -#: d7d77e807b3048c7bdf89558f76804cb +#: 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 -#: 8d9b8be147fc4a71922dde858842e543 +#: e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 -#: 34b7705416a745a6a42e6d402c0757ed +#: e3a7182f00f440b8b5461da91194a64b msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" msgstr "" #: ../../src/topics/workflows.md:491 -#: 257adcee9da64d5c987f3b64efd20ab0 +#: 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 -#: fa6ed5d0c14f42f4aa3c5144648db22c +#: b5338f39e8c74ff28e139da68089a742 msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 -#: 333e8ce458d54de394526769f96d12d2 +#: f6d92156d67c4a339bcfd194cff897df msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 -#: b819e8a5df6e4fa495924095709669ef +#: 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 -#: f1955468a1364d44a930db77c9c4b495 +#: d80ab383eec9402faba997b548fe42eb msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 -#: 8c3b9b645a204d02b2c73a205e8ec296 +#: f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 -#: 4d88b9c186cd4502adbf752e8a70b6ce +#: 49217c02f58c43ff9ec00f10da8d4e84 msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." msgstr "" #: ../../src/topics/workflows.md:527 -#: 9927673564024ba5833b5ac271737857 +#: 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 -#: 84f4ed7ce2004742b8db9087104a469a +#: 8dbd56473f8c40c0bb12a48be06117e3 msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 -#: 2b5f9757adca4490a149c7f45e14fcb5 +#: 78d7f3ede2c746d482042adef050b2c4 msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 -#: 0418de720813442f81ecff293c9448b5 +#: cbbf93c70fe04ba7932ba25758ddc611 msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 -#: 524eec63be8248ae982939c975ef50a2 +#: cfa1c1fde4454df283f87cc54a9c59ec msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 -#: 5e99f9912cc549a7890e2934425eb943 +#: 1a8be2950cbb475bbb2617e005f0fac9 msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 -#: b0121ee087d6424fbb0ea5957a7b0b8c +#: 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 -#: 49e9f6b3a06840289decf3f557860f87 +#: 5d83c56102e141cc978500f678dd0c1c msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 -#: ed9eebec0b3d4b72ba65507d37757a37 +#: c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 -#: bf9b255a24a84f3ba989a223492b8f41 +#: fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 -#: e79fa0b7f8b14810a3a20908ef92bc55 +#: 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 -#: 290e2035f903417cbecb5dc5f09d6ebe +#: b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 -#: d420730151534f1a89076588a3358f09 +#: b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 -#: a6b5378bbe1e4bee9e37a765bddf75f7 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 -#: 6e4d9465dc2b454d96b02d7ad1817795 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 -#: a649d4af5f434dac9395e013ec4836bb +#: 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 -#: 446190a298834b73bda068286e8490cf +#: cda73485875d4c8e9464679a20558616 msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 -#: 2f35c012ff174721bffe66a3f58a804f +#: 98cae24919b74c088a5d89706aec581b msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 -#: 43127c98c9d94aedac61cee67929c1a6 +#: b4b0940b4b5743c09637b36b964202d0 msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 -#: dc4fe561203c4c38a9caea5bd6eff2cd +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 -#: f924e4896db2424d99ce8c9da14c599a +#: 9ca3554d771d45998e88aaede525b227 msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 -#: bf7646f5f925485c842a6d34140e40b8 +#: 3fca839cede94cfd8e4f605c73ba699d msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 -#: c483e61dec8949fa96bb893d422888a0 +#: da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 -#: 85fcb523d0e34a499eae04d304887f7b +#: 3ded0f125249485c921994b6e6b93ac9 msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 -#: 83d47c8736a34f3cbf09e3997845e4f4 +#: 53ece35d309a4c8d99f1efb2122a7092 msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 -#: c698fb3d37bc403e9aeb679b8fc0e15e +#: d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 -#: ae8af2f0eeda4aec97201211dfa965c7 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 -#: 2ee87aa465cd41fda16a61e242f8c9d0 +#: fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 -#: 0a6fd4469ff24b61b3ad001b09eead18 +#: 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 -#: b96ba19bce9341d39c46054e1f10fe8f +#: 87bafb845c714b109874f6137b84462d msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 -#: 903f30af3d0c45cfb61063936a8097a7 +#: 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 -#: ede8db7c0a58432e8a1c416e937a06d2 +#: fcd05b1ef31a4046946a2399c7fc5575 msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 -#: c8b53615476a4a1fbef2420d93bac94e +#: f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 -#: ea03cb5525cc491f9feb5c4780b38fee +#: 859368c1f25c4a4aad57abfd046c63f5 msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." msgstr "" #: ../../src/tutorials.md:1 -#: 92fd3a5e31714eab859dd630af2e78cf +#: 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 -#: de660ecdb5b44c97a0e519d00b232497 +#: 5d92464923c245818c070fbef102be89 msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." msgstr "" #: ../../src/tutorials.md:7 -#: 5afc1e1288e74ed0985e61e5164479c7 +#: 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 -#: 862dc7ac81e54b1fb3d4c2f961b8810e +#: 13d7e2e92e96432787c712cf6a595424 msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 -#: e2c94c0e1c7048d38cd7aa2c465a859d +#: 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 -#: b63253780f51467a95207d820d13ac39 +#: 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 -#: 6d06ca7ed5df4560aaed286f4fe33928 +#: 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 -#: 5448df4a6a8f431d80e269bcd480e19e +#: a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/src/LICENSE.md b/src/LICENSE.md new file mode 100644 index 00000000..84798e58 --- /dev/null +++ b/src/LICENSE.md @@ -0,0 +1,2 @@ +```{include} ../LICENSE.md +``` diff --git a/src/LICENSE.rst b/src/LICENSE.rst deleted file mode 100644 index 68c5792f..00000000 --- a/src/LICENSE.rst +++ /dev/null @@ -1 +0,0 @@ -.. include:: ../LICENSE.rst diff --git a/src/index.md b/src/index.md index e1a0c0cb..8e10fa54 100644 --- a/src/index.md +++ b/src/index.md @@ -35,7 +35,7 @@ introduction/index.md topics/index.md tutorials.md faq.md -LICENSE.rst +LICENSE.md ``` [repo]: https://github.com/common-workflow-language/user_guide/issues From 3cf11ae4363e77095c9bb2a3c10355b71584b0f4 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 13:44:54 +0100 Subject: [PATCH 46/49] Makefile: drop default turn warnings into errors option --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 81bc3c77..83ba9e13 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS = "-W" +SPHINXOPTS = "" # was "-W" (turn warnings into errors) SPHINXBUILD = sphinx-build SOURCEDIR = src BUILDDIR = _build From 0efc0ad56cd7e96d32b5518b9fbdab291f528d8f Mon Sep 17 00:00:00 2001 From: Michael Crusoe Date: Fri, 27 Jan 2023 15:27:15 +0100 Subject: [PATCH 47/49] Translated using Weblate (Spanish) Currently translated at 3.4% (21 of 605 strings) Translated using Weblate (Portuguese) Currently translated at 2.1% (13 of 598 strings) Translated using Weblate (Spanish) Currently translated at 2.5% (15 of 598 strings) Translated using Weblate (Spanish) Currently translated at 100.0% (2 of 2 strings) Translated using Weblate (Portuguese) Currently translated at 100.0% (2 of 2 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/es/ Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/pt/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/es/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/pt/ Translation: Common Workflow Language/CWL User Guide Translation: Common Workflow Language/CWL User Guide: Sphinx --- locales/es/LC_MESSAGES/sphinx.po | 18 +- locales/es/LC_MESSAGES/user_guide.po | 2804 +++++++++++++++----------- locales/pt/LC_MESSAGES/sphinx.po | 18 +- locales/pt/LC_MESSAGES/user_guide.po | 2789 +++++++++++++++---------- 4 files changed, 3375 insertions(+), 2254 deletions(-) diff --git a/locales/es/LC_MESSAGES/sphinx.po b/locales/es/LC_MESSAGES/sphinx.po index 38526232..2bdf9af4 100644 --- a/locales/es/LC_MESSAGES/sphinx.po +++ b/locales/es/LC_MESSAGES/sphinx.po @@ -4,25 +4,27 @@ # Language User Guide package. # FIRST AUTHOR , 2023. # -#, fuzzy msgid "" msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" +"Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" +"PO-Revision-Date: 2023-01-26 13:55+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Spanish \n" +"Language: es\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" #: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" -msgstr "" +msgstr "Navegación principal" #: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "" - +msgstr "Sección Navegación" diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index ba080ed4..b1952aae 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -4,16 +4,15 @@ # Language User Guide package. # FIRST AUTHOR , 2023. # -#, fuzzy msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"PO-Revision-Date: 2023-01-27 14:27+0000\n" "Last-Translator: Michael Crusoe \n" "Language-Team: Spanish \n" +"user-guide/es/>\n" "Language: es\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" @@ -22,21 +21,23 @@ msgstr "" "X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 ../../LICENSE.rst:2 +#: dcdc2e8da0ec4d9e9453601fdd83bac5 msgid "Licenses" msgstr "Licencias" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 ../../LICENSE.rst:5 +#: 3e165520ca56481b8f8d494a8d471de3 msgid "Instructional Material" msgstr "Material didáctico" #: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " "cambios en la estructura también están disponibles bajo la [licencia " @@ -44,12 +45,14 @@ msgstr "" "legible por humanos (y no un sustituto) del [texto legal completo de la " "licencia CC BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 ../../LICENSE.rst:12 +#: b7a7a0fb40344fe087c1cc3ec19308aa msgid "You are free:" msgstr "Usted es libre de:" #: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" msgstr "" "**Compartir**---copiar y redistribuir el material en cualquier medio o " "formato" @@ -58,90 +61,93 @@ msgstr "" msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 ../../LICENSE.rst:18 +#: 430ff4de74924bc3a3b2c7e809ea4456 msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e ../../LICENSE.rst:20 +#: 8bc6672f4a33428296226112a1be6fbe msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms:" +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " -"términos de la licencia." +"términos de la licencia:" #: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." -msgstr "" -"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " -"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " -"Language Project» y, cuando sea práctico, con un enlace a https://www." -"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " -"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " -"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " -"licenciante." +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." +msgstr "" +"**Atribución**---Usted debe dar crédito de manera adecuada(mencionando que " +"su trabajo se deriva de un trabajo que tiene «Copyright © The Common " +"Workflow Language Project» y, cuando sea práctico, con un enlace a " +"https://www.commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], " +"e indicar si se han realizado cambios. Puede hacerlo en cualquier forma " +"razonable, pero no de forma tal que sugiera que usted o su uso tienen el " +"apoyo de la licenciante." #: ../../LICENSE.md:32 8161753b7526445db319210044566200 msgid "" "**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" msgstr "" "**No hay restricciones adicionales**---No puede aplicar términos legales ni " "medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " "permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 ../../LICENSE.rst:35 +#: 1798d65c10104040923c2fea2199bab2 msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 ../../LICENSE.rst:38 +#: c65198b804f8436ba783643d51bc72d9 msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " "necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " "publicidad, privacidad, o derechos morales pueden limitar la forma en que " "utilice el material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea ../../LICENSE.rst:44 +#: 3d7ca3f2cede4d5f998bf014bd970748 msgid "Software" msgstr "Software" #: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 msgid "" "Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " "disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " -"la [OSI][Osi]." +"la [OSI][osi]." #: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." msgstr "" "Unless required by applicable law or agreed to in writing, software " "distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " @@ -151,82 +157,97 @@ msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 #: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 +#: eab02dc13915490bb3c9ba744d78b6a7 271049c39d294b11b9bd94cb6be2857f +#: 61af90891e2d4542b5f45fb3ec6480af bf309fa01bed4355bf052ae4afbf9a67 msgid "" "CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." +"create workflows. Because CWL is a specification and not a specific piece of " +"software, tools and workflows described using CWL are portable across a " +"variety of platforms that support the CWL standard." msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 055f0e960450410585b59760ef3ad284 6294af2e32e04207a87399c7f0780011 msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: 6428125fc43c43bba8518ece2f5d150f msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" #: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: ce8fade1e88e4b03ac0d3fc71d16f844 msgid "FAQ" msgstr "" #: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +#: 9e7483b53a984b689964c69afcaa7123 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +#: 8c5a89257ef248cd99cba303713e5082 msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: 9e80d8eeefcf4a9d95fd5fe9d9fa124a msgid "" -"This example demonstrates how to change the name of an input file as part" -" of a tool description. This could be useful when you are taking files " -"produced from another step in a workflow, and don't want to work with the" -" default names that these files were given when they were created." +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +#: c2e5f62490f940aab19166403a840597 msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: ffcffabdf25a4c398e8e53bc817ea769 msgid "" -"This example demonstrates how to change the name of an output file from " -"the default name given to it by a tool:" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +#: c8a6b85cfca542ccb042a0269294e5e3 msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: 98f583e5e36941c1856d719a16e58e4a msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: fb9cac0954474b5284793330b7424949 msgid "" -"The first method involves adding the folder containing your scripts to " -"the `PATH` environment variable. This allows you to run the shell script " +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: cc45d609de1f423db86d58eea933e132 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: 27ee63895cb14321a1814f4372d3180f msgid "" -"After that, make the script executable with the command `chmod +x " -"scriptname.sh`" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" msgstr "" #: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: f1c841980f3d4364a2158a4eb2f0d257 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " @@ -234,117 +255,138 @@ msgid "" msgstr "" #: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: 6d53d38ddcf244fb997db37eae7fcf90 +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: b6d60d66f3744ab3aea1b175ecb23d4a msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" #: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: cf4fa3ae602841d393b4143e9f6f5e82 msgid "" -"The second method involves including an input of `type: File` in the " -"script itself:" +"The second method involves including an input of `type: File` in the script " +"itself:" msgstr "" #: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +#: 41a3c9aa55c5406f9b52af2243c79ccc msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#: 3b8eb247425a4a708f51c08cf258e30a msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: 388a6e091a054dc48afc928f46dac7b7 msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their " -"input binding makes use of `self`. Below is an example workaround for " -"this, pending a more sophisticated fix." +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +#: 28c59d12156e44ea833822fd3ecaf824 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: 8267843ff5c940c590b10047455f2102 msgid "" -"Below is an example showing how to specify different strings to be added " -"to a command line, based on the value given to a Boolean parameter." +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#: 6e6f55bc915e4cceb8e360544d6b4ae5 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: 1bc80953bd60405082a10a7798c1413d msgid "" -"Using " -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" along with [`linkMerge: " +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: a6cd4bf4dc314e66a951f7f1227c7bb7 msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: 7ab2440a92aa44b09e8a324cd67ca728 msgid "" -"The input must be an array consisting of exactly one entry for each input" -" link. If \"merge_nested\" is specified with a single link, the value " -"from the link must be wrapped in a single-item list." +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +#: 152a529dfa2c42c1b6f0083589fa5aeb msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: b278c137167d4b958c099c0509edb79c msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " -"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" -" destination step." +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." msgstr "" #: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +#: f0b38723838f479d9db8eb5142d28a1e msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: fc1e4a808e85422cbb4d128c5a1f4d0c msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" #: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: d74964c9d19241848f4dd92a201e201f msgid "" msgstr "" #: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +#: 859b8e18e05a4c3285fb20bbb44c1ed4 msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: eb6e932924a54afd9114c629b2d0e93b msgid "" -"For command line flags that require a specific input as the argument an " -"enum type can be declared in CWL. **Specifying null here is known as long" -" form style. It does the same thing as the question mark on the other " -"inputs.**" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: 31d70b41ddf042f6aa530b7bd6daae73 msgid "" msgstr "" #: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +#: 9aa3ff8c957b42c8a30f37167a8177fd msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: 777ac7f6bde2470b981efc91feb01c81 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " @@ -352,117 +394,138 @@ msgid "" msgstr "" #: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +#: 8647071efc0548a1807c03fe8a4ee54c msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: 4404233183124085990c44793a6b25f6 msgid "" -"To properly set fields in a record input type, you need to pass a " -"dictionary to the input to properly set the parameters. This is done by " -"using inline JavaScript and returning the dictionary with the key of the " -"field you want to set. The source field is set to indicate the input from" -" the workflow to be used as the value." +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." msgstr "" #: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +#: c5eecacfa07f47649f07ef9d888f4c5e msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: 1efef04061fd48f1ab39a99508b5bc0b msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +#: 57e8ace8e8d64e7a90510e1ccea69612 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: 138606e8d7be40bb960f278977f9107f msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +#: d0f668dc78464469a9f2bfc61a90aa76 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: f2a49a7663e1456cac6b2eac0c46c662 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: eefe4adebdba4063af0cac3ab5d46442 msgid "" -"For example, the filename `a space is here.txt` includes 3 space " -"characters." +"For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: 526f2816123a43ecbcf09c46904b4b5f msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#: 0ecf267c5f4d4557ad0d7ddef2f4b5e6 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: 935a253376854d12928f00c2870ed4c0 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: bc6c0bf679ae48e7822add7ab2cda220 msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: a63643806a2a4eee8ebd3502fd6ce2b5 msgid "The file is here" msgstr "" #: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: fc54964adcd648948d7baff02f47598e msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +#: aabc495306a149fdb15835ae1df93c42 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: 2930faead8be45a6b9adbf51dcdfef6e msgid "" -"If it is not possible to change the input identifier, then you can use an" -" alternative CWL Parameter Reference syntax:" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +#: f885e4716a8d4de0b25d2d3356789672 msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: 6487ff3c19c944eb8257b2cf60d0aac7 msgid "" -"The CWL standards are built around (optional) Docker format containers. " -"The reference runner and several other CWL implementations support " -"running those Docker format containers using the Singularity engine. " -"Directly specifying a Singularity format container is not part of the CWL" -" standards." +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +#: 4cbacce539ce4f6cb5bb8ccf1574640c msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: 27321576de714cd5b82c67f59b2e3e6f msgid "" -"You can use the --js-console option of cwltool," -" or you can try creating a JavaScript or TypeScript project for your " -"code, and load it using expressionLib, e.g.: " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" #: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: 6afded7ba21247099c9bfcedf40c9171 msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: 17c386e7cd25496784207140f9876b90 msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " @@ -470,267 +533,275 @@ msgid "" msgstr "" #: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: 3bfd9bcf826a4400935dfad338612b12 msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: 4b38f1439da44ebb967b5b1e3df8f78a msgid "" -"If you find that something is missing from this guide, or if you would " -"like to provide other feedback, file an Issue on the [project repository " -"for this guide][repo]. You can also suggest changes directly in a Pull " -"Request by clicking the \"Edit this page\" button at the right sidebar of" -" each page." +"If you find that something is missing from this guide, or if you would like " +"to provide other feedback, file an Issue on the [project repository for this " +"guide][repo]. You can also suggest changes directly in a Pull Request by " +"clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: a4a60a8d010448b0b8ad1e05cbc78f2b msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: e23e00e89c81410ba8381fd81bc73b3c msgid "" -"If you are a beginner user get started with the " -"[Introduction](/introduction/index.md) section. For advanced users the " -"subsections of the [Topics](/topics/index.md) have detailed information " -"about the most common topics for CWL." +"If you are a beginner user get started with the [Introduction](/introduction/" +"index.md) section. For advanced users the subsections of the [Topics](/" +"topics/index.md) have detailed information about the most common topics for " +"CWL." msgstr "" #: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: 7274d92e678a440eb0d3ae3109f4157a msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each " -"page, and the Search form is on the left sidebar." +"subsections. The right sidebar contains links to the sections of each page, " +"and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: 6ad5f2d254a24ac1b3faf382d08b58aa msgid "Table of Contents" msgstr "" #: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: 7208cbccb84d45d58c7d5becec74b7d3 msgid "Basic Concepts" msgstr "" #: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: 8b9809abb49840b195a89943ba15f78a msgid "" "This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are " -"expected to be familiar with workflow managers, YAML, and comfortable " -"with following instructions for the command-line. The other sections of " -"the user guide cover the same concepts, but in more detail. If you are " -"already familiar with CWL or you are looking for more advanced content, " -"you may want to skip this section." +"working with Common Workflow Language (CWL) workflows. Readers are expected " +"to be familiar with workflow managers, YAML, and comfortable with following " +"instructions for the command-line. The other sections of the user guide " +"cover the same concepts, but in more detail. If you are already familiar " +"with CWL or you are looking for more advanced content, you may want to skip " +"this section." msgstr "" #: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: 9a934bf0848b438aaef7c4f00e0f2901 msgid "The CWL Specification" msgstr "" #: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: 5a299600dc304fd886b7153de1a706f7 msgid "" "The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered " -"in this user guide is the {{ cwl_version }}." +"community. The specification has different versions. The version covered in " +"this user guide is the {{ cwl_version }}." msgstr "" #: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: 55f7696f07d64277ad1b39d283175b37 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" "incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes " -"that are backward-compatible. The last number is used for bug fixes, like" -" typos and other corrections to the specification." +"number is the minor release, used for new features or smaller changes that " +"are backward-compatible. The last number is used for bug fixes, like typos " +"and other corrections to the specification." msgstr "" #: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: b854ca0af98347d2b66e74754eb92a50 msgid "" -"The model used for the specification version is called Semantic " -"Versioning. See the end of this section to [learn more](#learn-more) " -"about it." +"The model used for the specification version is called Semantic Versioning. " +"See the end of this section to [learn more](#learn-more) about it." msgstr "" #: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: d9785269c51e4902bf3a70e917d33238 msgid "Implementations" msgstr "" #: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: b57a31b8d26545d1823fcd1fa2c83316 msgid "" -"An implementation of the CWL specification is any software written " -"following what is defined in a version of the specification document. " -"However, implementations may not implement every aspect of the " -"specification. CWL implementations are licensed under both Open Source " -"and commercial licenses." +"An implementation of the CWL specification is any software written following " +"what is defined in a version of the specification document. However, " +"implementations may not implement every aspect of the specification. CWL " +"implementations are licensed under both Open Source and commercial licenses." msgstr "" #: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: 4e264b1a40bd4935abb5bdeb75fa5c64 msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud" -" and high performance computing environments where tasks are scheduled in" -" parallel across many nodes." +"CWL is well suited for describing large-scale workflows in cluster, cloud " +"and high performance computing environments where tasks are scheduled in " +"parallel across many nodes." msgstr "" #: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: 791b02bb1ee6459d8d8332fc2dee353c msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: a5ebc727fb3443f78e81d6b7ed5ac750 17300bbe695044e7b8917d23bd0aa597 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: 86e6a06992dc4228bfda7add48e28ca3 526614f195614818a614fc9a576e7cb5 msgid "" -"A process is a computing unit that takes inputs and produces outputs. The" -" behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification" -" {{ cwl_version }}:" +"A process is a computing unit that takes inputs and produces outputs. The " +"behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification " +"{{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 8c9772f96caf4169924d22eb929a4f0f 7b47991653054f2d9f49a91720754abf msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 4fac209a62114798b79e4810f7a0148b aa8838c0ee0a4b4285cb1b5dc6eb5d31 msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: b97ba368fd664caab0494e2392795697 457c73a37cb143d98005ebf6e67f5bf1 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: 903a6796e3304a19ad885b2428b0e80f c28057f3b7814f8395dbc3ad54d5f6f9 msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 6e352ac1f8e144c392ac5adf18c28298 83afed0785cd4b0bb86863c2841ce982 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: cf2922f645904ac7955428ecddc37b8a f332864bcc1e49d582a82f3d721ff3cf msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: 5f47aae608c041aeb4134d59dad314d2 3005c6d669de412ab7f8e30d00752a20 msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be " -"used to simplify workflows and command-line tools, moving common parts of" -" a workflow execution into reusable JavaScript code that takes inputs and" -" produces outputs like a command-line tool." +"An expression tool is a wrapper for a JavaScript expression. It can be used " +"to simplify workflows and command-line tools, moving common parts of a " +"workflow execution into reusable JavaScript code that takes inputs and " +"produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: f6f589481d0c4891beaccb63160619ef 2e4041cb402e4054a53ea5890b938ac1 msgid "" -"Operation is an abstract process that also takes inputs, produces " -"outputs, and can be used in a workflow. But it is a special operation not" -" so commonly used. It is discussed in the [Operations " -"section](../topics/operations.md) of this user guide." +"Operation is an abstract process that also takes inputs, produces outputs, " +"and can be used in a workflow. But it is a special operation not so commonly " +"used. It is discussed in the [Operations section](../topics/operations.md) " +"of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 972f9a1e64394a63be3258d3af0b1d79 msgid "" -"The workflow is a process that contains steps. Steps can be other " -"workflows (nested workflows), command-line tools, or expression tools. " -"The inputs of a workflow can be passed to any of its steps, while the " -"outputs produced by its steps can be used in the final output of the " -"workflow." +"The workflow is a process that contains steps. Steps can be other workflows " +"(nested workflows), command-line tools, or expression tools. The inputs of a " +"workflow can be passed to any of its steps, while the outputs produced by " +"its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 4ace6b92f4e04a07aa202840ebe36417 a572f0789084402fb2d216ac845bbfdb msgid "" "The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through " -"*requirements*. There are many requirements defined in the CWL " -"specification, for instance:" +"functionality and specify prerequisites to workflows through *requirements*. " +"There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 c7c5c9a1e98e47c0a5a6dfa69e96f921 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: 2d9f53b6ed5041dbb6c0b54835897856 357d42768e794286bf5463ca5850a7ed msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 907674a4ecff4826a2b880e28fc38f33 61966aab989744c1b9b93f7751f35ebc msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input " -"directory." +"`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 037cd0e5ceda482eaeaca03d51745aee e14a2082d2c44f3690a07d3cee5b13d1 msgid "" -"Some CWL runners may provide requirements that are not in the " -"specification. For example, GPU requirements are supported in `cwltool` " -"through the `cwltool:CUDARequirement` requirement, but it is not part of " -"the {{ cwl_version }} specification and may not be supported by other CWL" -" runners." +"Some CWL runners may provide requirements that are not in the specification. " +"For example, GPU requirements are supported in `cwltool` through the " +"`cwltool:CUDARequirement` requirement, but it is not part of the " +"{{ cwl_version }} specification and may not be supported by other CWL " +"runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: e4643938445b48cc80eb8973ceeb126e c128a76992e04d20bcc3edae8b6c0bc0 msgid "" -"Hints are similar to requirements, but while requirements list features " -"that are required, hints list optional features. Requirements are " -"explained in detail in the [Requirements](../topics/requirements-and-" -"hints.md) section." +"Hints are similar to requirements, but while requirements list features that " +"are required, hints list optional features. Requirements are explained in " +"detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: c4c3315c96714e81b364f8cc003b87e6 42953a3d591c48c6b4e80e9ea4b97bb3 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: 3eb6a013a2a4478ca2ad134661f65c58 e3762a763ba24571a9627efafe172441 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " "machine accessibility and that all digital assets should be Findable, " "Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created." -" It is thus important that workflows support the creation of FAIR data " -"and adhere to the FAIR principles. — [FAIR Computational " -"Workflows](https://workflows.community/groups/fair/), Workflows Community" -" Initiative." +"which the scientific process is conducted and via which data are created. It " +"is thus important that workflows support the creation of FAIR data and " +"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" +"workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: 074af9633627470485e5225326d5f20a be8e01a012ed45d6b7e4e6aab1afcc32 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\"," -" CWL tasks are isolated, and you must be explicit about your inputs and " +"execution, based on dependencies between tasks. However, unlike \"make\", " +"CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: 847951c055b94a83b1e081594cef22ee cf31aca4294d486cb0e25c6436996d17 msgid "" -"The benefit of explicitness and isolation are flexibility, portability, " -"and scalability; tools and workflows described with CWL can transparently" -" leverage technologies such as Docker and be used with CWL " -"implementations from different vendors." +"The benefit of explicitness and isolation are flexibility, portability, and " +"scalability; tools and workflows described with CWL can transparently " +"leverage technologies such as Docker and be used with CWL implementations " +"from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: 44bde1fae06b4678bcac4f3224601296 cc7adbdc66df4aeaad1429f7268c90c0 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" @@ -738,264 +809,306 @@ msgstr "" #: ../../src/introduction/prerequisites.md:196 #: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 #: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +#: 71beb059c9e54a9ab5430f0dc44e07ea 84679c5b03a3469294de849d9abe0a82 +#: fd690fdd46344e0e8d9fc546f6d4013b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 9d5100c7d0a040aea1020bf633ad17de 89ddaddb64f64b0c86c7e89da0edfaae msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: 36eb4b3b966640af90faa55db3789cb6 e920a824207746ffae63242d33137ac7 msgid "" -"The CWL Specification page in the CWL website: " -"" +"The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 2ccb956baa6b4376a04ad9fcc4654631 51d619152aa44651889ff2006c8f5800 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 72889b830c514afe9a7cb1e64b5666a0 88f3f5dd8aa6401793b89e8de3b8c7a7 msgid "" -"The list of Implementations in the CWL website: " -"" +"The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: e29bd7f973544600be589c3b3f84cf63 f1f9ee90d07c4381a8bb0851bdac231e msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: c377a7f5dbe645cebbb6c7eccf831a0b e3b710dabec2482d8ec1072d64d4e1f8 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" #: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: 418699fcb6c241dcbeeed81d82e9f84f msgid "Introduction" msgstr "" #: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: 28b6521a55aa4ab190ca998a59c52609 msgid "" "This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that" -" are useful to know before reading the rest of the user guide." +"prerequisites for following this user guide, and some basic concepts that " +"are useful to know before reading the rest of the user guide." msgstr "" #: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: 0e4969399eda48b98d883a3fc1540633 msgid "Prerequisites" msgstr "" #: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: 6d59f082157b494ebcfff2f649abc524 msgid "" -"The software and configurations listed in this section are prerequisites " -"for following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements " -"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" -"compatible runner or workflow system, but the results and interface may " -"look different (though the exact workflow outputs should be identical)." +"The software and configurations listed in this section are prerequisites for " +"following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements focuses " +"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " +"runner or workflow system, but the results and interface may look different " +"(though the exact workflow outputs should be identical)." msgstr "" #: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: 2b83beccbc1b43969b705156b9c29482 msgid "CWL Implementations" msgstr "" #: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: 594fe5e0aaf0499ebfa9218aaad4d08d msgid "" -"There are many implementations of the CWL standards. Some are complete " -"CWL runners, while others could be plug-ins or extensions to workflow " -"engines. We have a better explanation in the [Implementations](basic-" -"concepts.md#implementations) section." +"There are many implementations of the CWL standards. Some are complete CWL " +"runners, while others could be plug-ins or extensions to workflow engines. " +"We have a better explanation in the [Implementations](basic-concepts." +"md#implementations) section." msgstr "" #: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: f69c7c75a36048f5af0ed1b56df9320d msgid "Operating System" msgstr "" #: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: f28638ffb8394ccead4ac52f30adc627 msgid "" -"We recommend using an up-to-date operating system. You can choose any of " -"the following options for your operating system:" +"We recommend using an up-to-date operating system. You can choose any of the " +"following options for your operating system:" msgstr "" #: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: 8993d7d5c8d24fc5a9c7005800c0a1f1 msgid "Linux" msgstr "" #: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: 2073109799e748d68304f5558c82b105 msgid "macOS" msgstr "" #: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: 9fb2c31bd36d495786397c7a7d6b3417 msgid "Windows" msgstr "" #: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: 43e1957537034c5886574118fc2533da msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem" -" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " -"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" -"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " -"details on installing WSL2. Your operating system also needs internet " -"access and a recent version of Python (3.6+)." +"If you are using Windows, you will have to install the [Windows Subsystem " +"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " +"installing WSL2. Your operating system also needs internet access and a " +"recent version of Python (3.6+)." msgstr "" #: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: e3a3d9b94b1e44c48f298dfcdcd27104 msgid "CWL Runner" msgstr "" #: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: 8a385803ed3945ff81d38a3543a69d94 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL " -"community. It is also the CWL reference runner, which means it must " -"support everything in the current CWL specification, {{ cwl_version }}." +"`cwltool` is a Python Open Source project maintained by the CWL community. " +"It is also the CWL reference runner, which means it must support everything " +"in the current CWL specification, {{ cwl_version }}." msgstr "" #: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: bf56727d93994d3995b0af0c68c2c583 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create " -"and activate a Python virtual environment using the `venv` module, and " -"install `cwltool` in that environment:" +"environment like `venv` or `conda`. The following commands will create and " +"activate a Python virtual environment using the `venv` module, and install " +"`cwltool` in that environment:" msgstr "" #: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +#: 9a959bd914d543b78f9625f03df95765 msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" #: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: 198ce7d893a04fcb806ec1671838d588 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` " -"and `conda`." +"language/cwltool#install) for other ways to install `cwltool` with `apt` and " +"`conda`." msgstr "" #: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: cc2be8feeab54a22a0b64a2a72991003 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: 749c672e8c234c1c9a5eb2cc9b77c4e3 msgid "`true.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: 29c64936318a4a2ba882e1eae8f03f57 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the " -"CWL standards. However, these actions will be performed without running " -"the document. To validate CWL workflows (or even a standalone command " -"line tool description like the above) pass the `--validate` option to the" -" `cwltool` command:" +"errors, and verify that the workflow descriptions are compliant with the CWL " +"standards. However, these actions will be performed without running the " +"document. To validate CWL workflows (or even a standalone command line tool " +"description like the above) pass the `--validate` option to the `cwltool` " +"command:" msgstr "" #: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +#: 44106744147f45bab675eb66148531c7 msgid "Validating `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 -msgid "You can run the CWL tool description by omitting the `--validate` option:" +#: 6d84c6890f564b4baf7b34f6a52cbfc4 +msgid "" +"You can run the CWL tool description by omitting the `--validate` option:" msgstr "" #: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: 7eb67993e8ca48dc929e1a992f78cb39 msgid "Running `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: 52886c54c3c54b83896c52ebd7d53fad msgid "Cwl-runner Python Module" msgstr "" #: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: 097945c33f7542e2bae2e9f7ba1cf84d msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be " -"invoked independently, and is not reliant on a particular CWL runner " -"program name. Users can invoke `cwl-runner` instead of invoking a CWL " -"runner like `cwltool` directly. The `cwl-runner` is installed by a system" -" administrator or user to point to the preferred CWL implementation. This" -" is convenient for environments with multiple CWL runners." +"runner. This simply means that the `cwl-runner` alias command can be invoked " +"independently, and is not reliant on a particular CWL runner program name. " +"Users can invoke `cwl-runner` instead of invoking a CWL runner like " +"`cwltool` directly. The `cwl-runner` is installed by a system administrator " +"or user to point to the preferred CWL implementation. This is convenient for " +"environments with multiple CWL runners." msgstr "" #: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: 3853bfc6a85747019c615a50c7ca6b40 msgid "" -"The CWL community publishes a Python package with the name `cwlref-" -"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +"The CWL community publishes a Python package with the name `cwlref-runner` " +"that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" #: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: 662230f538504f44941c6f4801f6251c msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" #: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: 1c9eb9e2bb9e40a9985ada16c34eea2d msgid "" -"Now you can validate and run your workflow with the `cwl-runner` " -"executable, which will invoke `cwltool`. You should have the same results" -" and output as in the previous section." +"Now you can validate and run your workflow with the `cwl-runner` executable, " +"which will invoke `cwltool`. You should have the same results and output as " +"in the previous section." msgstr "" #: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: 7f53ba159979461393c0f278fe97fb30 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: 7e8077c2dd584eda89ead60ecc5eabf3 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: 1787a3c749ee48218b87c8401f6255d7 msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For" -" that, the first thing you need to do is copy `true.cwl` workflow into a " -"new file: `true_shebang.cwl`, and include a special first line, a " -"*shebang*:" +"Another way to execute `cwl-runner` is by invoking the file directly. For " +"that, the first thing you need to do is copy `true.cwl` workflow into a new " +"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" #: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: a52ca4ce9a184e938c3a5cac9cb882ca msgid "`true_shebang.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +#: 41d3287a9a774a73aefd49bd709764bf +msgid "" +"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" #: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: 3b9d30094611400b85b55db163cb303e msgid "Making `true.cwl` executable." msgstr "" #: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: b6ea77357b4f45528ed1379f8fe67cfd msgid "" -"And finally, you can execute it directly in the command-line. On " -"execution, the program specified in the shebang (`cwl-runner`) will be " -"used to execute the rest of the file." +"And finally, you can execute it directly in the command-line. On execution, " +"the program specified in the shebang (`cwl-runner`) will be used to execute " +"the rest of the file." msgstr "" #: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: 8797ce327d7443fdb3d4617d3fc2cf7f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" #: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: 896b6896b1e44d0cab5f35e7d0dd88e3 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute " -"the script using the executable specified after the shebang. It is " -"considered a good practice to use `/usr/bin/env ` rather than" -" using a hard-coded location, since `/usr/bin/env ` looks for" -" the `` program in the system `PATH`," +"script. When the script is executable, the operating system will execute the " +"script using the executable specified after the shebang. It is considered a " +"good practice to use `/usr/bin/env ` rather than using a hard-" +"coded location, since `/usr/bin/env ` looks for the " +"`` program in the system `PATH`," msgstr "" #: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +#: 4b839d23d72f4d3fbe4f1ce7e568b20b msgid "Text Editor" msgstr "" #: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: a42b9ab315b5402493e4ce0067d0a18e msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " @@ -1003,379 +1116,429 @@ msgid "" msgstr "" #: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: 2f63483960634a7782f95e9e2feaa5a6 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting" -" and better auto-complete:" +"integration with CWL, and features such as customized syntax highlighting " +"and better auto-complete:" msgstr "" #: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: 3471105073204d7998aaf790b73f785d msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " -"" +"Visual Studio Code with the Benten (CWL) plugin - " msgstr "" #: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: 0b8b47511b5e4296b7438be0ad2604ed msgid "" -"cwl-plugin for IntelliJ - " +"cwl-plugin for IntelliJ - " msgstr "" #: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: 3e3eec00f23f4f21873ddb005204a875 msgid "" -"The CWL community also maintains a list of editors and viewers: " -"" +"The CWL community also maintains a list of editors and viewers: " msgstr "" #: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: 2ceb25f2668442839e3e9f4512772a03 msgid "Docker" msgstr "" #: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: 20c753c5371b43ed834fa741b0ce7692 msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: " -"." +"documentation to install it for your operating system: ." msgstr "" #: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: a19c4fc9fa404912a0389337536d9c25 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models " -"with and without containers." +"examples, and to clarify the differences between the execution models with " +"and without containers." msgstr "" #: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: a0f38c1e28ca4850b3986617625acbf2 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for " -"pulling images." +"Singularity. You can also use alternative container registries for pulling " +"images." msgstr "" #: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: 37e1162f30894a1ca7dada9870ffa3da msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the " -"next section, Basic Concepts." +"The [Implementations](basic-concepts.md#implementations) topic in the next " +"section, Basic Concepts." msgstr "" #: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: 1c25a51edf6f47c5979c721b19cf11b5 msgid "The Python `venv` module: " msgstr "" #: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: ace930cf878d45a99f12b71bf0987a87 msgid "Quick Start" msgstr "" #: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: 46587a5e0d534af5867ae4f70a116bee msgid "" -"This section will show you a brief overview of what CWL is, and where you" -" can learn more about it. No previous knowledge of CWL is required, but " -"you must be comfortable following instructions for the command-line." +"This section will show you a brief overview of what CWL is, and where you " +"can learn more about it. No previous knowledge of CWL is required, but you " +"must be comfortable following instructions for the command-line." msgstr "" #: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: a0774d4e779e46f7a983922425203066 msgid "“Hello World”" msgstr "" #: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: 1658ee6f3cac4d04afc732aa758b1f48 msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " -"The example below shows a simple CWL “Hello World” workflow annotated " -"with comments. Note that comments start with `#`:" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " +"example below shows a simple CWL “Hello World” workflow annotated with " +"comments. Note that comments start with `#`:" msgstr "" #: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: d8e2bc671b894f3fa8a091261754c728 msgid "`hello_world.cwl`" msgstr "" #: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: 683a469bf4824c64a8ea32e048d5df73 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the" -" same result as the command-line `echo \"Hello World\"`." +"Running the workflow above with the default input values will produce the " +"same result as the command-line `echo \"Hello World\"`." msgstr "" #: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: b7c50413f7864a86815f3b581561cdb5 msgid "" -"In CWL, there is a distinction between a command-line tool and a " -"workflow. But for the sake of simplicity, we are using the term " -"“workflow” here. You will learn more about this in the [basic concepts" -"](basic-concepts.md) section." +"In CWL, there is a distinction between a command-line tool and a workflow. " +"But for the sake of simplicity, we are using the term “workflow” here. You " +"will learn more about this in the [basic concepts](basic-concepts.md) " +"section." msgstr "" #: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: d2ed66bdfcab4f7dad95b00c95d4a3d6 msgid "Installing a CWL Runner" msgstr "" #: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: 4dcbe776a70645e5a6c7513348fa6bee msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the " -"CWL *Reference Runner* for the specification, and it is compliant with " -"the latest version of the specification: {{ cwl_version }}. You can " -"install `cwltool` using `pip`:" +"`cwltool` is an implementation of the CWL specification. It is also the CWL " +"*Reference Runner* for the specification, and it is compliant with the " +"latest version of the specification: {{ cwl_version }}. You can install " +"`cwltool` using `pip`:" msgstr "" #: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: bae5b03fb74541e6ad79277a576e0516 msgid "Installing `cwltool` with `pip`." msgstr "" #: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: 8ff0d7a8d37b48488e4504ff8e3adcc5 msgid "" -"If installing the cwltool using the pip command doesn't work for you, the" -" [prerequisites](prerequisites.md) section contains other ways to install" -" `cwltool` and a more detailed list of software and libraries used for " +"If installing the cwltool using the pip command doesn't work for you, the " +"[prerequisites](prerequisites.md) section contains other ways to install " +"`cwltool` and a more detailed list of software and libraries used for " "following the rest of this user guide." msgstr "" #: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: 6255b499b9b144128afaeed64fabe8e5 msgid "Running \"Hello World\"" msgstr "" #: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: e861db9c43ed4b8ba262af8e435a350a msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the " -"`hello_world.cwl` workflow without specifying any option:" +"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " +"workflow without specifying any option:" msgstr "" #: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: c6318f06bcd74cda8c1f0caef9452b51 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: c862e745217244d28cd4c2f0842e203f msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" #: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: eba007736b92434a9711f683e64bb153 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" #: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: aebc2caf5d1b47f1b7cc0aa53e5a684e msgid "" -"Another way of passing values to your workflow input parameters is via an" -" *Inputs Object*. This is a file containing the input fields with their " +"Another way of passing values to your workflow input parameters is via an " +"*Inputs Object*. This is a file containing the input fields with their " "corresponding values. The Inputs Objects file can be written in JSON or " "YAML. For example:" msgstr "" #: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: 1242171f8b854562bb7848b06d2d065d msgid "`hello_world-job.json`" msgstr "" #: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: 24e82ecf7926428386a89f18a34eb00c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" #: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: 00e75efe03554835bc33ebaed0652626 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: 4ba34ec455704844a9cfcbac3522ea0c msgid "" "We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but " -"it is not a requirement. You can choose any name for your workflows and " -"Inputs Object files." +"files. The *-job.json* suffix is very common in Inputs Object files, but it " +"is not a requirement. You can choose any name for your workflows and Inputs " +"Object files." msgstr "" #: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: c0e9673440db454bb51af04432aeddbb msgid "Continue reading the next sections of this User Guide!" msgstr "" #: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: 39a23a9d02ab4bccb36d6a714639509b +msgid "" +"[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" #: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: 23a878e0166b40d78984a2263f63b760 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" #: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: 5d9c435820674bf4b1c5d3fef5df736d msgid "" -"[Common Workflow Language at " -"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." msgstr "" #: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: e724ee53db1940b9b09a909f4db531a4 msgid "" -"[YAML.org](http://yaml.org/) and [YAML at " -"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." +"org/wiki/YAML)." msgstr "" #: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: 7820eb801a8145feb603145f153263b9 msgid "" -"The {{'[CWL Specification " -"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " -"cwl_version_text) }}." +"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." +"replace('VERSION', cwl_version_text) }}." msgstr "" #: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: e8db3f10be294f13abe3a4418bbae4b6 msgid "" -"[Workflow management system at " -"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." msgstr "" #: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: 95211ea6924148a6a1fa5ae8facc2c7b msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. The information on this page has been migrated to the " -"[FAQ](/faq.md) section of the new user guide." +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 9c87c76c690948ac8e18088a0fffe679 b742a74d586e42e6b0480b7af3e49c9e msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: ad00d94d4fb64bbdac356e64dd3803b9 cd3da03d43044ec9843e476a54e704be msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: d8110ed19da94ad8a9f56e7006c4a2cf 0d48e2f07d784504a17cad0ae20262c2 msgid "" "In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files " -"in the same directory as the source file. However, CWL input files (and " -"the directories in which they appear) may be read-only, so we need to " -"instruct \"javac\" to write the class file to the designated output " -"directory instead." +"file to a class file. By default, \"javac\" will create the class files in " +"the same directory as the source file. However, CWL input files (and the " +"directories in which they appear) may be read-only, so we need to instruct " +"\"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: a74935dc31664e979ca8f90a6a4ba53c 4d372b89f0ce451db2a505b1754b8356 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: f357755f6dcb4971bade8636064f8dd1 573e903ef3d34514ab7b20e79c446567 +#: cfb40fbe52174d3799a6bec175db60a5 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: 6359191b4f684d5aa3602e4aaf394883 95841b1c75c84f01bd5fcb7cf3afe78d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: 9643449da1da46d7861866dce490cbcb c8bca3654ebb4b29bf3f028b4c65fa35 msgid "" -"And now invoke `cwltool` providing the tool description and the input " -"object on the command line:" +"And now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: 713666580a0a4466b4ba6e3eb2b54f0a 1432105e38014a6d9d0cf80007141007 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: d50574c8b9694f83aa376d39b9a6fcd6 bcad473b34ec43f7906253123a1661fa msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include " -"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " -"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " -"Environment][runtime] section of the CWL specification for details." +"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" +"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." +"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " +"specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: e1c8949e663b4debaf87735f1d62a2fc msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: dcc991b647d34ffc8ea3bf9c3a38258d msgid "" -"The following are a set of recommended good practices to keep in mind " -"when writing a Common Workflow Language description for a tool or " -"workflow. These guidelines are presented for consideration on a scale of " -"usefulness: although more is better, not all are required." +"The following are a set of recommended good practices to keep in mind when " +"writing a Common Workflow Language description for a tool or workflow. These " +"guidelines are presented for consideration on a scale of usefulness: " +"although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: f26c222638e54187b8bb62fe30b66bc3 msgid "" -"No `type: string` parameters for names of input or reference " -"files/directories; use `type: File` or `type: Directory` as appropriate." +"No `type: string` parameters for names of input or reference files/" +"directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: 23720e4ab3d1407597f1d1c2a4d4d90c msgid "" "A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that" -" the usual rules of software licensing apply to this document. For " -"example, if the workflow is shared publicly, licensing terms must be " -"clear so that a future user understands under what conditions they can " -"run the workflow, modify it and/or combine it with other workflows. For " -"this reason, please consider including a license field in the document. " -"The authors of this guide urge you to choose a pre-existing license " -"rather than trying to write your own (see the link below to learn more " -"about choosing a license), and our recommended practice is to choose a " -"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" -"license]." +"`Dockerfile`s) is software code. Workflow developers should be aware that " +"the usual rules of software licensing apply to this document. For example, " +"if the workflow is shared publicly, licensing terms must be clear so that a " +"future user understands under what conditions they can run the workflow, " +"modify it and/or combine it with other workflows. For this reason, please " +"consider including a license field in the document. The authors of this " +"guide urge you to choose a pre-existing license rather than trying to write " +"your own (see the link below to learn more about choosing a license), and " +"our recommended practice is to choose a license that allows for re-use by " +"anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: b3638183c59744c897246af7dab5d10e msgid "" -"If possible, the license should be specified with its corresponding [SPDX" -" identifier][spdx]. Construct the metadata field for the license by " -"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " -"`SPDX-ID` is taken from the list of identifiers linked above. See the " -"example snippet below for guidance. For non-standard licenses without an " -"SPDX identifier, provide a URL to the license." +"If possible, the license should be specified with its corresponding [SPDX " +"identifier][spdx]. Construct the metadata field for the license by providing " +"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " +"taken from the list of identifiers linked above. See the example snippet " +"below for guidance. For non-standard licenses without an SPDX identifier, " +"provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: 2c0291133b964ad8b751f8a8ed2338fc msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: 325c8c4058f045aa8fbd705238122798 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: 05333866485b43479352f7ee9326c7fd msgid "" -"For more examples of providing metadata within CWL descriptions, see " -"[the Metadata and Authorship section of this User Guide](../topics" -"/metadata-and-authorship.md)." +"For more examples of providing metadata within CWL descriptions, see [the " +"Metadata and Authorship section of this User Guide](../topics/metadata-and-" +"authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: f8140ec6e9cc41ee88ec4bde61a44d47 msgid "" -"Include [attribution information][license-example] for the author(s) of " -"the CWL tool or workflow description. Use unambiguous identifiers like " -"[ORCID][orcid]." +"Include [attribution information][license-example] for the author(s) of the " +"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" +"[orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: 1d68f50dafaf4cc1851e2d67b3e78603 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: b283942434c54456a3f29fbb0960b6c4 msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in " -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" +"identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: 0b4477c5b0184e59aa0c07161008a7bf msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1384,24 +1547,26 @@ msgid "" msgstr "" #: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: 9741651d51f249ffba1820694ab78e92 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: 5e76d4a9708244ff91f2587350d684a4 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " -"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" -"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " -"types). For non-bioinformatics tools, use or build an appropriate " -"ontology/controlled vocabulary in the same way. Please edit this page to " -"let us know about it." +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" +"$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. " +"[Full IANA media type list][iana-types] (also known as MIME types). For non-" +"bioinformatics tools, use or build an appropriate ontology/controlled " +"vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: 89e7028e55b54f968e87b9c1c3caeecf msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " @@ -1409,158 +1574,175 @@ msgid "" msgstr "" #: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: 88e2338fb2614ef29dc497d8c01a2f2f msgid "" -"Each `CommandLineTool` description should focus on a single operation " -"only, even if the (sub)command is capable of more. Don't overcomplicate " -"your tool descriptions with options that you don't need or use." +"Each `CommandLineTool` description should focus on a single operation only, " +"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: 0f3aad35924344659eb5a6719ab2b8f0 msgid "" -"Custom types should be defined with one external YAML per type definition" -" for re-use." +"Custom types should be defined with one external YAML per type definition " +"for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: 877cbb1d537b46d3b6d05b2d8c025e70 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: 5c0debbc1c1b428ebb32b589b99fe17d msgid "" -"If useful, include a top-level `doc` as well. This should provide a " -"longer, more detailed description than was provided in the top-level " -"`label` (see above)." +"If useful, include a top-level `doc` as well. This should provide a longer, " +"more detailed description than was provided in the top-level `label` (see " +"above)." msgstr "" #: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: 1ff97183191240edb98f0cc365cc028b msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list" -" of valid values." +"Use `type: enum` instead of `type: string` for elements with a fixed list of " +"valid values." msgstr "" #: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: 22f7725deb07422fa0a7bc2e6f01e4d0 msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. " -"One common example: manipulating `File` names and paths? Consider whether" -" one of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc., could be used instead." +"Evaluate all use of JavaScript for possible elimination or replacement. One " +"common example: manipulating `File` names and paths? Consider whether one of " +"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: 982313839ccc4f5a8527fe9a854c78eb msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: 267c9d10ab5e4b6c8a6104952deb1690 msgid "" -"Complex workflows with individual components which can be abstracted " -"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" -" their workflow modular and allow sections of them to be easily reused." +"Complex workflows with individual components which can be abstracted should " +"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " +"workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: 2eff0eec58c94f4d8986a4cb91b14b8e msgid "" "Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics" -" software\"][containers] (also useful to other disciplines)." +"[\"Recommendations for the packaging and containerizing of bioinformatics " +"software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: f38db701740b442c89ce58e937bd35c5 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: 034aac9e186645e384c28bb2a739cfff msgid "" -"A command-line tool is a type of Process object that can be run by itself" -" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " -"`tar`, etc. The command-line tool is defined in the `baseCommand` " -"attribute of the command-line tool CWL document." +"A command-line tool is a type of Process object that can be run by itself or " +"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " +"etc. The command-line tool is defined in the `baseCommand` attribute of the " +"command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: 5f835cdfc0ae4f378d8dad6ae7ab1855 msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The " -"following example contains a minimal example of a CWL command-line tool " -"for the `echo` Linux command, using inputs and outputs." +"A CWL command-line tool must also have `inputs` and `outputs`. The following " +"example contains a minimal example of a CWL command-line tool for the `echo` " +"Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: 02900cb8ae4c4da89d264b76a984d6cd msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: 753e48d6dfd54a88a12773b996f182d7 msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: c7ed6d1654c54bf390e933ef0f847b99 msgid "" -"The example above uses a simplified form to define inputs and outputs. " -"You will learn more about in the [Inputs](../topics/inputs.md) and in the" -" [Outputs](../topics/outputs.md) sections." +"The example above uses a simplified form to define inputs and outputs. You " +"will learn more about in the [Inputs](../topics/inputs.md) and in the " +"[Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: 0a0f855ce34449a0a37c036105c65839 msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#: c4300454f49548f49e4bd186192515a1 msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network " -"access. If a command-line tool is written manually in CWL v1.1+, there is" -" a need to specify when network access is required." +"This indicates whether a process requires outgoing IPv4/IPv6 network access. " +"If a command-line tool is written manually in CWL v1.1+, there is a need to " +"specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: f985d58070de4c0fb5f5a491fd4dc31c msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " -"Network Access automatically." +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " +"Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b 2f4e2c85677a4e56a35b6bef36d67334 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: 0cf51b6da6884065ae42032abc20eb0d 13c6d5600a30406c81ffa25ce42eb0c8 msgid "" -"Sometimes you need to create a file on the fly from input parameters, " -"such as tools that expect to read their input configuration from a file " -"rather than the command line parameters, or need a small wrapper shell " -"script." +"Sometimes you need to create a file on the fly from input parameters, such " +"as tools that expect to read their input configuration from a file rather " +"than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: 2df3a3a9094d4b79b1d5dd99195f3bff 3bf773b8560e44a3a37c68b6fcdc6a23 msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: d3f74c3b094a427fbec831afab657d50 68b8578d2f6442929941ed2522b218ad msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: cfffc518ba6e4ed1a80762ed6f7d25df 755149ed46c348c2b723b49c3b3152a8 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the " -"value at the input `message`." +"expanded by the CWL engine before creating the file. Here, insert the value " +"at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: 9454a330b9324744b89448f2694b1b03 54b7ff590d52454eb87d9f23fca44501 msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later" -" during command line tool invocation. That means that any genuine need " -"for the character `$` must be **escaped** with `\\`. For instance, " -"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " -"be evaluated by the shell script instead of the CWL engine." +"The _CWL expressions_ are independent of any _shell variables_ used later " +"during command line tool invocation. That means that any genuine need for " +"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " +"above is expanded to `${PREFIX}` in the generated file to be evaluated by " +"the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: 7f8d99a30b644457a62ac1523d0c72aa a7c74a4a74c9414e9f29fa20bab7e295 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1569,32 +1751,33 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 #: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 +#: ca03defa3ad14cf698171cb09e3055c1 0cbf233379024800bcebb963e0a3eb6f +#: ae3bc02e4f3b404c89f3c461a62c5bc4 dc32a2bacf2d4c8cb841be6eb8b839ad msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: 10d1373bb14a4a3cacd3b92a2f83382d 34a56bc23af44353a003ee295fb2c609 msgid "" -"Before we run this, let us look at each step in a little more detail. The" -" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"Before we run this, let us look at each step in a little more detail. The " +"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " "command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 70e257091bdb456e8957f90a8fa90e8c c7855ec1f09d4945afcb0aec22567b31 msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " -"YAML array, we need a `-` on the first line of each element of the array," -" in this case we have just one element. `entryname:` can have any value, " -"but it must match what was specified in the `baseCommand`. The final part" -" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " -"means that you are using a multiline string (without it, we would need to" -" write the whole script on one line)." +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " +"array, we need a `-` on the first line of each element of the array, in this " +"case we have just one element. `entryname:` can have any value, but it must " +"match what was specified in the `baseCommand`. The final part is `entry:`, " +"this is followed by `|-` which is YAML quoting syntax, and means that you " +"are using a multiline string (without it, we would need to write the whole " +"script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: 1741804e33aa43ce88b4320c11ae5973 5c60492e27014735bb9a86307ee654d6 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1606,221 +1789,258 @@ msgstr "" #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 #: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f #: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 +#: f924d65fed0c4cb5b0a019b084a8b535 80a9c04358e64ca28ef4879ad74ef733 +#: a2b470f06ad94871970b7d95339fd369 dc65b4b5e48e48a6ada03da0fac18a51 +#: ea2360c5286b43ccabac202dfa97fbe7 ee4ca94dadf64ab69a70b6cd4eaf451a msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line:" msgstr "" #: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: 285d23ef9bbc46c9890ae7957d487c12 msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: 3edd322daad940d8957f88a2637876b5 msgid "" -"Sometimes you may want to write your own custom types for use and reuse " -"in CWL descriptions. Use of such custom types can reduce redundancy " -"between multiple descriptions that all use the same type, and also allow " -"for additional customisation/configuration of a tool/analysis without the" -" need to fiddle with the CWL description directly." +"Sometimes you may want to write your own custom types for use and reuse in " +"CWL descriptions. Use of such custom types can reduce redundancy between " +"multiple descriptions that all use the same type, and also allow for " +"additional customisation/configuration of a tool/analysis without the need " +"to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: a1bd9b0dfa234e6caa6a684e981d89b5 msgid "" -"The example below is a CWL description of the [biom convert format][biom]" -" tool for converting a standard biom table file to hdf5 format." +"The example below is a CWL description of the [biom convert format][biom] " +"tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: 0aeacb6ac20f4ebca3600425ca32f5f4 msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: 1c813ebce2904f008b5b33656f673ebc msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: cc36359e94c841d3aa5cbb26a094e1d5 msgid "" -"___Note:___ To follow the example below, you need to [download the " -"example input file](https://github.com/common-workflow-" -"language/user_guide/blob/main/src/_includes/cwl/custom-" -"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " -"`wget`:" +"___Note:___ To follow the example below, you need to [download the example " +"input file](https://github.com/common-workflow-language/user_guide/blob/main/" +"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " +"*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: dc79668b05e8439591a0beb4b57acc66 msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to " -"be used in the table conversion are imported as a custom object:" +"On line 29, in `inputs:table_type`, a list of allowable table options to be " +"used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: 08aba4f77aa442d4a34aa1535f78c49e msgid "" -"The reference to a custom type is a combination of the name of the file " -"in which the object is defined (`biom-convert-table.yaml`) and the name " -"of the object within that file (`table_type`) that defines the custom " -"type. In this case the `symbols` array from the imported `biom-convert-" -"table.yaml` file define the allowable table options. For example, in " -"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" -" to create an OTU table in hdf5 format." +"The reference to a custom type is a combination of the name of the file in " +"which the object is defined (`biom-convert-table.yaml`) and the name of the " +"object within that file (`table_type`) that defines the custom type. In this " +"case the `symbols` array from the imported `biom-convert-table.yaml` file " +"define the allowable table options. For example, in `custom-types.yml`, we " +"pass `OTU table` as an `input` that tells the tool to create an OTU table in " +"hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e -msgid "The contents of the YAML file describing the custom type are given below:" +#: 63431a972f994bccacf55d5fac0d614e +msgid "" +"The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: 55e7695aca4f4319b1cf7551105a8782 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: 0c5ab34ebbf54ff6940b8ce3f080d744 msgid "" -"In order for the custom type to be used in the CWL description, it must " -"be imported. Imports are described in " -"`requirements:SchemaDefRequirement`, as below in the example `custom-" -"types.cwl` description:" +"In order for the custom type to be used in the CWL description, it must be " +"imported. Imports are described in `requirements:SchemaDefRequirement`, as " +"below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: f97e18d2d3b946468c4fac227920e011 msgid "" "Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number " -"of cores required for the tool to run successfully, as well as details of" -" the version of the software that the description was written for and " -"other useful metadata. These features are discussed further in other " -"chapters of this user guide." +"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " +"cores required for the tool to run successfully, as well as details of the " +"version of the software that the description was written for and other " +"useful metadata. These features are discussed further in other chapters of " +"this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: 62644031403548898ff36addbc0b1f6f msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: 595630b0687c4467aa65bfed289281f4 msgid "" -"Tools run in a restricted environment and do not inherit most environment" -" variables from the parent process. You can set environment variables " -"for the tool using `EnvVarRequirement`." +"Tools run in a restricted environment and do not inherit most environment " +"variables from the parent process. You can set environment variables for " +"the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: 34e005c135864a89a00e817d79118e2e msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: b624f9f99c294e6996f212c8b62f20b0 msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: 14df63ab847e4efca820f712548cd076 msgid "" -"An expression tool is a type of Process that can be run by itself or as a" -" Workflow step. It executes a pure JavaScript expression. It is meant to " -"be used as a way to isolate complex JavaScript expressions that need to " -"operate on input data and produce some result as output." +"An expression tool is a type of Process that can be run by itself or as a " +"Workflow step. It executes a pure JavaScript expression. It is meant to be " +"used as a way to isolate complex JavaScript expressions that need to operate " +"on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: 91d4224b41c6473f936c03bd0ab9d370 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: 519989399dab493ea41941ed85cb9670 msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: 28dd1cf24309404eaf717d417272e094 msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: 3f536ad8c86d442c8bbe61777dbb1a54 msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains" -" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"We had to use an `InlineJavascriptRequirement` as our expression contains a " +"JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: b9e9894c6d024e60929d020dbaa553f0 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: 482debe1a40f490b90d4ece1b3f9d732 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by " -"the CWL runner." +"legal you can provide a fragment of Javascript that will be evaluated by the " +"CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: 708346038be745d097685970cc462f4a msgid "" -"JavaScript expressions should only be used when absolutely necessary. " -"When manipulating file names, extensions, paths etc, consider whether one" -" of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " -"practices](best-practices.md)." +"JavaScript expressions should only be used when absolutely necessary. When " +"manipulating file names, extensions, paths etc, consider whether one of the " +"[built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc, could be used instead. See the [list of best practices](best-" +"practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: 99347b6b2c404a4b9bbcc96e0b4bd925 msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: e6629f0914324c76a08fe179575b73d5 msgid "" -"As this tool does not require any `inputs` we can run it with an (almost)" -" empty job file:" +"As this tool does not require any `inputs` we can run it with an (almost) " +"empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: 2287002a87184fb9b95d775a368f0e46 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: c23d4543d9f949a9a7015fdcbb40dcd0 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object" -" is represented simply by a set of empty brackets." +"descriptions are contained inside curly brackets `{}`, so an empty object is " +"represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: c04a9dcc84b84f37bcf32c3790672038 msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: 9f27c79365db455d9d31053576ebe05e msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: a2b3ad1e2c884e24948a915c3305aee1 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" #: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: dd7665bbc5e9449588c9539e3c1910de msgid "" "Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" -" describe the additional command line arguments." +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " +"describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: 0972c757f7c74ea9beabf6b9ef9dbf4c msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: 175de3b9854546568f60a20cc19887de msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: 0c286e5ba1714a059a95b566fe49be31 msgid "" -"From " -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: 1acb064f7a4a482aa0174bdc847c6382 3029c1dfe5424c2b812597b03ea76178 +#: a5503b6c524e4848aa308b0f4c26d774 msgid "`arguments`" msgstr "" @@ -1831,32 +2051,39 @@ msgstr "" #: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e #: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 #: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 0e03befa46c74dc2b09420e1eb2a6fbd +#: 50f81e7ab73a4713bbc60f6f5609b906 718dc3def33c462786174fb42097981f +#: 9c2acd930553458eb105f96213b5d7b0 d4bf86a995d546c0a9159b3f29a84125 +#: e98424244f554c7399e9e7ad560849a6 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: 17ac6d2c703b466f9720b7489209a2ff 2be930b5da674874a0b634eca3ad9346 +#: ce445ad0f00f403985eed1328103a500 msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 2fe48d6404864ea39ef0634169f67be1 +#: 43453d90db244c558a815ca872dc716c msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: 37392218309d4baebe62fc38bf50efe9 78eaa318ba81407e9ca9c2c1702ead11 +#: f5da7058f7f146d584314a5bf4de5498 msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: 7189f4415d204fb388c4a7e927e15b71 msgid "" -"From " -"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" #: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 @@ -1868,7 +2095,11 @@ msgstr "" #: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd #: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 #: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ed875a006df64f9e8a55fa5e9fa87404 17a83cc91963434e89822a3e46df8401 +#: 194d3e48d38c476fa8f731e3bc2d8c7f 3a3000a6446b4ef4ac66a28acb13b136 +#: 5cc35210e95e4f2ba6a1a6f118926fdd 68b3d1481a4e4375b1b0c4fca8285374 +#: 94f2bc195bc0487da014bc3f4d2dc8fa b92b4eff2429437d9da911ca68cef954 +#: fc0a1353e87e479d8c8b6c973d547465 msgid "`format`" msgstr "" @@ -1881,800 +2112,914 @@ msgstr "" #: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d #: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f #: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 +#: f760465a49d64d4c8468ad9c4fea62b1 5478cbeadc64412bbb32619fae9b9958 +#: 6950cbe52d334fe58bf4fa20e5f1f8ca 6b5bda581d0047819c6d92edd8ac9045 +#: 8248329fbe504b3a96bcd890908b070f 978c0fea8ed1481a9f06b6abb31ebd21 +#: a24ba514d66d49cea281fd4c9c7a2b8d b6e2c8e7abf74d64b2915063dda8479b +#: bc184adfad0e4642bc864d367b8779b7 msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: 5bba2d465e0a4c5d9575406d1294a225 msgid "" -"From " -"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: da385d3cde614749887e195ea6d95291 msgid "" -"From " -"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: 487c95417f8e48be8391163578ca9519 msgid "" -"From " -"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: d193ce0123db4535a4f0b11405ad0322 48437402c00147d4b4ca8bd6b38a5823 +#: bdcb3920048f4e578a4005fc2e30233b msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 +#: d555a3d991e344a5a8e1289168d7c6d1 121556d49d584cc491a15ef8404ce462 +#: 183ba52666744f7ca5772939db2efd6c msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: e9fa9430535c424fa3e8be5d460d2ba4 08ad064936d8406f8c3852526f4f863d +#: 30c927925c6b483b80b583ca7c735437 msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: 32a26dd9c5f84e88995f093cda953ac9 msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff +#: b0290d1a477b48119e17cf1fed9d6dff 05ee6df2f9b247629d148fd59c293660 +#: e7b7d782b6ac49b3aa0c8d8ce7ff04d1 msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: b0cccc07e5bb4effb60424623351499e msgid "" -"From " -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 +#: e1cde4aa32c041238ed2596173c6d824 4e5281c8663c4b6e8851be10f50143f1 +#: b5c22c66397e4268b4b3d53b9a253a3a msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 +#: c2a92d3eca7f4ee39cec649170eeea53 98a28fec818e42af9e177e17fa12aa7a +#: c37d0b1fd75e44a28b3b6409f912e865 msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: dcc42c6c49964a4ca7bcf2124e26ebfd msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](https://www." +"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: d2ba352ac5fe427ea7ceb0bde01458ba msgid "" -"From " -"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: d0eec6969d174b258e0f010800884cc6 235cfd6e9baf48698102447fcb83e0e1 +#: 8aad01df8d8d4ab7905a5da7ce7f6bbf msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 +#: 718ceee9973240ec9c100977bbcc8921 058ba8c9c2da4ebf8b2291600dafd611 +#: cea47d3e10f641a2b64f08ee100ea6bf msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: c07ab08eb75d4528949c56a3d7c12b28 3b039de5ad144207ae337aa88b3b1a1f +#: e0ecfe44b34e45dea513459b6b3e44a6 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: b885e108dced4981a445e5fa0a044394 1cfc6cb0be4e4ddd90f546adb796b805 +#: b62f6eaa7c394792929dda83a187c632 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: e9f5306ae6ea49bbb6801dcce9be2d67 8b13b0e4071444179b26401929de8a10 +#: 8ffb471129c04fc6bb52b782fbd09f9b msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: 58bf8016f5f04c26b645025f405e2288 331f58b998cd4d309940ebfcc60a44f8 +#: 5041700e6ccc48989e395a6dcb1be3c4 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: 7c817029d55b4700ae8e84be4d0f0ca0 14402b41c64548f8a9691c3b7ccaf3ac +#: cb4837a2b25343d2880a07143f85f40e msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 #: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 1d1c2894600544b686a8ec3c36cdf767 eaa30e987ec543ef8d6f7171de5525f0 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: 065c97a553904db6ba61c20cf9d9939c msgid "" -"From " -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 #: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 36be05289972455ea4a60aa1f0b9cbdf 49e1ab5bc5734debb83060759d5c3236 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: f8e37cd35aea4bbb92d28e8d7e803ebb msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 #: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +#: de816d1dc9f24c0cbef86fd6a09eff6b e265df9d1cfe439bb798ab6cd32485af msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 #: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +#: 0363e32e12604eb896f4bdf6bbefd550 8b5289393b7f477699d007ded45a4df1 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 #: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: 2c704cae43d64ecbbed33d18eb3f66f3 89acc8f8387d4643a844ac3efb186000 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: 0597c6c214924e75ba2f212cd6b0c9f2 msgid "" -"From " -"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 #: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 1eb1c2432dd943f6a27a1f8b92e3981b 5b9ba9380f10425b809c6157a1f0b052 msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +#: b4cc7cc55cf04449b291a27514fc99ae +msgid "" +"Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: cdb48eff43e7459fbf3ed21eb7791d66 msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" -" attribute that allows users to load external JavaScript files, or to " -"provide inline JavaScript code." +"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " +"attribute that allows users to load external JavaScript files, or to provide " +"inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: 67a4dc675c0e444585d579954b99614e msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts" -" of the CWL document." +"files or to create JavaScript functions that can be called in other parts of " +"the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: ea3238db48494ab7b044bab9f96590af msgid "" -"The CWL standards (versions 1.0 through 1.2) " -"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" -" that the only version of JavaScript valid in CWL expressions is " -"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " -"that any code that you include or write in your CWL Document must be " -"compliant with ECMAScript 5.1." +"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." +"org/v1.0/CommandLineTool.html#Expressions) that the only version of " +"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" +"international.org/5.1/). This means that any code that you include or write " +"in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: baf2f6ac8d514705a1f7bf7ea8c71d2e msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a " -"JavaScript function inline in `expressionLib`. That function can then be " -"used in other parts of the CWL document:" +"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " +"function inline in `expressionLib`. That function can then be used in other " +"parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: ef45f4e14fb943cd9fbf179f5d3680e5 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: 030261615c38485d83ed986c9c98ce15 msgid "" -"Running this CWL workflow will invoke the JavaScript function and result " -"in the `echo` command printing the input message with capital initial " -"letters:" +"Running this CWL workflow will invoke the JavaScript function and result in " +"the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: 1728e2370cbb49ab97bee4c2f74fff2d msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: 4514fc0c99ac4688a37bf30bffe139e8 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: 33804649720143e5a70e890af9ad9119 msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: c114496be4c243d6834776e17bf15010 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: c784e86f14f54e4982db206741fbd96e msgid "" -"The `custom-functions.js` file is included in the CWL document with the " -"`$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the `" +"$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: f9de69aad9b44afabded71221c84adc2 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: b853c964611e45c2b37a8ac3c34a4133 msgid "" -"Finally, note that you can have both inline and external JavaScript code " -"in your CWL document. In this final example we have added another entry " -"to the `expressionLib` attribute with the new function " -"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" -" the external file `custom-functions.js`." +"Finally, note that you can have both inline and external JavaScript code in " +"your CWL document. In this final example we have added another entry to the " +"`expressionLib` attribute with the new function `createHelloWorldMessage`, " +"that calls the `capitalizeWords` function from the external file `custom-" +"functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: a10d143210b94f83857f62e972d69134 msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: b07734b172664040aff04f83bd4395a5 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: 1f9a5377a1f04ee3b8a9ae22390e0cae msgid "" -"The `$include` statement can be used to include a file from the local " -"disk or from a remote location. It works with both relative and absolute " -"paths. Read the [text about " -"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " -"the CWL specification to learn more about it." +"The `$include` statement can be used to include a file from the local disk " +"or from a remote location. It works with both relative and absolute paths. " +"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: 359bb6448aa140f8b940baf769c13db6 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: c4aba730bee14931b051d6aead7c2dae msgid "" "Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This " -"helps document for others how to use your tool while allowing you to do " -"some simple type-checking when creating parameter files." +"output. We also recommend indicating the format for `File` types. This helps " +"document for others how to use your tool while allowing you to do some " +"simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: c4dfcff573424bccb97580fdd1ef27a1 msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM" -" in our example), reference a local ontology for your institution, or do " -"not add a file format initially for quick development before sharing your" -" tool with others. You can browse existing [IANA file format " -"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +"For file formats, we recommend referencing existing ontologies (like EDAM in " +"our example), reference a local ontology for your institution, or do not add " +"a file format initially for quick development before sharing your tool with " +"others. You can browse existing [IANA file format listings][IANA] and [EDAM " +"file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: 1457fa489c894f1bae8a3949ef200527 msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` " -"section of the document in greater detail, so don't worry about these for" -" now." +"In the next tutorial, we explain the `$namespaces` and `$schemas` section " +"of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: cc4fa87d57b344ed8961c31bc4397e71 msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: 091815ab1d824787a1460ce11ffb834d msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 #: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 414b68dac4654163b3dc13e140ffdbf8 96fad38b4aea461493bf0827476163bd msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: 4f71de1140974e73ab033fe7dd9dc165 msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: b84e3294c8f648aab634e59b6f58441e msgid "" -"Below is an example of a parameter file for the example above. We " -"encourage checking in working examples of parameter files for your tool. " -"This allows others to quickly work with your tool, starting from a " -"\"known good\" parameterization." +"Below is an example of a parameter file for the example above. We encourage " +"checking in working examples of parameter files for your tool. This allows " +"others to quickly work with your tool, starting from a \"known good\" " +"parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: 6d9ae44900d64532906532432881d29d msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: 5b99384b3a854832bcca2fb02bdfc1b6 msgid "" -"___Note:___ To follow the example below, you need to download the example" -" input file, *file-formats.bam*. The file is available from " -" and can be downloaded e.g. via `wget`:" +"___Note:___ To follow the example below, you need to download the example " +"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: 3141fc6828024c3e8201e88ca10e19ee msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: 5f8c8ea68d7f46fead000315226ec164 msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: 86c18e5105b1400d86d413e28ad72f48 msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: fa15037f9b0b4a2c9a1f4cff9b8fde43 msgid "" -"The `inputs` of a tool is a list of input parameters that control how to " -"run the tool. Each parameter has an `id` for the name of parameter, and " -"`type` describing what types of values are valid for that parameter." +"The `inputs` of a tool is a list of input parameters that control how to run " +"the tool. Each parameter has an `id` for the name of parameter, and `type` " +"describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: fba6d2b7843e466abee33183103cf47d msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*," -" and *null*; complex types are *array* and *record*; in addition there " -"are special types *File*, *Directory* and *Any*." +"Available primitive types are *string*, *int*, *long*, *float*, *double*, " +"and *null*; complex types are *array* and *record*; in addition there are " +"special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: 09f5a55611d14e39b2266245b79ed763 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: bdfb39c2656040858616afe731111d1a msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: c306335ff07e4c03955fe87cad16efd1 msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: 50bd3db6bfb348eea13ba4714ecb2a20 msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: 5d32cfb6f6ed4dd8b11ed316830edba8 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: b90fb1b2d38b42c1bad2d9667aaa22fd msgid "" -"You can use `cwltool` to create a template input object. That saves you " -"from having to type all the input parameters in a input object file:" +"You can use `cwltool` to create a template input object. That saves you from " +"having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: 6029a96abf9c4d7295eb86d435a1f58d msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template " -"inp.cwl > inp-job.yml`, and then modify the default values with your " -"desired input values." +"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " +"> inp-job.yml`, and then modify the default values with your desired input " +"values." msgstr "" #: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: 902e9df74f78431ca9cf1421a26e097a msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: 9760d15bad144e70a86dc0a8da72363a msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" -" command line." +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " +"command line." msgstr "" #: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: 75bf3fae131049308441bc496f543f6e msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " -"following boxed text describes these two commands and the expected output" -" from the command line:" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " +"boxed text describes these two commands and the expected output from the " +"command line:" msgstr "" #: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: 38d8a9c157404bb496bc49f1e427bf99 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not " -"explicitly specified" +"that the tools aren't accidentally accessing files that were not explicitly " +"specified" msgstr "" #: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: 502994ee84234f048e545633bb04cd3c msgid "" -"The field `inputBinding` is optional and indicates whether and how the " -"input parameter should appear on the tool's command line. If " -"`inputBinding` is missing, the parameter does not appear on the command " -"line. Let's look at each example in detail." +"The field `inputBinding` is optional and indicates whether and how the input " +"parameter should appear on the tool's command line. If `inputBinding` is " +"missing, the parameter does not appear on the command line. Let's look at " +"each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: 551b06b8a3064bcd8d0f1693a4c0ee94 msgid "" -"Boolean types are treated as a flag. If the input parameter " -"\"example_flag\" is \"true\", then `prefix` will be added to the command " -"line. If false, no flag is added." +"Boolean types are treated as a flag. If the input parameter \"example_flag" +"\" is \"true\", then `prefix` will be added to the command line. If false, " +"no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: 1838e7438be5449c91c6406a7e40d8cb msgid "" -"String types appear on the command line as literal values. The `prefix` " -"is optional, if provided, it appears as a separate argument on the " -"command line before the parameter . In the example above, this is " -"rendered as `--example-string hello`." +"String types appear on the command line as literal values. The `prefix` is " +"optional, if provided, it appears as a separate argument on the command line " +"before the parameter . In the example above, this is rendered as `--example-" +"string hello`." msgstr "" #: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: 098bb02c941a4bf2a8d4dd9ab3bf052e msgid "" -"Integer (and floating point) types appear on the command line with " -"decimal text representation. When the option `separate` is false (the " -"default value is true), the prefix and value are combined into a single " -"argument. In the example above, this is rendered as `-i42`." +"Integer (and floating point) types appear on the command line with decimal " +"text representation. When the option `separate` is false (the default value " +"is true), the prefix and value are combined into a single argument. In the " +"example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: b43194d2b3ef4fc6a8c4b58741317b29 msgid "" "File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the " -"parameter is optional. In the example above, this is rendered as " -"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " -"parameter were not provided in the input, nothing would appear on the " -"command line." +"parameter type ends with a question mark `?` it indicates that the parameter " +"is optional. In the example above, this is rendered as `--file=/tmp/random/" +"path/whale.txt`. However, if the \"example_file\" parameter were not " +"provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: e17c55c9ed034dd68f4d24272a61d2f1 msgid "" -"Input files are read-only. If you wish to update an input file, you must" -" [first copy it to the output directory](staging-input-files.md)." +"Input files are read-only. If you wish to update an input file, you must " +"[first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: c97a6945e4bc49888d280bbc43c3c069 msgid "" -"The value of `position` is used to determine where parameter should " -"appear on the command line. Positions are relative to one another, not " -"absolute. As a result, positions do not have to be sequential, three " -"parameters with positions 1, 3, 5 will result in the same command line as" -" 1, 2, 3. More than one parameter can have the same position (ties are " -"broken using the parameter name), and the position field itself is " -"optional. The default position is 0." +"The value of `position` is used to determine where parameter should appear " +"on the command line. Positions are relative to one another, not absolute. " +"As a result, positions do not have to be sequential, three parameters with " +"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " +"than one parameter can have the same position (ties are broken using the " +"parameter name), and the position field itself is optional. The default " +"position is 0." msgstr "" #: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: 503666cda07b4d7397c65561714d8034 msgid "" -"The `baseCommand` field will always appear in the final command line " -"before the parameters." +"The `baseCommand` field will always appear in the final command line before " +"the parameters." msgstr "" #: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: e5463be0a00d42e386aa6fd3dfacaeaf msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: 14b98bd0ef4a4065a24e66443458d607 msgid "" "It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to " -"provide `type` field with `type: array` and `items` defining the valid " -"data types that may appear in the array. Alternatively, brackets `[]` may" -" be added after the type name to indicate that input parameter is array " -"of that type." +"line. There are two ways to specify an array parameter. First is to provide " +"`type` field with `type: array` and `items` defining the valid data types " +"that may appear in the array. Alternatively, brackets `[]` may be added " +"after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: 98fa5dab117e41d4a42da8d78c533c64 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: 116c212444da4488b32abdbd725db98a msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 #: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +#: 065e556e01b34c35b6be4b54b7cc0203 4745f370dcbd4ee8bbf4b3a20ac5b9fe +#: d11761f2d576464f8a2c63bdec02d410 msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" +"Now invoke `cwltool` providing the tool description and the input object on " +"the command line:" msgstr "" #: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: b3bf1d7e95704682b1bae17472eaa4bc msgid "" -"The `inputBinding` can appear either on the outer array parameter " -"definition or the inner array element definition, and these produce " -"different behavior when constructing the command line, as shown above. In" -" addition, the `itemSeparator` field, if provided, specifies that array " -"values should be concatenated into a single argument separated by the " -"item separator string." +"The `inputBinding` can appear either on the outer array parameter definition " +"or the inner array element definition, and these produce different behavior " +"when constructing the command line, as shown above. In addition, the " +"`itemSeparator` field, if provided, specifies that array values should be " +"concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: 04bc655130234786b06b2d5b9e693635 msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` " -"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " -"lines, where array values that are not defined with an associated key are" -" marked by a leading `-`. This will be demonstrated in the next lesson " -"and is discussed in more detail in the [YAML Guide](yaml-" -"guide.md#arrays). You can specify arrays of arrays, arrays of records, " -"and other complex types." +"Note that the arrays of inputs are specified inside square brackets `[]` in " +"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " +"where array values that are not defined with an associated key are marked by " +"a leading `-`. This will be demonstrated in the next lesson and is discussed " +"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " +"arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: e2c18a43b2794448b45c489dd2fa951e msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: 38968ed627514ef38e43b3d1e4a5e25f msgid "" "Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be " -"provided together (they are exclusive). You can use records and type " -"unions to group parameters together to describe these two conditions." +"together (they are dependent) or several arguments that cannot be provided " +"together (they are exclusive). You can use records and type unions to group " +"parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: 06aab84eceeb41d087b7e295ffa21586 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: a0317edb8b964cd2a36c59eaa6df302a msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: 5a3d1b82c79c4ccdb7d06381f4d0acda msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" #: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: e1fc6c3a324a46ee84b0eb59f8396552 msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: f22e7d9e23b541ef88f3254095147519 msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the " -"first matching item (`itemC`) is added to the command line and remaining " -"item (`itemD`) is ignored." +"In the second example, `itemC` and `itemD` are exclusive, so only the first " +"matching item (`itemC`) is added to the command line and remaining item " +"(`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: d473d2fa11f64e8fa86554b5777c98e4 msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: 290461c321d14d23b39003b93008a7cb msgid "" -"In the third example, only `itemD` is provided, so it appears on the " -"command line." +"In the third example, only `itemD` is provided, so it appears on the command " +"line." msgstr "" #: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: add43f7531bb4c6988053ae799c366f0 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: b12b6f5e34c14dbc9b40458d92e6797f msgid "" -"If you use exclusive input parameters combined with expressions, you need" -" to be aware that the `inputs` JavaScript object will contain one of the " +"If you use exclusive input parameters combined with expressions, you need to " +"be aware that the `inputs` JavaScript object will contain one of the " "exclusive input values. This means that you might need to use an **or** " "boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: 4d8f38679952486095a77692387db2d3 msgid "" "Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from" -" an enum." +"parameter that accepts `null` (i.e. no value provided), or any value from an " +"enum." msgstr "" #: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: 47ec49759e274e59834192b794ec2d9b msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: 0657044c742348fe9e63f662692570a1 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you " -"provide a valid value, such as “fasta” (one of the values of the enum), " -"your command should execute successfully:" +"parameter without taking into consideration a `null` value. If you provide a " +"valid value, such as “fasta” (one of the values of the enum), your command " +"should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: 30c21cafda144f848bfe79d8e232296e msgid "" -"However, if you do not provide any input value, then `file_format` will " -"be evaluated to a `null` value, which does not match the expected type " -"for the output field (a `string`), resulting in failure when running your" -" workflow." +"However, if you do not provide any input value, then `file_format` will be " +"evaluated to a `null` value, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: 1cc8ea6abb684470b7790808acea2be1 msgid "" -"To correct it, you must remember to use an or operator in your JavaScript" -" expression when using exclusive parameters, or any parameter that allows" -" `null`. For example, the expression could be changed to " -"`$(inputs.file_format || 'auto')`, to have a default value if none was " -"provided in the command line or job input file." +"To correct it, you must remember to use an or operator in your JavaScript " +"expression when using exclusive parameters, or any parameter that allows " +"`null`. For example, the expression could be changed to `$(inputs." +"file_format || 'auto')`, to have a default value if none was provided in the " +"command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: d33aa2353ad44fb885d3a1ee48263dc4 c3b84742343449f9b3866285d98b53bb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: cd64d2d828834cbbb24ea5358caf5405 0a1b08fe707c41089ad3d4895960ba17 msgid "" -"Implementation extensions not required for correct execution (for " -"example, fields related to GUI presentation) and metadata about the tool " -"or workflow itself (for example, authorship for use in citations) may be " -"provided as additional fields on any object. Such extensions fields (e.g." -" `format: edam:format_2572`) can use a namespace prefix listed in the " -"`$namespaces` section of the document (e.g. edam: " -"http://edamontology.org/) as described in the [Schema Salad specification" -"][schema-salad]. Once you add the namespace prefix, you can access it " -"anywhere in the document as shown below. Otherwise, one must use full " -"URLs: `format: http://edamontology.org/format_2572`." +"Implementation extensions not required for correct execution (for example, " +"fields related to GUI presentation) and metadata about the tool or workflow " +"itself (for example, authorship for use in citations) may be provided as " +"additional fields on any object. Such extensions fields (e.g. `format: edam:" +"format_2572`) can use a namespace prefix listed in the `$namespaces` section " +"of the document (e.g. edam: http://edamontology.org/) as described in the " +"[Schema Salad specification][schema-salad]. Once you add the namespace " +"prefix, you can access it anywhere in the document as shown below. " +"Otherwise, one must use full URLs: `format: http://edamontology.org/" +"format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 80af387fe3ff4e2da999903385bd602b 5bc4ef6584c74b948ffd5c0bddf8e569 msgid "" "For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to " -"cite your tool." +"tool and workflows. This example includes metadata allowing others to cite " +"your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 47ee25d60a4a4faa80476797954ec7a9 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: d402bf528c7f4eb69aaaa275be2bf1d4 195d4a8d5aad41159beffafd198d4640 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 b0c5946fbf79415aa74c8e72fa88cf85 msgid "" -"For those that are highly motivated, it is also possible to annotate your" -" tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints" -" at hardware requirements in order to use the tool, and a few more " -"metadata fields." +"For those that are highly motivated, it is also possible to annotate your " +"tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints at " +"hardware requirements in order to use the tool, and a few more metadata " +"fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 2dfbd4d580044ed083992f3ceb1bc64e a98236fc1be745a69271855e1b5eecdb msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: 5f0da8d7e06a47fda38053dbadcbec18 msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: 23d41792b0524742878a6ab8f3ff0fe1 msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-" -"line tool, or an expression tool. It is a step of a workflow that " -"specifies inputs and outputs, but it does not provide enough information " -"to be executed." +"An Operation is a type of CWL process, just like a workflow, a command-line " +"tool, or an expression tool. It is a step of a workflow that specifies " +"inputs and outputs, but it does not provide enough information to be " +"executed." msgstr "" #: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: c0f723242f11464392dfc32f67a3b67b msgid "" -"You can create operations to visualize a workflow during development, " -"before you are ready to submit the workflow to a CWL runner:" +"You can create operations to visualize a workflow during development, before " +"you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: c9f3a48a3a064cb3b1759effe724301d msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: fbad0b0144984ae78b84307ea68d0a03 msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like" -" a command line tool or an expression. You can also plot it with the CWL " -"Viewer or `cwltool`:" +"The `uppercase` step of the workflow is an operation. It can be used like a " +"command line tool or an expression. You can also plot it with the CWL Viewer " +"or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: 59e9ff3276454ff19eb351ff33737f12 msgid "" -"The output of the command above can be rendered with a Graphviz renderer." -" The following image is rendered with the Sphinx Graphviz directive (this" -" user guide is built with Sphinx):" +"The output of the command above can be rendered with a Graphviz renderer. " +"The following image is rendered with the Sphinx Graphviz directive (this " +"user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: ba74f2ab7f6d4c178f3c4c43c461afbd msgid "" -"If you try running it with `cwltool`, the command will fail since " -"`cwltool` does not have enough information to know how to execute it:" +"If you try running it with `cwltool`, the command will fail since `cwltool` " +"does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: 93c8b61a12134991ae9bb78223e2017e msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: cbbdba36dc3841f2b1d820f369a8c680 msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A" -" CWL runner could, for instance, use abstract operations with ID's that " +"CWL runners may come up with ways to bind operations to concrete steps. A " +"CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: 4649c8d743f448ab94ee589a1b3a342a msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: 1a9d6e2e33244d01b820cf11fe2beaff msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: 233c8865faac4d6c8ec7704e9a997719 msgid "" "The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name" -" of parameter, and `type` describing what types of values are valid for " -"that parameter." +"returned after running the tool. Each parameter has an `id` for the name of " +"parameter, and `type` describing what types of values are valid for that " +"parameter." msgstr "" #: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: 5aab1c0db3d5449cbb4a0f0dad615d87 msgid "" -"When a tool runs under CWL, the starting working directory is the " -"designated output directory. The underlying tool or script must record " -"its results in the form of files created in the output directory. The " -"output parameters returned by the CWL tool are either the output files " -"themselves, or come from examining the content of those files." +"When a tool runs under CWL, the starting working directory is the designated " +"output directory. The underlying tool or script must record its results in " +"the form of files created in the output directory. The output parameters " +"returned by the CWL tool are either the output files themselves, or come " +"from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: 46b4eeb3ce8946dca0f8a94c399b4c96 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: 8d322609948a4d6e87d7962b3d29df2f msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: 9fdcb55e965444ee8b5d74a2a9870d27 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2683,464 +3028,520 @@ msgid "" msgstr "" #: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: e4c490f599a0469a821aa8e74f4ef0ef msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: b8ed6ebe6928455cb094ea430e21e5d4 msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: 3e65c52d218946fc83b8c3e6adcb21fe msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: 03751b45cdf647b689a3a69156989db5 msgid "" -"And now invoke `cwltool` with the tool description and the input object " -"on the command line:" +"And now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "" #: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: 1b6f59623f5d4cd984426da21b8438bf msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" #: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: 095902cca30944d19a0d5f17f582e3b0 msgid "" -"The `glob` field consists of the name of a file in the output directory. " -"If you don't know name of the file in advance, you can use a wildcard " -"pattern like `glob: '*.txt'`." +"The `glob` field consists of the name of a file in the output directory. If " +"you don't know name of the file in advance, you can use a wildcard pattern " +"like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: 6d95fbfa321144a9932f26ab5f9ddc74 msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: 8be7ef160e8b421a89124a639dc7fd84 msgid "" -"To capture a tool's standard output stream, add the `stdout` field with " -"the name of the file where the output stream should go. Then add `type: " -"stdout` on the corresponding output parameter." +"To capture a tool's standard output stream, add the `stdout` field with the " +"name of the file where the output stream should go. Then add `type: stdout` " +"on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: fcf4490c351d4cd6a208345308168ef7 msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: 00f1bb92a38b4f3a8c0065ac75530689 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: 1477d0fc5c4c4f82bcc1c8e6ba8eed4d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" #: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: dee904cb678d4eb49dc829d6590b267a msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: a21c1fd3194a49ae992a743023653dc5 msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: e72c526da47a455da4b10e33938d1600 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions" -" to mark entries in arrays, as demonstrated in several of the upcoming " -"sections." +"marked by a leading `-`. This format can also be used in CWL descriptions to " +"mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: 6447f4b8bb5f4f93bd8ec2c7b1fb09cb msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: 1faea30495a440a68dbd1647dacc404c msgid "" "In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file " -"we were interested in was called \"hello.txt\", and this was written into" -" the `.cwl` file. This is not the best way to do this, as the " -"\"hello.txt\" filename may vary or be dependent on the input file(s) " -"used. To avoid this we can specify the name of the file we want in the " -"job parameters file (`.yml`). In this example, you will see how to " -"reference the value of input parameters dynamically from other fields, " -"which will allow us to then specify the name of the file to extract." +"However, that example was very limited because it assumed that the file we " +"were interested in was called \"hello.txt\", and this was written into the `." +"cwl` file. This is not the best way to do this, as the \"hello.txt\" " +"filename may vary or be dependent on the input file(s) used. To avoid this " +"we can specify the name of the file we want in the job parameters file (`." +"yml`). In this example, you will see how to reference the value of input " +"parameters dynamically from other fields, which will allow us to then " +"specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: 0c0a3f58a93f492dbfca14523809aacc msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: 460842f202db493dbb901be73a02797f msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: 2591c2cf9e5f402281031ea8dd41a251 msgid "" -"Create your input files and invoke `cwltool` with the tool description " -"and the input object on the command line:" +"Create your input files and invoke `cwltool` with the tool description and " +"the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: b093abbff3614b2ba0141f07376a5220 msgid "" -"Certain fields permit parameter references which are enclosed in " -"`$(...)`. These are evaluated and replaced with value being referenced." +"Certain fields permit parameter references which are enclosed in `$(...)`. " +"These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: fda3718113354215bd2ac212553fb2d4 msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " -"`$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" +"$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: 271e78089c274154a0233289d705e628 msgid "" -"The value of the \"inputs\" variable is the input object provided when " -"the CWL tool was invoked." +"The value of the \"inputs\" variable is the input object provided when the " +"CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: 29ab4fa0876b4c11a0c7482cca56ed80 msgid "" -"Note that because `File` parameters are objects, to get the path to an " -"input file you must reference the path field on a file object; to " -"reference the path to the tar file in the above example you would write " -"`$(inputs.tarfile.path)`." +"Note that because `File` parameters are objects, to get the path to an input " +"file you must reference the path field on a file object; to reference the " +"path to the tar file in the above example you would write `$(inputs.tarfile." +"path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: 78e1857c5bd54af1b7ca4728879e6219 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: dae7873015254aa7874379164c90a8d0 msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: 7a45deb4682b49fd86d62fae41831db8 msgid "" -"From " -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: 442f77a69b314cba8e8857470263c706 msgid "" -"From " -"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: d4455241f14549b791e59fc1f942c8cb msgid "" -"From " -"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: ff4b1c05c5804ec7846043ae8814ad21 msgid "" -"From " -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: 119e026b595f49c090d62aa7b7c77de4 msgid "" -"From " -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: 5449d9c5687544a3bfbf8b2b25640a83 msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: b3191a7bd03d4ff18802ae0f5d419676 msgid "" -"From " -"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: ea9cfbbd4cbd4f26ba4b0cb50d58635b msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: 7d39ed2a3a724dc1a75e6b2cdf87d91d msgid "" -"From " -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 5d8bed66282c408695292ea92a03b2c4 a1306ee650344278ae39d6086b1ed7d9 msgid "" -"From " -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: 958178d1fa8843aaa0541e2bb115cfd4 21d76d22f3044460b925fee68ac74454 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 6b8a5c59217c4928874710ead1456622 msgid "" -"From " -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: aac74f957774479a83aab4c6ff1390ae a9f6d09055c24029a5f85c3a663c4202 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: b75d29d1d55d44488338f9689f156855 d3948618f9274ad0a333722567efeea5 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: 574d93d1d592458a985f259519c036cb 44623c81141345a0b0080e719e1418ab msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may " -"also help to avoid confusion about which version of a tool the " -"description was written for." +"include a `SoftwareRequirement` field in the `hints` section. This may also " +"help to avoid confusion about which version of a tool the description was " +"written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 82e48b3e3c3f451480cc0b6a529271f6 6e80d82ed57b441b8292961ec3163213 msgid "" -"In this example, the software requirement being described is InterProScan" -" version 5.21-60." +"In this example, the software requirement being described is InterProScan " +"version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: 02e40154eac74ecc98d0447d03475b44 fc61f369e720463f8a5cd6c751d1d5e6 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the " -"[dependency resolvers configuration][dependencies]." +"enable these checks with the reference implementation, use the [dependency " +"resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the " -"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" -" looked up in the [SciCrunch][scicrunch] registry, which provides a " -"portal for finding, tracking, and referring to scientific resources " -"consistently. If you want to specify a tool as a `SoftwareRequirement`, " -"search for the tool on SciCrunch and use the RRID that it has been " -"assigned in the registry. (Follow this [Adding a Resource Tutorial" -"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " -"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " -"field of your requirement description. Other good choices, in order of " -"preference, are to include the DOI for the main tool citation and the URL" -" to the tool." +#: 8cb1c5d9b1a54c40924099494eb766c6 f20aadbfc13243498ad199376c314e72 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the tool " +"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " +"up in the [SciCrunch][scicrunch] registry, which provides a portal for " +"finding, tracking, and referring to scientific resources consistently. If " +"you want to specify a tool as a `SoftwareRequirement`, search for the tool " +"on SciCrunch and use the RRID that it has been assigned in the registry. " +"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " +"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." +"org][identifiers]) in the `specs` field of your requirement description. " +"Other good choices, in order of preference, are to include the DOI for the " +"main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: e66956313b8f4f02bb96cfb256e2a7d4 msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: f18c5a8fcbe84135a6e06cbf8008cd63 msgid "" -"Normally, input files are located in a read-only directory separate from " -"the output directory. This causes problems if the underlying tool " -"expects to write its output files alongside the input file in the same " -"directory. You use `InitialWorkDirRequirement` to stage input files into" -" the output directory. In this example, we use a JavaScript expression to" -" extract the base name of the input file from its leading directory path." +"Normally, input files are located in a read-only directory separate from the " +"output directory. This causes problems if the underlying tool expects to " +"write its output files alongside the input file in the same directory. You " +"use `InitialWorkDirRequirement` to stage input files into the output " +"directory. In this example, we use a JavaScript expression to extract the " +"base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: 87fe14c9a0594602aa56a7706e089458 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: 6e10063f55b747e1b07d6109ab7b046b msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: e8831832b32449f4a8a3dde3c1b479cd msgid "" -"In this section you will find ways to troubleshoot when you have problems" -" executing CWL. We focus on `cwltool` here but some of these techniques " -"may apply to other CWL Runners." +"In this section you will find ways to troubleshoot when you have problems " +"executing CWL. We focus on `cwltool` here but some of these techniques may " +"apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: 9c86467137864626a2079cb6cecb71c0 msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: 24b66a3e2e464ec6a85b5dfbaad1cbf4 msgid "" "You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor " -"output files, but created while your workflow is running). By default, " -"these files are created in a temporary directory but writing them to a " -"separate directory makes accessing them easier." +"`cwltool` to cache intermediate files (files that are not input nor output " +"files, but created while your workflow is running). By default, these files " +"are created in a temporary directory but writing them to a separate " +"directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: 6d28f1cd40c045f384313c4d74073ed2 msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " -"World\" | rev`, which would print the message \"Hello World\" reversed, " -"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," -" where instead of executing the `rev` command it tries to execute `revv`," -" which fails." +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " +"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " +"olleH\". However, the second step, `step_b`, **has a typo**, where instead " +"of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: 5235ff0c35c54396aceb799a65f6158e msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: fc49344510594559b4f888bc45093b51 msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " -"value (`cwltool` will create the directory for you if it does not exist " -"already):" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " +"(`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: 6e62be8d7d1344e8917904278b508518 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. " -"You can inspect the intermediate files created:" +"successfully and its output has been cached in your `cachedir` location. You " +"can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: c91b3a2818b143f58bd37da63479c560 msgid "" -"Each workflow step has received a unique ID (the long value that looks " -"like a hash). The `${HASH}.status` files display the status of each step " -"executed by the workflow. And the `step_a` output file `stdout.txt` is " -"visible in the output of the command above." +"Each workflow step has received a unique ID (the long value that looks like " +"a hash). The `${HASH}.status` files display the status of each step executed " +"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " +"output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: 86f283bc522c4be2adfac16256f01b0e msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" -" in the `step_b`). After fixing the typo, when you execute `cwltool` with" -" the same arguments as the previous time, note that now `cwltool` output " -"contains information about pre-cached outputs for `step_a`, and about a " -"new cache entry for the output of `step_b`. Also note that the status of " -"`step_b` is now of success." +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " +"the `step_b`). After fixing the typo, when you execute `cwltool` with the " +"same arguments as the previous time, note that now `cwltool` output contains " +"information about pre-cached outputs for `step_a`, and about a new cache " +"entry for the output of `step_b`. Also note that the status of `step_b` is " +"now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: 5362aa1d28344968953ab9cb389ccd8e msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had" -" been cached, and there was no change in its execution or output. " +"In this example the workflow step `step_a` was not re-evaluated as it had " +"been cached, and there was no change in its execution or output. " "Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for" -" troubleshooting your CWL documents and also as a way to prevent " -"`cwltool` to re-evaluate steps unnecessarily." +"`step_b` after we fixed the executable name. This technique is useful for " +"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " +"re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: 4bb1aafde4f745a083d3a276497523dc msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: b00987baf6974ff9b7e3b8cdfd7abd9a msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: 9ac51c5a2a0a45859e14d9e388edd5f0 msgid "" -"[Docker][docker] containers simplify software installation by providing a" -" complete known-good runtime for software and its dependencies. However," -" containers are also purposefully isolated from the host system, so in " -"order to run a tool inside a Docker container there is additional work to" -" ensure that input files are available inside the container and output " -"files can be recovered from the container. A CWL runner can perform this" -" work automatically, allowing you to use Docker to simplify your software" -" management while avoiding the complexity of invoking and managing Docker" -" containers." +"[Docker][docker] containers simplify software installation by providing a " +"complete known-good runtime for software and its dependencies. However, " +"containers are also purposefully isolated from the host system, so in order " +"to run a tool inside a Docker container there is additional work to ensure " +"that input files are available inside the container and output files can be " +"recovered from the container. A CWL runner can perform this work " +"automatically, allowing you to use Docker to simplify your software " +"management while avoiding the complexity of invoking and managing Docker " +"containers." msgstr "" #: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: 5494ccdb1a354b2386c82bd9a6f0b6a9 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the " -"container." +"input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: 4cfa8fc2bb224883946d5f63b372de82 msgid "" -"This example runs a simple Node.js script inside a Docker container which" -" will then print \"Hello World\" to the standard output." +"This example runs a simple Node.js script inside a Docker container which " +"will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: e16c1922527a46e28bb5d933614cdaf7 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: 7498a71704be462abef71c42e6b83d1b msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: ac0689bff9db46ea8bff8cd35cde86f3 msgid "" "Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that " -"is really new is the `dockerRequirement` section." +"Most of this has been explained in previous sections, the only part that is " +"really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: c4b7da5575674ca3ae734424022ef090 msgid "" -"`baseCommand: node` tells CWL that we will be running this command using " -"the Node Js runtime that is meant for Javascript files. We then need to " -"specify some `hints` for how to find the container we want. In this case" -" we list just our requirements for the docker container in " -"`DockerRequirements`. The `dockerPull:` parameter takes the same value " -"that you would pass to a `docker pull` command. That is, the name of the " -"container image (you can even specify the tag, which is good idea for " -"best practices when using containers for reproducible research). In this " -"case we have used a container called `node:slim`." +"`baseCommand: node` tells CWL that we will be running this command using the " +"Node Js runtime that is meant for Javascript files. We then need to specify " +"some `hints` for how to find the container we want. In this case we list " +"just our requirements for the docker container in `DockerRequirements`. The " +"`dockerPull:` parameter takes the same value that you would pass to a " +"`docker pull` command. That is, the name of the container image (you can " +"even specify the tag, which is good idea for best practices when using " +"containers for reproducible research). In this case we have used a container " +"called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: d24fcecc17d0461cbd8689067f770c0d msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` " -"providing the tool description and the input object on the command line:" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " +"the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: 833d4d3b3f0e4c7cb8b1d35cb9a78a7e msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: 50fc0573276e4dd4a47208ed81109991 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" #: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: f72e10e746604421904057ddf7078d3e msgid "" -"In this example, the path to the script `hello.js` is " -"`/home/me/cwl/user_guide/hello.js` outside the container but " -"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " -"reflected in the invocation of the `node` command." +"In this example, the path to the script `hello.js` is `/home/me/cwl/" +"user_guide/hello.js` outside the container but `/var/lib/cwl/" +"job369354770_examples/hello.js` inside the container, as reflected in the " +"invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: ee126833f6014e378c7841c4048dae85 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: 0325bd610aa747b0b657afa0c978a1eb msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " @@ -3148,239 +3549,265 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: 7c901105cf6949909d87be5681331368 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: 74138d0c2ded4311bf688df4a28387b5 msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier " -"examples." +"command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: 1ec4773e7319414b997d746d1965ff56 msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: 5f860dd70e3b435188c61a538e5de0ef msgid "" -"A command-line tool or expression tool can also be written directly in " -"the same CWL document as the workflow. For example, we can rewrite the " -"`echo-uppercase.cwl` workflow as a single file:" +"A command-line tool or expression tool can also be written directly in the " +"same CWL document as the workflow. For example, we can rewrite the `echo-" +"uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: a9c56df6dca441dfabda7fa54fbe56c6 msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: 586d561ddf724319b3da9ae857828648 msgid "" -"Having separate files helps with modularity and code organization. But it" -" can be helpful writing everything in a single file for development. " -"There are other ways to combine multiple files into a single file (e.g. " -"`cwltool --pack`) discussed further in other sections of this user guide." +"Having separate files helps with modularity and code organization. But it " +"can be helpful writing everything in a single file for development. There " +"are other ways to combine multiple files into a single file (e.g. `cwltool --" +"pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: f3e80b1903534065a30323611c267e9b msgid "" "For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this" -" user guide in more detail." +"`SubworkflowFeatureRequirement`. It is covered in another section of this " +"user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: 6ed53c6f9fb94d4ab3d10532c605c46b msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: 3fcfdf43b0a049388634625c45e0b1bb msgid "" -"This workflow extracts a java source file from a tar file and then " -"compiles it." +"This workflow extracts a java source file from a tar file and then compiles " +"it." msgstr "" #: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: 49415efafae64f94b66cb46ca2bbd40a msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 #: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 4806a2ef982944e8b073fafd416d3d74 d45701eeaa6e42feb4ef79d2fc4af756 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: 155cd684ff304258ae374b2e13090e5f msgid "" -"[![Visualization of 1st-" -"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" +"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" "workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" +"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" +"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: d8bdb44011274f94b606277799a6fa6f msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a" -" run:" +"Use a YAML or a JSON object in a separate file to describe the input of a " +"run:" msgstr "" #: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: 9e1d9bc2f83743ea9964ec418d225200 msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: a1240eab3ef746cf82a2c5451042b888 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: a73cdc43a8e44973808027c29903afa3 msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: 4277837a9fd443378d5ca3d9252993c9 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a " -"workflow." +"document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: 09b714af60ee4ecc8ab1b95eac8284dd msgid "" -"The `inputs` section describes the inputs of the workflow. This is a " -"list of input parameters where each parameter consists of an identifier " -"and a data type. These parameters can be used as sources for input to " -"specific workflows steps." +"The `inputs` section describes the inputs of the workflow. This is a list " +"of input parameters where each parameter consists of an identifier and a " +"data type. These parameters can be used as sources for input to specific " +"workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: 3e99a3be9265463daf74b00a21d89cff msgid "" -"The `outputs` section describes the outputs of the workflow. This is a " -"list of output parameters where each parameter consists of an identifier " -"and a data type. The `outputSource` connects the output parameter " -"`classfile` of the `compile` step to the workflow output parameter " -"`compiled_class`." +"The `outputs` section describes the outputs of the workflow. This is a list " +"of output parameters where each parameter consists of an identifier and a " +"data type. The `outputSource` connects the output parameter `classfile` of " +"the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: 1c4a959d43b74686ab801a26ef412b3d msgid "" "The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second " -"step compiles the file from the first step using the java compiler. " -"Workflow steps are not necessarily run in the order they are listed, " -"instead the order is determined by the dependencies between steps (using " -"`source`). In addition, workflow steps which do not depend on one " -"another may run in parallel." +"example, the first step extracts a file from a tar file, and the second step " +"compiles the file from the first step using the java compiler. Workflow " +"steps are not necessarily run in the order they are listed, instead the " +"order is determined by the dependencies between steps (using `source`). In " +"addition, workflow steps which do not depend on one another may run in " +"parallel." msgstr "" #: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: 55daf180336d4045ac0cc4c14af98cfc msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input" -" parameters, `tarfile` and `extractfile` and one output parameter " +"[Parameter References](parameter-references.md)). This tool has two input " +"parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: 5ae40eb04d5440d5ba882a74aa5b9708 msgid "" -"The ``in`` section of the workflow step connects these two input " -"parameters to the inputs of the workflow, `tarball` and " -"`name_of_file_to_extract` using `source`. This means that when the " -"workflow step is executed, the values assigned to `tarball` and " -"`name_of_file_to_extract` will be used for the parameters `tarfile` and " -"`extractfile` in order to run the tool." +"The ``in`` section of the workflow step connects these two input parameters " +"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " +"`source`. This means that when the workflow step is executed, the values " +"assigned to `tarball` and `name_of_file_to_extract` will be used for the " +"parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: f93e9b776a4544018877b7a13399609b msgid "" -"The `out` section of the workflow step lists the output parameters that " -"are expected from the tool." +"The `out` section of the workflow step lists the output parameters that are " +"expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: 0e587435e3884334bc51a4abf4b4d785 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described " -"previously in [Additional Arguments and Parameters](additional-arguments-" -"and-parameters.md)). The output of this step `classfile` is connected to " -"the `outputs` section for the Workflow, described above." +"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " +"in [Additional Arguments and Parameters](additional-arguments-and-parameters." +"md)). The output of this step `classfile` is connected to the `outputs` " +"section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: 81b98764289245c79f18fcff478f4a9b msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: 9baddec4015f40ad82ea2dee30305654 msgid "" -"Workflows are ways to combine multiple tools to perform a larger " -"operations. We can also think of a workflow as being a tool itself; a CWL" -" workflow can be used as a step in another CWL workflow, if the workflow " -"engine supports the `SubworkflowFeatureRequirement`:" +"Workflows are ways to combine multiple tools to perform a larger operations. " +"We can also think of a workflow as being a tool itself; a CWL workflow can " +"be used as a step in another CWL workflow, if the workflow engine supports " +"the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: 986c3dd9460b42b3b20e2d01ba1fbe51 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" #: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: 4558f174fea445fd97b80d963fc74f43 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: 532823a13154401090e9fee3e018fda9 msgid "" -"This two-step workflow starts with the `create-tar` step which is " -"connected to the `compile` step in orange; `compile` is another workflow," -" diagrammed on the right. In purple we see the fixed string " -"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +"This two-step workflow starts with the `create-tar` step which is connected " +"to the `compile` step in orange; `compile` is another workflow, diagrammed " +"on the right. In purple we see the fixed string `\"Hello.java\"` being " +"supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: 7b6f46b70bac4f848a956ea160243621 msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows.cwl" +"\"> \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: 3861b4a31f71471b97bf9dc18cc80594 msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " -"its CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " -"mapped to become the step's input/outputs." +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " +"CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " +"to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: a10c37f65ac14ef2a5971872bc9b8f9a msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and " -"`*.java` filename. This is generally best-practice, as it means it can be" -" reused in multiple parent workflows, or even in multiple steps within " -"the same workflow." +"running it we had to provide a job file to denote the tar file and `*.java` " +"filename. This is generally best-practice, as it means it can be reused in " +"multiple parent workflows, or even in multiple steps within the same " +"workflow." msgstr "" #: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: 34175f932716406f836840732618caee msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar" -" file at `tarball`, which we will prepare in the `create-tar` step. At " -"this point it is probably a good idea to refactor `1st-workflow.cwl` to " -"have more specific input/output names, as those also appear in its usage " -"as a tool." +"`name_of_file_to_extract` input, however our workflow also requires a tar " +"file at `tarball`, which we will prepare in the `create-tar` step. At this " +"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " +"specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: 0d132dc39cdf4818bc8e20132073f669 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3389,186 +3816,212 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: 9f8c45f077974cf79612ee83df3d152b msgid "" -"In this case our step can assume `Hello.java` rather than be " -"parameterized, so we can use hardcoded values `hello.tar` and " -"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +"In this case our step can assume `Hello.java` rather than be parameterized, " +"so we can use hardcoded values `hello.tar` and `Hello.java` in a " +"`baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: 435f80d0599b4d93ae1339e8c7bc020a msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This " -"is generally not best practice, as the tool then can't be reused. The " -"reason for doing it in this case is because the command line is hard-" -"coded with filenames that only make sense within this workflow." +"separate file, but rather embedded it within the CWL Workflow file? This is " +"generally not best practice, as the tool then can't be reused. The reason " +"for doing it in this case is because the command line is hard-coded with " +"filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: d39b024a1a8d4eae8d7fd3c929a782e9 msgid "" -"In this example we had to prepare a tar file outside, but only because " -"our inner workflow was designed to take that as an input. A better " -"refactoring of the inner workflow would be to take a list of Java files " -"to compile, which would simplify its usage as a tool step in other " -"workflows." +"In this example we had to prepare a tar file outside, but only because our " +"inner workflow was designed to take that as an input. A better refactoring " +"of the inner workflow would be to take a list of Java files to compile, " +"which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: 3cbbe074843d4306b762d2fbc6fe9850 msgid "" "Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL" -" Tool description, care must be taken to improve its usability in " -"multiple workflows." +"functional and reusable workflow units - but just like for creating a CWL " +"Tool description, care must be taken to improve its usability in multiple " +"workflows." msgstr "" #: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: 7118b6e09b9f44129c7d98d90570f2c2 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: 70f3e73ee3714f22ad6ee43dd5ece703 msgid "" "Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish " -"to run a tool or workflow multiple times over a list of inputs. The " -"workflow then takes the input(s) as an array and will run the specified " -"step(s) on each element of the array as if it were a single input. This " -"allows you to run the same workflow on multiple inputs without having to " -"generate many different commands or input yaml files." +"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " +"run a tool or workflow multiple times over a list of inputs. The workflow " +"then takes the input(s) as an array and will run the specified step(s) on " +"each element of the array as if it were a single input. This allows you to " +"run the same workflow on multiple inputs without having to generate many " +"different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: 279495257ead4a4fa725c7d68c504162 msgid "" -"The most common reason a new user might want to use scatter is to perform" -" the same analysis on different samples. Let's start with a simple " -"workflow that calls our first example (`hello_world.cwl`) and takes an " -"array of strings as input to the workflow:" +"The most common reason a new user might want to use scatter is to perform " +"the same analysis on different samples. Let's start with a simple workflow " +"that calls our first example (`hello_world.cwl`) and takes an array of " +"strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: 86d1d742bb5c4a9898aa573ce648f0ec msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: f4987847f46e4a2db54127ec7ebcadf7 msgid "" -"Aside from the `requirements` section including " -"`ScatterFeatureRequirement`, what is going on here?" +"Aside from the `requirements` section including `ScatterFeatureRequirement`, " +"what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: 80e7c22dfe4d40749f2e9c3bf02bf8bc msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" #: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: e930bb5d430a41d9b5bf49e473dd2ed1 msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This " -"field tells the runner that we'd like to scatter over this input for this" -" particular step. Note that the input name listed after scatter is the " -"one of the step's input, not a workflow level input." +"Here we've added a new field to the step `echo` called `scatter`. This field " +"tells the runner that we'd like to scatter over this input for this " +"particular step. Note that the input name listed after scatter is the one of " +"the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: 4076e9eb67ed4bd5942f089e394bad26 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if " -"you expect that the final output of your workflow will now have multiple " -"outputs to collect, be sure to update that to an array type as well!" +"collect any outputs, we still use `outputs: []` in our workflow, but if you " +"expect that the final output of your workflow will now have multiple outputs " +"to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: 1b44092e87b840de8f1d022676d0990d msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: a8afac626f5d4240a57267085b9bef26 msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: 0896efc674bc402495c6e73c6c352523 msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" -" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " +"calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: 91a53d918d4b47bdbe0b0a6d4adfc0dc msgid "" -"You can see that the workflow calls echo multiple times on each element " -"of our `message_array`. Ok, so how about if we want to scatter over two " -"steps in a workflow?" +"You can see that the workflow calls echo multiple times on each element of " +"our `message_array`. Ok, so how about if we want to scatter over two steps " +"in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: 8325682d51d8421b9ea507f424f71e73 msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding " -"the following lines instead of `outputs: []`" +"Let's perform a simple echo like above, but capturing `stdout` by adding the " +"following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: 503d068602d8477a820b91d835fa3f28 msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: 4e768b91eb274a5cb157f1e3fe2f85cd msgid "" -"And add a second step that uses `wc` to count the characters in each " -"file. See the tool below:" +"And add a second step that uses `wc` to count the characters in each file. " +"See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: 18ec5231b7bf4c9ea59361b325fcdd01 msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: 87fd118dc2774cf08db0a3ba56520da5 msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under " -"each step:" +"Now, how do we incorporate scatter? Remember the scatter field is under each " +"step:" msgstr "" #: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: 8168ffcb23124b3f839a9862a7ec0958 msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 -msgid "" -"Here we have placed the scatter field under each step. This is fine for " -"this example since it runs quickly, but if you're running many samples " -"for a more complex workflow, you may wish to consider an alternative. " -"Here we are running scatter on each step independently, but since the " -"second step is not dependent on the first step completing all languages, " -"we aren't using the scatter functionality efficiently. The second step " -"expects an array as input from the first step, so it will wait until " -"everything in step one is finished before doing anything. Pretend that " -"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " -"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " -"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " -"could finish in 4 minutes, it will actually finish in 8 minutes because " -"the first step must wait on `echo Hallo welt!`. You can see how this " -"might not scale well." +#: 37c222ea14904fd4a8fa93a1e0103239 +msgid "" +"Here we have placed the scatter field under each step. This is fine for this " +"example since it runs quickly, but if you're running many samples for a more " +"complex workflow, you may wish to consider an alternative. Here we are " +"running scatter on each step independently, but since the second step is not " +"dependent on the first step completing all languages, we aren't using the " +"scatter functionality efficiently. The second step expects an array as input " +"from the first step, so it will wait until everything in step one is " +"finished before doing anything. Pretend that `echo Hello World!` takes 1 " +"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " +"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " +"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " +"actually finish in 8 minutes because the first step must wait on `echo Hallo " +"welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: d392813fc6d14851a294a391426d41f6 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can" -" make an entire workflow a single step in another workflow! Convert our " -"two-step workflow to a single step subworkflow:" +"samples? Remember from [Nested Workflows](#nested-workflows), that we can " +"make an entire workflow a single step in another workflow! Convert our two-" +"step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: 652155460eaa42b6856c16cffdb845c0 msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: 6313cb377dc249e0b2262a3fe732fe32 msgid "" -"Now the scatter acts on a single step, but that step consists of two " -"steps so each step is performed in parallel." +"Now the scatter acts on a single step, but that step consists of two steps " +"so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: 11f73cf24fb044e3a3afb3adb6137708 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: def9e62bf73f49eebce09677954e2a92 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " @@ -3576,252 +4029,357 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: 200dfe47d09d4b0b9e4acf29b7e038da msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: 858bda7fb6524e9dbfb35596ce6a6d07 msgid "" -"The first thing you'll notice is that this workflow is only compatible " -"for version 1.2 or greater of the CWL standards." +"The first thing you'll notice is that this workflow is only compatible for " +"version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: 28897819504247a3a6cf9a9d9476b63b msgid "" "The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when`" -" is where the condition validation takes place. In this case only when " -"`in1` from the workflow contains a value `< 1` this step will be " -"executed." +"will execute foo.cwl when the conditions are met. The new property `when` is " +"where the condition validation takes place. In this case only when `in1` " +"from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: 4f8fd11e29b048e1851299002c3a48c4 msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" -" will pass the first conditional step and will therefore be executed and " -"is shown in the log by `INFO [step step1] start` whereas the second step " -"is skipped as indicated by `INFO [step step2] will be skipped`." +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " +"will pass the first conditional step and will therefore be executed and is " +"shown in the log by `INFO [step step1] start` whereas the second step is " +"skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: ed33196347d949eda752a081c7af4657 msgid "" -"When a value of 3 is given the first conditional step will not be " -"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +"When a value of 3 is given the first conditional step will not be executed " +"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: 738c67568dbb4f2bbb5756fc5e727c01 msgid "" -"If no conditions are met for example when using `--val 2` the workflow " -"will raise a permanentFail." +"If no conditions are met for example when using `--val 2` the workflow will " +"raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: 19b016a1fec14056a9812c1c195c7c90 msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: a513367d60a74f559339c05d8ef10eb7 msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers " -"and humans. This guide introduces the features of YAML that are relevant " -"when writing CWL descriptions and input parameter files." +"[YAML][yaml] is a file format designed to be readable by both computers and " +"humans. This guide introduces the features of YAML that are relevant when " +"writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: 5e30680941164047a47f98417e916188 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: ca02f2bf1d754d5190f296674245b936 msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: 466615194bb541fdbe2e6515b50531b3 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: 33e664d59a30407891336db290a8a5b2 msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: 3e52ab079dcf4fc6a3f052a517f4d31b msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: abcad6b7d37a4342a90c2d5952ea1232 msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: 500a489e4fae4d1abaa8883f632d1a24 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: 546c1ef51a63487c91c98059dd46b0cb msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: 72b4262833054edd9efe6078381de654 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the " -"`:` is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have " -"special meaning in the CWL specification and underscored key names " -"otherwise. For example:" +"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " +"is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have special " +"meaning in the CWL specification and underscored key names otherwise. For " +"example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#: 7b7e8242660744b791ba3868e4ed7e37 msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, " -"`age_years`, and `home` - with their four respective values. Values can " -"be character strings, numeric (integer, floating point, or scientific " -"representation), Boolean (`true` or `false`), or more complex nested " -"types (see below)." +"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " +"and `home` - with their four respective values. Values can be character " +"strings, numeric (integer, floating point, or scientific representation), " +"Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#: 492d994a541c4c948fb5da9041153bcf msgid "" -"Values may be wrapped in quotation marks, but be aware that this may " -"change the way that they are interpreted i.e. `\"1234\"` will be treated " -"as a character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a" -" command: in CWL all parts of `baseCommand` must be strings so, if you " -"want to specify a fixed numeric value to a command, make sure that you " -"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +"Values may be wrapped in quotation marks, but be aware that this may change " +"the way that they are interpreted i.e. `\"1234\"` will be treated as a " +"character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a " +"command: in CWL all parts of `baseCommand` must be strings so, if you want " +"to specify a fixed numeric value to a command, make sure that you wrap that " +"numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: e2209269db394f3988f18b147a57677c msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: e15c39c65aca47f690264d8008463bec msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program " -"interpreting the YAML. For example:" +"characters to the right of ` #` will be ignored by the program interpreting " +"the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: afa546fcb7fb447d939d4a167f206f79 msgid "" -"If there is anything on the line before the comment, be sure to add at " -"least one space before the `#`!" +"If there is anything on the line before the comment, be sure to add at least " +"one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: 7dd375e0fd964413af4957396d2a0474 msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: af8ef039a64a4c0783d7229dbdac65ef msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, " -"these hierarchical structures are described in YAML by providing " -"additional key-value pairs as the value of any key. These pairs " -"(sometimes referred to as \"children\") are written on new lines under " -"the key to which they belong (the \"parent\"), and should be indented " -"with two spaces (⇥tab characters are not allowed). For example:" +"construct more complex, nested representations. Referred to as _maps_, these " +"hierarchical structures are described in YAML by providing additional key-" +"value pairs as the value of any key. These pairs (sometimes referred to as " +"\"children\") are written on new lines under the key to which they belong " +"(the \"parent\"), and should be indented with two spaces (⇥tab characters " +"are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: 3ce968cb39a443059f6a828b3c8c2f33 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and " -"`inputBinding`, while one of these children, `inputBinding`, contains a " -"further two key-value pairs (`position` and `prefix`). See the " -"[Arrays](#arrays) section below for more information about providing " -"multiple values/key-value pairs for a single key. For comparison with the" -" example YAML above, here is a graphical representation of the `inputs` " -"object it describes." +"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " +"while one of these children, `inputBinding`, contains a further two key-" +"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " +"below for more information about providing multiple values/key-value pairs " +"for a single key. For comparison with the example YAML above, here is a " +"graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: 3c2f48a8e616400b9a8ffb4b6f7efc9b msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: c432b1656e0e49ef87aa3d6e42acad84 msgid "" "In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) " -"section above, more than one key-value pair can be mapped to a single " -"key. However, it is also possible to define multiple values for a key " -"without having to provide a unique key for each value. We can achieve " -"this with an _array_, where each value is defined on its own line and " -"preceded by `-`. For example:" +"objects for a single key. As we've already seen in the [Maps](#maps) section " +"above, more than one key-value pair can be mapped to a single key. However, " +"it is also possible to define multiple values for a key without having to " +"provide a unique key for each value. We can achieve this with an _array_, " +"where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: cac5e52767f74ce98693e2a19ee1eb0d msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: 101666907f8b4fb994e25ceffcf04a13 msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: 5461960a469042a487b89e440f856aea msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " -"arrays can also be defined in YAML using the native JSON syntax. For " -"example:" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " +"can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: e31349c164c84a9da46e2fb1861793df msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: 49a0b3dfdc9e4d58b6bc966db979ace8 msgid "" -"Native JSON can be useful in indicating where a field is intentionally " -"left empty (such as `[]` for an empty array), as well as where it makes " -"more sense for the values to be located on the same line (For example, " -"when providing option flags and their values in a shell command). " -"However, as the second example above shows, it can severely affect the " -"readability of a YAML file, and should be used sparingly." +"Native JSON can be useful in indicating where a field is intentionally left " +"empty (such as `[]` for an empty array), as well as where it makes more " +"sense for the values to be located on the same line (For example, when " +"providing option flags and their values in a shell command). However, as the " +"second example above shows, it can severely affect the readability of a YAML " +"file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: e08ec8c473e847f98e8a18b9ca0f2670 msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: 6ee7bfb4a9e04dd19b5180bca5b02705 msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" -" us while we wrote this guide, though it also covers features that are " -"not valid in CWL." +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " +"while we wrote this guide, though it also covers features that are not valid " +"in CWL." msgstr "" #: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: 42614ab7ba1546f89abeb8f48991271c msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: b8df5b8393ed4d869c066640fe83ec7b msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to " -"the list." +"this page` link in the menu if you would like to add another tutorial to the " +"list." msgstr "" #: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: 5b9aee5af41f438b9f4208294bf97f4a msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: a71d3022dcfc44979cca4655ea51ad42 msgid "" -"[Introduction to Workflows with Common Workflow Language: For " -"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" -"tutorial/)" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: 42b5a982e86f46dfbfcd7bfcc99d72a5 msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: 12dc402d053044b78d69927dd391fe9d msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: 687c20e2e4bc4f869c7ee9390e61476a msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: a975fbb3ea7d467881ce0245de538295 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" +#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee +msgid "" +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the `Creative Commons " +"Attribution license `_. The following is a human-readable " +"summary of (and not a substitute for) the `full legal text of the CC BY 4.0 " +"license `_." +msgstr "" +"Todo el material instructivo del proyecto Common Workflow Language y los " +"cambios en la estructura también están disponibles bajo la `licencia " +"Creative Commons Attribution `_. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del `texto legal completo de la " +"licencia CC BY 4.0 `_." + +#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 +msgid "to **Share**—copy and redistribute the material in any medium or format" +msgstr "" +"**Compartir**—copiar y redistribuir el material en cualquier medio o formato" + +#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 +msgid "to **Adapt**—remix, transform, and build upon the material" +msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" + +#: ../../LICENSE.rst:23 be38276e7b374f57b9997391bf898a62 +msgid "" +"**Attribution**—You must give appropriate credit (mentioning that your work " +"is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a `link to the license `_, and indicate if changes " +"were made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." +msgstr "" +"**Atribución**---Usted debe dar crédito de manera adecuada(mencionando que " +"su trabajo se deriva de un trabajo que tiene «Copyright © The Common " +"Workflow Language Project» y, cuando sea práctico, con un enlace a " +"https://www.commonwl.org/ ), brindar un `enlace a la licencia `" +"_, e indicar si se han realizado cambios. Puede hacerlo en cualquier forma " +"razonable, pero no de forma tal que sugiera que usted o su uso tienen el " +"apoyo de la licenciante." + +#: ../../LICENSE.rst:31 f00d5c3846034c2ea116c2f74786d9fc +msgid "" +"**No additional restrictions**—You may not apply legal terms or " +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" +msgstr "" +"**No hay restricciones adicionales**---No puede aplicar términos legales ni " +"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " +"permitido por la licencia. Con el entendimiento de que:" + +#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the " +"`OSI`_-approved `Apache 2.0 license `_." +msgstr "" +"Excepto cuando se indique lo contrario, los programas de ejemplo y otro " +"software proporcionado por el proyecto Common Workflow Language están " +"disponibles bajo la `licencia Apache 2.0 `_ aprobada por la " +"`OSI`_." + +#: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." +msgstr "" diff --git a/locales/pt/LC_MESSAGES/sphinx.po b/locales/pt/LC_MESSAGES/sphinx.po index 38526232..fc56cb08 100644 --- a/locales/pt/LC_MESSAGES/sphinx.po +++ b/locales/pt/LC_MESSAGES/sphinx.po @@ -4,25 +4,27 @@ # Language User Guide package. # FIRST AUTHOR , 2023. # -#, fuzzy msgid "" msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" +"Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" +"PO-Revision-Date: 2023-01-26 13:55+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Portuguese \n" +"Language: pt\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" #: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" -msgstr "" +msgstr "Navegação principal" #: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "" - +msgstr "Seção Navegação" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index 3584ce39..fd0da8d1 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -12,8 +12,8 @@ msgstr "" "POT-Creation-Date: 2023-01-24 17:23+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Portuguese \n" +"Language-Team: Portuguese \n" "Language: pt\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" @@ -21,21 +21,23 @@ msgstr "" "Plural-Forms: nplurals=2; plural=n > 1;\n" "X-Generator: Weblate 4.16-dev\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 ../../LICENSE.rst:2 +#: 75de2be8809847b8bf1ccd42aa694a24 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 ../../LICENSE.rst:5 +#: 2edd71801f6245ef821887a74f21b94c msgid "Instructional Material" msgstr "" #: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." msgstr "" "Todo o material instrucional do projeto Common Workflow Language e " "alterações na estrutura também são disponibilizados sob a [licença Creative " @@ -43,12 +45,14 @@ msgstr "" "humanos de (e não um substituto para) o [texto legal completo da licença CC " "BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 ../../LICENSE.rst:12 +#: 90cc755d172e4c82b882b4ee620fe652 msgid "You are free:" msgstr "Você tem o direito de:" #: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" msgstr "" "**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " "formato" @@ -57,27 +61,28 @@ msgstr "" msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 ../../LICENSE.rst:18 +#: 430ff4de74924bc3a3b2c7e809ea4456 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e ../../LICENSE.rst:20 +#: 2173e2af49be41ee97a74c4e879faf25 msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms:" +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms:" msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " -"termos da licença." +"termos da licença:" #: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." msgstr "" "Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " "trabalho deriva de um trabalho que é «Copyright © The Common Workflow " @@ -90,136 +95,153 @@ msgstr "" #: ../../LICENSE.md:32 8161753b7526445db319210044566200 msgid "" "**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" msgstr "" "**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " "medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " "algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 ../../LICENSE.rst:35 +#: f6aae4a5cd0547118c8a3240ca2b4be6 msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." msgstr "" "Não tem de cumprir com os termos da licença relativamente a elementos do " "material que estejam no domínio público ou cuja utilização seja permitida " "por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 ../../LICENSE.rst:38 +#: a40c173be35b4c1b92e83f42bfe2382c msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." msgstr "" "Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " "autorizações necessárias para o uso pretendido. Por exemplo, outros " "direitos, tais como direitos de imagem, de privacidade ou direitos morais, " "podem limitar o uso do material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea ../../LICENSE.rst:44 +#: 3d7ca3f2cede4d5f998bf014bd970748 msgid "Software" msgstr "Software" #: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 msgid "" "Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" -"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " +"[licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." #: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 #: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 +#: eab02dc13915490bb3c9ba744d78b6a7 5ad4be9b62d54c95a913795b514676fd +#: bdd540403a5746ff99edf2dcad0e3122 dfc7702e073140c985cf47272a20214d msgid "" "CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." +"create workflows. Because CWL is a specification and not a specific piece of " +"software, tools and workflows described using CWL are portable across a " +"variety of platforms that support the CWL standard." msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: 3060770b3bef41d7bcfcdfb413d7689c msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" #: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: 48bb9f628b344ba1a3b67ae1cb264e3c msgid "FAQ" msgstr "" #: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +#: 7e3684e9672643738846756e1ebafd18 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +#: 187ceabb7fd9480bb8cf0f2da47f65ef msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: b548b76bcc85420a9b30792386105139 msgid "" -"This example demonstrates how to change the name of an input file as part" -" of a tool description. This could be useful when you are taking files " -"produced from another step in a workflow, and don't want to work with the" -" default names that these files were given when they were created." +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +#: 9ce692b78ead47e4b0f8cdae8837d35b msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: 6df1201c159343da9e7515379980d6a0 msgid "" -"This example demonstrates how to change the name of an output file from " -"the default name given to it by a tool:" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +#: f9ab1d0dc1c842b6abb5385268c1d3bd msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: 9f6a84ab6a9343b6ad7db826f8964362 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: fa50e4fa990b42d1ba4c0f4ae1e5caa1 msgid "" -"The first method involves adding the folder containing your scripts to " -"the `PATH` environment variable. This allows you to run the shell script " +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: 3a871012fcfd4f3ebeca0cb86ec93435 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: d954edfff2584288ac8c600733070d2e msgid "" -"After that, make the script executable with the command `chmod +x " -"scriptname.sh`" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" msgstr "" #: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: af6b1e37d6be4450a761854480ec9aab msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " @@ -227,117 +249,138 @@ msgid "" msgstr "" #: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: 31f4a2d43062493ca64c648f80afc8e9 +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: 41c54e71b6cd4f63b2a619a515240d34 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" #: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: 8edc3541ad134ab5a1d23c724f1f0a4e msgid "" -"The second method involves including an input of `type: File` in the " -"script itself:" +"The second method involves including an input of `type: File` in the script " +"itself:" msgstr "" #: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +#: ac0ea81eba8842a18801ab03cbf80a57 msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#: 52be1a5640234feabe958ff7ade33653 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: c6db734d5aef4f4f99676bdebf9c83c9 msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their " -"input binding makes use of `self`. Below is an example workaround for " -"this, pending a more sophisticated fix." +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +#: a9f7b47c0dd741739795da39bf114879 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: e3fdd9228b924905a4a1f4b2b7ad7159 msgid "" -"Below is an example showing how to specify different strings to be added " -"to a command line, based on the value given to a Boolean parameter." +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#: 3f7cda1437cc48f18745a827ebb74582 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: 5aeaba2cae64442e816bbd458aee833a msgid "" -"Using " -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" along with [`linkMerge: " +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: 5af827a402834978addd82c70be6b5ab msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: 6d69e42bd8e443c4b19d80807c7efd6b msgid "" -"The input must be an array consisting of exactly one entry for each input" -" link. If \"merge_nested\" is specified with a single link, the value " -"from the link must be wrapped in a single-item list." +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +#: 404640397b6e40c2a2cd5cf85ab3b1c0 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: 1682c2486e224770b62269709a8663cf msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " -"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" -" destination step." +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." msgstr "" #: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +#: 9078fc009bc145808813c9cc2b734b58 msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: d4b5a54a400c409cb7984428f6a03ec8 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" #: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: 9e8dbee6e8f84d08b1a54fffa06394ef msgid "" msgstr "" #: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +#: 1d846bfb5f054d09a4afad1da8e4b642 msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: 2d0e95fec8084787b734388d60188574 msgid "" -"For command line flags that require a specific input as the argument an " -"enum type can be declared in CWL. **Specifying null here is known as long" -" form style. It does the same thing as the question mark on the other " -"inputs.**" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: eccc4a364330470fa474dcaaa3433390 msgid "" msgstr "" #: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +#: e945f6a337af4e4686bed482a4fe6c39 msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: 8a3efaa0ad1548428bcfd6e01d135cdc msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " @@ -345,117 +388,138 @@ msgid "" msgstr "" #: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +#: cdab644adc5643708870fb08c06cbfca msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: 089a5a0b076b44aeaab4d69ee3c79f97 msgid "" -"To properly set fields in a record input type, you need to pass a " -"dictionary to the input to properly set the parameters. This is done by " -"using inline JavaScript and returning the dictionary with the key of the " -"field you want to set. The source field is set to indicate the input from" -" the workflow to be used as the value." +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." msgstr "" #: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +#: 561172559c6f41a68819608fd9e58bb0 msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: c5ee4946d2e840abaa3dc796a62652c7 msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +#: 4f2069a2113c414db18eca95550e9e09 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: 31f3390e6771414ba7bf57c044c4b0c4 msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +#: 3b77ce4930ae46d5be9f6965e8c54727 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: 06f36bbe4d3840229b7374f27b86ae80 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: 3cb2f70d00274a4dafd972ccd8c519c2 msgid "" -"For example, the filename `a space is here.txt` includes 3 space " -"characters." +"For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: 093a1529262043ef84a99675054938e0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#: 45b6d9acbfaa47e5984184f7da554d0a msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: 5705c9bacca5405ca6f14315a5575db8 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: 82bfc285b59a439ca97d3278997f0fce msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: 181d5130101d45ccb22aebae3d154c2f msgid "The file is here" msgstr "" #: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: e864390b5ddb423aaa10e9d33d257dc1 msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +#: fe637c32fb15427a9045679b5da42ec5 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: 1f8004b9df8547029d82e57f9abdc979 msgid "" -"If it is not possible to change the input identifier, then you can use an" -" alternative CWL Parameter Reference syntax:" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +#: 70990dc5a0034099921ceb89c89e2dcc msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: f679e26f18d9455f945fd13361a9c906 msgid "" -"The CWL standards are built around (optional) Docker format containers. " -"The reference runner and several other CWL implementations support " -"running those Docker format containers using the Singularity engine. " -"Directly specifying a Singularity format container is not part of the CWL" -" standards." +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +#: fcd0273dbdd84e728cfd8fbe239f2a01 msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: 173ddbd1e7c64927a8dcb12a2a2140f8 msgid "" -"You can use the --js-console option of cwltool," -" or you can try creating a JavaScript or TypeScript project for your " -"code, and load it using expressionLib, e.g.: " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" #: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: 662fe273e2fb4042b688512955e450a1 msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: a15b52205f0145feaac298510e4d678a msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " @@ -463,267 +527,275 @@ msgid "" msgstr "" #: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: 512aa0c7166b429e8116f71eef007f79 msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: b1b19e17a18540939cb3bb7f8a700cab msgid "" -"If you find that something is missing from this guide, or if you would " -"like to provide other feedback, file an Issue on the [project repository " -"for this guide][repo]. You can also suggest changes directly in a Pull " -"Request by clicking the \"Edit this page\" button at the right sidebar of" -" each page." +"If you find that something is missing from this guide, or if you would like " +"to provide other feedback, file an Issue on the [project repository for this " +"guide][repo]. You can also suggest changes directly in a Pull Request by " +"clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: d58b36ac43ac44139897be752fbb1f87 msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: 6726cf3585a646a8b4cbeb543cf84a38 msgid "" -"If you are a beginner user get started with the " -"[Introduction](/introduction/index.md) section. For advanced users the " -"subsections of the [Topics](/topics/index.md) have detailed information " -"about the most common topics for CWL." +"If you are a beginner user get started with the [Introduction](/introduction/" +"index.md) section. For advanced users the subsections of the [Topics](/" +"topics/index.md) have detailed information about the most common topics for " +"CWL." msgstr "" #: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: 2e504aa7c46a426fa959e7254e9a84a5 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each " -"page, and the Search form is on the left sidebar." +"subsections. The right sidebar contains links to the sections of each page, " +"and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: e7be0df0838b432d9c7f296d777f120b msgid "Table of Contents" msgstr "" #: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: 173e0816db20432c8d9dba1de5393dee msgid "Basic Concepts" msgstr "" #: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: 30eacc583f6841719e2142d283811d97 msgid "" "This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are " -"expected to be familiar with workflow managers, YAML, and comfortable " -"with following instructions for the command-line. The other sections of " -"the user guide cover the same concepts, but in more detail. If you are " -"already familiar with CWL or you are looking for more advanced content, " -"you may want to skip this section." +"working with Common Workflow Language (CWL) workflows. Readers are expected " +"to be familiar with workflow managers, YAML, and comfortable with following " +"instructions for the command-line. The other sections of the user guide " +"cover the same concepts, but in more detail. If you are already familiar " +"with CWL or you are looking for more advanced content, you may want to skip " +"this section." msgstr "" #: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: 791b8f38a14147bbaa174c7eb595f17e msgid "The CWL Specification" msgstr "" #: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: 1a3989dcbb9844b39d84bf6df6b352ed msgid "" "The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered " -"in this user guide is the {{ cwl_version }}." +"community. The specification has different versions. The version covered in " +"this user guide is the {{ cwl_version }}." msgstr "" #: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: db1bbc6e980f404f9f3fcd08e92ee9a3 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" "incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes " -"that are backward-compatible. The last number is used for bug fixes, like" -" typos and other corrections to the specification." +"number is the minor release, used for new features or smaller changes that " +"are backward-compatible. The last number is used for bug fixes, like typos " +"and other corrections to the specification." msgstr "" #: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: acc7887c65974114996f700a38a7eccc msgid "" -"The model used for the specification version is called Semantic " -"Versioning. See the end of this section to [learn more](#learn-more) " -"about it." +"The model used for the specification version is called Semantic Versioning. " +"See the end of this section to [learn more](#learn-more) about it." msgstr "" #: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: d2476d9bcff44f21b8d84a3a0d87a246 msgid "Implementations" msgstr "" #: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: f86415e4d78e48c4a8a76ced81221b98 msgid "" -"An implementation of the CWL specification is any software written " -"following what is defined in a version of the specification document. " -"However, implementations may not implement every aspect of the " -"specification. CWL implementations are licensed under both Open Source " -"and commercial licenses." +"An implementation of the CWL specification is any software written following " +"what is defined in a version of the specification document. However, " +"implementations may not implement every aspect of the specification. CWL " +"implementations are licensed under both Open Source and commercial licenses." msgstr "" #: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: c5524d73708c4c779980528864506fd4 msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud" -" and high performance computing environments where tasks are scheduled in" -" parallel across many nodes." +"CWL is well suited for describing large-scale workflows in cluster, cloud " +"and high performance computing environments where tasks are scheduled in " +"parallel across many nodes." msgstr "" #: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: ac46a9f8850a434bac5bc2b41ee6294e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: a5ebc727fb3443f78e81d6b7ed5ac750 9bba7c4f783942e4a299603430601363 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: 86e6a06992dc4228bfda7add48e28ca3 e2140e0f0e7747ef8383887c20a7945a msgid "" -"A process is a computing unit that takes inputs and produces outputs. The" -" behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification" -" {{ cwl_version }}:" +"A process is a computing unit that takes inputs and produces outputs. The " +"behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification " +"{{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 8c9772f96caf4169924d22eb929a4f0f 15bf490724cd46dcbcfab44633c5a9a2 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 4fac209a62114798b79e4810f7a0148b 51d52d051e654a8395239f88df7c9d8c msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: b97ba368fd664caab0494e2392795697 eb496cc818524fa7bae5a22ddd00a19c msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: 903a6796e3304a19ad885b2428b0e80f c4a22d12e7f149ff901d27de32b9361d msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 6e352ac1f8e144c392ac5adf18c28298 7618de899a7043989d77baacf62eb7b2 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: cf2922f645904ac7955428ecddc37b8a 6f1544a220664b79b04bf008058b5a91 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: 5f47aae608c041aeb4134d59dad314d2 fbd14ac9a2f541478a320ed4cbc69e13 msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be " -"used to simplify workflows and command-line tools, moving common parts of" -" a workflow execution into reusable JavaScript code that takes inputs and" -" produces outputs like a command-line tool." +"An expression tool is a wrapper for a JavaScript expression. It can be used " +"to simplify workflows and command-line tools, moving common parts of a " +"workflow execution into reusable JavaScript code that takes inputs and " +"produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: f6f589481d0c4891beaccb63160619ef da4dba50d25d4533b3dbb92f54d32a30 msgid "" -"Operation is an abstract process that also takes inputs, produces " -"outputs, and can be used in a workflow. But it is a special operation not" -" so commonly used. It is discussed in the [Operations " -"section](../topics/operations.md) of this user guide." +"Operation is an abstract process that also takes inputs, produces outputs, " +"and can be used in a workflow. But it is a special operation not so commonly " +"used. It is discussed in the [Operations section](../topics/operations.md) " +"of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 ce11c9f8d65c4268984d0384d95144cc msgid "" -"The workflow is a process that contains steps. Steps can be other " -"workflows (nested workflows), command-line tools, or expression tools. " -"The inputs of a workflow can be passed to any of its steps, while the " -"outputs produced by its steps can be used in the final output of the " -"workflow." +"The workflow is a process that contains steps. Steps can be other workflows " +"(nested workflows), command-line tools, or expression tools. The inputs of a " +"workflow can be passed to any of its steps, while the outputs produced by " +"its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 4ace6b92f4e04a07aa202840ebe36417 3a201aa497e84f70855bb2251e7e3281 msgid "" "The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through " -"*requirements*. There are many requirements defined in the CWL " -"specification, for instance:" +"functionality and specify prerequisites to workflows through *requirements*. " +"There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 b78f7fa2be1c4bb090f6da895457ad1e msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: 2d9f53b6ed5041dbb6c0b54835897856 f7e95d264ffa4e2db0864faccd9e5a0e msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 907674a4ecff4826a2b880e28fc38f33 3f1e5b01e49a4dc1b1c99936a4589afc msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input " -"directory." +"`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 037cd0e5ceda482eaeaca03d51745aee 03c3048f38ae4938a484cf02001877b3 msgid "" -"Some CWL runners may provide requirements that are not in the " -"specification. For example, GPU requirements are supported in `cwltool` " -"through the `cwltool:CUDARequirement` requirement, but it is not part of " -"the {{ cwl_version }} specification and may not be supported by other CWL" -" runners." +"Some CWL runners may provide requirements that are not in the specification. " +"For example, GPU requirements are supported in `cwltool` through the " +"`cwltool:CUDARequirement` requirement, but it is not part of the " +"{{ cwl_version }} specification and may not be supported by other CWL " +"runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: e4643938445b48cc80eb8973ceeb126e f9715b5ec65c405c849bb030c1927060 msgid "" -"Hints are similar to requirements, but while requirements list features " -"that are required, hints list optional features. Requirements are " -"explained in detail in the [Requirements](../topics/requirements-and-" -"hints.md) section." +"Hints are similar to requirements, but while requirements list features that " +"are required, hints list optional features. Requirements are explained in " +"detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: c4c3315c96714e81b364f8cc003b87e6 442662f50e9e4620970ce32b1b127969 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: 3eb6a013a2a4478ca2ad134661f65c58 2b34c786af3840e88f29d214e19dc837 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " "machine accessibility and that all digital assets should be Findable, " "Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created." -" It is thus important that workflows support the creation of FAIR data " -"and adhere to the FAIR principles. — [FAIR Computational " -"Workflows](https://workflows.community/groups/fair/), Workflows Community" -" Initiative." +"which the scientific process is conducted and via which data are created. It " +"is thus important that workflows support the creation of FAIR data and " +"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" +"workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: 074af9633627470485e5225326d5f20a dd6aadff8cf54ce78ea6b317afbaddb0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\"," -" CWL tasks are isolated, and you must be explicit about your inputs and " +"execution, based on dependencies between tasks. However, unlike \"make\", " +"CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: 847951c055b94a83b1e081594cef22ee fe7f1f0b28434f8aaf0f6ac6589a83f0 msgid "" -"The benefit of explicitness and isolation are flexibility, portability, " -"and scalability; tools and workflows described with CWL can transparently" -" leverage technologies such as Docker and be used with CWL " -"implementations from different vendors." +"The benefit of explicitness and isolation are flexibility, portability, and " +"scalability; tools and workflows described with CWL can transparently " +"leverage technologies such as Docker and be used with CWL implementations " +"from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: 44bde1fae06b4678bcac4f3224601296 d10cf45b3c7f49dc98bc0e5d1246f224 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" @@ -731,264 +803,306 @@ msgstr "" #: ../../src/introduction/prerequisites.md:196 #: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 #: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +#: 332b6e8b831e4bc5aed3745938230a57 ce7fc63b808d4499b9bf9828c2dafe35 +#: ebf339ed376a4d3b89b15b4d5afe593b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 9d5100c7d0a040aea1020bf633ad17de 8badec9987ba40609cf1f626172b2b2d msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: 36eb4b3b966640af90faa55db3789cb6 c75a8b4bf0e24781bf6713cf6f013cd1 msgid "" -"The CWL Specification page in the CWL website: " -"" +"The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 2ccb956baa6b4376a04ad9fcc4654631 79b146ffe6d74e1b8f6019251dc4b7c2 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 72889b830c514afe9a7cb1e64b5666a0 07cca9a33d8f4b77ac6ad35ca8b95655 msgid "" -"The list of Implementations in the CWL website: " -"" +"The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: e29bd7f973544600be589c3b3f84cf63 31db11c8ddf2423192a8b2063b3e91c2 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: c377a7f5dbe645cebbb6c7eccf831a0b d81dd96143ea444aa78ff45cfa0584b3 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" #: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: c54984605872472190ae7771809a20db msgid "Introduction" msgstr "" #: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: 01a237b8ec2f46c9acd31d142591ce75 msgid "" "This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that" -" are useful to know before reading the rest of the user guide." +"prerequisites for following this user guide, and some basic concepts that " +"are useful to know before reading the rest of the user guide." msgstr "" #: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: 3fb9888b666945eab1e3ff109646c574 msgid "Prerequisites" msgstr "" #: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: 5fb0486762354f93853fff209f835c08 msgid "" -"The software and configurations listed in this section are prerequisites " -"for following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements " -"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" -"compatible runner or workflow system, but the results and interface may " -"look different (though the exact workflow outputs should be identical)." +"The software and configurations listed in this section are prerequisites for " +"following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements focuses " +"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " +"runner or workflow system, but the results and interface may look different " +"(though the exact workflow outputs should be identical)." msgstr "" #: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: 5f1e7a608e0b455196d191c845a5c98e msgid "CWL Implementations" msgstr "" #: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: 7ba4b5c51be24f5392949d06ee42e018 msgid "" -"There are many implementations of the CWL standards. Some are complete " -"CWL runners, while others could be plug-ins or extensions to workflow " -"engines. We have a better explanation in the [Implementations](basic-" -"concepts.md#implementations) section." +"There are many implementations of the CWL standards. Some are complete CWL " +"runners, while others could be plug-ins or extensions to workflow engines. " +"We have a better explanation in the [Implementations](basic-concepts." +"md#implementations) section." msgstr "" #: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: e2d3e6dd13b14d819a504c35da6fe8e7 msgid "Operating System" msgstr "" #: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: 91251d1f0efb4d4cb083b4517ff3107a msgid "" -"We recommend using an up-to-date operating system. You can choose any of " -"the following options for your operating system:" +"We recommend using an up-to-date operating system. You can choose any of the " +"following options for your operating system:" msgstr "" #: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: 6ad263e267514c5fb05794d3d76d418d msgid "Linux" msgstr "" #: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: 8a3bfd72dccf4a8c874a96aebcbe5cb7 msgid "macOS" msgstr "" #: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: 5195706d9c6c4573aff135fd539759a2 msgid "Windows" msgstr "" #: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: 9c4506915e4c40599527bc1d2b18645b msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem" -" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " -"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" -"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " -"details on installing WSL2. Your operating system also needs internet " -"access and a recent version of Python (3.6+)." +"If you are using Windows, you will have to install the [Windows Subsystem " +"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " +"installing WSL2. Your operating system also needs internet access and a " +"recent version of Python (3.6+)." msgstr "" #: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: 37d9eb784ec1425786158f98e3f63890 msgid "CWL Runner" msgstr "" #: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: 572f493a985141a1b92dafbdba92790d msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL " -"community. It is also the CWL reference runner, which means it must " -"support everything in the current CWL specification, {{ cwl_version }}." +"`cwltool` is a Python Open Source project maintained by the CWL community. " +"It is also the CWL reference runner, which means it must support everything " +"in the current CWL specification, {{ cwl_version }}." msgstr "" #: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: 9606d3c4849f4b17b2e55a298210f055 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create " -"and activate a Python virtual environment using the `venv` module, and " -"install `cwltool` in that environment:" +"environment like `venv` or `conda`. The following commands will create and " +"activate a Python virtual environment using the `venv` module, and install " +"`cwltool` in that environment:" msgstr "" #: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +#: 754fc59967d94ffa935284676d55ffed msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" #: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: 2905c6362d4146e8b35bc74744841972 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` " -"and `conda`." +"language/cwltool#install) for other ways to install `cwltool` with `apt` and " +"`conda`." msgstr "" #: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: 091278ece252483a9838fb771de3e04e msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: 0928a5c668c3414a945bc9eda147892c msgid "`true.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: 56f3c481762848298214a88e559fc0f9 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the " -"CWL standards. However, these actions will be performed without running " -"the document. To validate CWL workflows (or even a standalone command " -"line tool description like the above) pass the `--validate` option to the" -" `cwltool` command:" +"errors, and verify that the workflow descriptions are compliant with the CWL " +"standards. However, these actions will be performed without running the " +"document. To validate CWL workflows (or even a standalone command line tool " +"description like the above) pass the `--validate` option to the `cwltool` " +"command:" msgstr "" #: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +#: 710c266ab4a5477b84d6ea987420fa20 msgid "Validating `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 -msgid "You can run the CWL tool description by omitting the `--validate` option:" +#: cc353db5da2546bb88a77ce1a202ff9d +msgid "" +"You can run the CWL tool description by omitting the `--validate` option:" msgstr "" #: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: b62df08ec96f4cdb887600079856dd76 msgid "Running `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: 97e02557293440d1a58ba659dad21113 msgid "Cwl-runner Python Module" msgstr "" #: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: 0935c3ff01634c75b5c91546dc36c7b9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be " -"invoked independently, and is not reliant on a particular CWL runner " -"program name. Users can invoke `cwl-runner` instead of invoking a CWL " -"runner like `cwltool` directly. The `cwl-runner` is installed by a system" -" administrator or user to point to the preferred CWL implementation. This" -" is convenient for environments with multiple CWL runners." +"runner. This simply means that the `cwl-runner` alias command can be invoked " +"independently, and is not reliant on a particular CWL runner program name. " +"Users can invoke `cwl-runner` instead of invoking a CWL runner like " +"`cwltool` directly. The `cwl-runner` is installed by a system administrator " +"or user to point to the preferred CWL implementation. This is convenient for " +"environments with multiple CWL runners." msgstr "" #: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: cfb37fd605164a8d9cc75bf892ce97c0 msgid "" -"The CWL community publishes a Python package with the name `cwlref-" -"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +"The CWL community publishes a Python package with the name `cwlref-runner` " +"that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" #: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: 5f06a7a6aae343d989a5b30979c600f6 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" #: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: 5f956260f3874b6dbeaf3ad7ecc09c9a msgid "" -"Now you can validate and run your workflow with the `cwl-runner` " -"executable, which will invoke `cwltool`. You should have the same results" -" and output as in the previous section." +"Now you can validate and run your workflow with the `cwl-runner` executable, " +"which will invoke `cwltool`. You should have the same results and output as " +"in the previous section." msgstr "" #: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: d35e4effec554a638d6c3047ef3fd05f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: 15a1f944a0d642729d3736ed1c907074 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: fa34c808bb494ddfa3f3926bc42e650c msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For" -" that, the first thing you need to do is copy `true.cwl` workflow into a " -"new file: `true_shebang.cwl`, and include a special first line, a " -"*shebang*:" +"Another way to execute `cwl-runner` is by invoking the file directly. For " +"that, the first thing you need to do is copy `true.cwl` workflow into a new " +"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" #: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: 0c15f62eb7534e809f625f3fa213e92d msgid "`true_shebang.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +#: d67719a6f0ce4ba1bb6152a10507b729 +msgid "" +"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" #: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: 1c96e75281844bfab0578bab2e816854 msgid "Making `true.cwl` executable." msgstr "" #: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: bece1fc3c3f842b0b30d8f1b7fbfc200 msgid "" -"And finally, you can execute it directly in the command-line. On " -"execution, the program specified in the shebang (`cwl-runner`) will be " -"used to execute the rest of the file." +"And finally, you can execute it directly in the command-line. On execution, " +"the program specified in the shebang (`cwl-runner`) will be used to execute " +"the rest of the file." msgstr "" #: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: a7caa36b0f83448b91ef2e76e30abc51 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" #: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: 39321e93e9994fcca20b425aa45c2894 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute " -"the script using the executable specified after the shebang. It is " -"considered a good practice to use `/usr/bin/env ` rather than" -" using a hard-coded location, since `/usr/bin/env ` looks for" -" the `` program in the system `PATH`," +"script. When the script is executable, the operating system will execute the " +"script using the executable specified after the shebang. It is considered a " +"good practice to use `/usr/bin/env ` rather than using a hard-" +"coded location, since `/usr/bin/env ` looks for the " +"`` program in the system `PATH`," msgstr "" #: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +#: 601cf500d76c4e0287af4429a46b36d2 msgid "Text Editor" msgstr "" #: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: b286d5359e184ef58054c72df4014629 msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " @@ -996,379 +1110,429 @@ msgid "" msgstr "" #: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: e14423edd829401faed0950772123240 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting" -" and better auto-complete:" +"integration with CWL, and features such as customized syntax highlighting " +"and better auto-complete:" msgstr "" #: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: 889c44360bd54a0e85e7f0e61aa6593c msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " -"" +"Visual Studio Code with the Benten (CWL) plugin - " msgstr "" #: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: 7b9bff73624947ac90a99c7880e2e911 msgid "" -"cwl-plugin for IntelliJ - " +"cwl-plugin for IntelliJ - " msgstr "" #: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: c5ff687c86ef4ccaae25d8bcfbd5f873 msgid "" -"The CWL community also maintains a list of editors and viewers: " -"" +"The CWL community also maintains a list of editors and viewers: " msgstr "" #: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: 0a610a9632064deb824afd0719429d3a msgid "Docker" msgstr "" #: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: ec0c47438a5242cb99dffa7a4997e95a msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: " -"." +"documentation to install it for your operating system: ." msgstr "" #: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: aae94ac2114641f186eac0f4117223eb msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models " -"with and without containers." +"examples, and to clarify the differences between the execution models with " +"and without containers." msgstr "" #: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: 209e072724ed4d27b37e9bff6d55d811 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for " -"pulling images." +"Singularity. You can also use alternative container registries for pulling " +"images." msgstr "" #: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: 3bf47876e3694e6cadb05123326459cb msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the " -"next section, Basic Concepts." +"The [Implementations](basic-concepts.md#implementations) topic in the next " +"section, Basic Concepts." msgstr "" #: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: 459a65b8e67c4a9aaa03138c1abe94ad msgid "The Python `venv` module: " msgstr "" #: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: 898eb29ac7714c69840b795633953a05 msgid "Quick Start" msgstr "" #: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: 2a658bd2d8ce4533ab7e056fc3a3ffcf msgid "" -"This section will show you a brief overview of what CWL is, and where you" -" can learn more about it. No previous knowledge of CWL is required, but " -"you must be comfortable following instructions for the command-line." +"This section will show you a brief overview of what CWL is, and where you " +"can learn more about it. No previous knowledge of CWL is required, but you " +"must be comfortable following instructions for the command-line." msgstr "" #: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: 32dd2e28cf0f40b6930750f0162355eb msgid "“Hello World”" msgstr "" #: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: 471c47d311074ecfac071b6d52d9cfb6 msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " -"The example below shows a simple CWL “Hello World” workflow annotated " -"with comments. Note that comments start with `#`:" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " +"example below shows a simple CWL “Hello World” workflow annotated with " +"comments. Note that comments start with `#`:" msgstr "" #: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: 5078140028ea4d04973cb9cd20f0607e msgid "`hello_world.cwl`" msgstr "" #: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ab127d4ba0a44526ab129587a8160923 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the" -" same result as the command-line `echo \"Hello World\"`." +"Running the workflow above with the default input values will produce the " +"same result as the command-line `echo \"Hello World\"`." msgstr "" #: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: d5cc6b4295a74f3586f022b0227759b3 msgid "" -"In CWL, there is a distinction between a command-line tool and a " -"workflow. But for the sake of simplicity, we are using the term " -"“workflow” here. You will learn more about this in the [basic concepts" -"](basic-concepts.md) section." +"In CWL, there is a distinction between a command-line tool and a workflow. " +"But for the sake of simplicity, we are using the term “workflow” here. You " +"will learn more about this in the [basic concepts](basic-concepts.md) " +"section." msgstr "" #: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: 585a4fe583ce44e180a062742b3b0849 msgid "Installing a CWL Runner" msgstr "" #: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: 0d81b0c9ea58420789d1d71cca32ce88 msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the " -"CWL *Reference Runner* for the specification, and it is compliant with " -"the latest version of the specification: {{ cwl_version }}. You can " -"install `cwltool` using `pip`:" +"`cwltool` is an implementation of the CWL specification. It is also the CWL " +"*Reference Runner* for the specification, and it is compliant with the " +"latest version of the specification: {{ cwl_version }}. You can install " +"`cwltool` using `pip`:" msgstr "" #: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: ea4ab0782d8049d8b1b89cea4ae60048 msgid "Installing `cwltool` with `pip`." msgstr "" #: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: f6f3b7453a254f828bd4c9e9fef92bed msgid "" -"If installing the cwltool using the pip command doesn't work for you, the" -" [prerequisites](prerequisites.md) section contains other ways to install" -" `cwltool` and a more detailed list of software and libraries used for " +"If installing the cwltool using the pip command doesn't work for you, the " +"[prerequisites](prerequisites.md) section contains other ways to install " +"`cwltool` and a more detailed list of software and libraries used for " "following the rest of this user guide." msgstr "" #: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: 3bf9050175d4444ebbbabe219412574f msgid "Running \"Hello World\"" msgstr "" #: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: e03f72a14dcf4bf38ce8232598ca761d msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the " -"`hello_world.cwl` workflow without specifying any option:" +"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " +"workflow without specifying any option:" msgstr "" #: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: 3dcfb2facd324dccb3084c02487625dc msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: b8531da183964b02bca19f818ec076d4 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" #: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: 7ba1ddebeb2843179fe99fc410b193c6 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" #: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: a6dc303e9d284b60bf1102212505ca27 msgid "" -"Another way of passing values to your workflow input parameters is via an" -" *Inputs Object*. This is a file containing the input fields with their " +"Another way of passing values to your workflow input parameters is via an " +"*Inputs Object*. This is a file containing the input fields with their " "corresponding values. The Inputs Objects file can be written in JSON or " "YAML. For example:" msgstr "" #: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: 59ac7830ae3e4d7cb1bf503e8c90fe30 msgid "`hello_world-job.json`" msgstr "" #: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: 6d1d6f42ada2418ba0a1de1371825b9f msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" #: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: 1cd924fe8ace4a82ad8701f37b5e7d84 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: aa297c52cd964291a47bb91c0135156b msgid "" "We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but " -"it is not a requirement. You can choose any name for your workflows and " -"Inputs Object files." +"files. The *-job.json* suffix is very common in Inputs Object files, but it " +"is not a requirement. You can choose any name for your workflows and Inputs " +"Object files." msgstr "" #: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: 28b02c90397745bfbacc03c3b1034939 msgid "Continue reading the next sections of this User Guide!" msgstr "" #: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: ef2a4f39f01049b891868b84d968c0dd +msgid "" +"[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" #: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: 89e3fa8dceda4f0cb1cfdfd1f17fe4df msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" #: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: 7cd178223ba94d1ab3ee8cc5f13a8dcf msgid "" -"[Common Workflow Language at " -"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." msgstr "" #: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: 46f6f8d050ce4f8c897056167d9707a7 msgid "" -"[YAML.org](http://yaml.org/) and [YAML at " -"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." +"org/wiki/YAML)." msgstr "" #: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: 5ee00ee409b746dc951ca1d4c360e624 msgid "" -"The {{'[CWL Specification " -"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " -"cwl_version_text) }}." +"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." +"replace('VERSION', cwl_version_text) }}." msgstr "" #: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: d4af972281174b8999eab55ee0ab1a0e msgid "" -"[Workflow management system at " -"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." msgstr "" #: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: 80401cfffae042ab9ec4b3754af04b25 msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. The information on this page has been migrated to the " -"[FAQ](/faq.md) section of the new user guide." +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 9c87c76c690948ac8e18088a0fffe679 32f86f911ebe4a4c94975f81742333f3 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: ad00d94d4fb64bbdac356e64dd3803b9 d5f1ad2b95ad46d48f8f2ca5e357bb5d msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: d8110ed19da94ad8a9f56e7006c4a2cf c53ceee943ad4acea779e072b9137889 msgid "" "In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files " -"in the same directory as the source file. However, CWL input files (and " -"the directories in which they appear) may be read-only, so we need to " -"instruct \"javac\" to write the class file to the designated output " -"directory instead." +"file to a class file. By default, \"javac\" will create the class files in " +"the same directory as the source file. However, CWL input files (and the " +"directories in which they appear) may be read-only, so we need to instruct " +"\"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: a74935dc31664e979ca8f90a6a4ba53c 7dfe9dffbf5744299bf232599644c7f6 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: f357755f6dcb4971bade8636064f8dd1 00709fa451134ee09a0d808e101f28ed +#: 991172e201ec4796992a349dee44f090 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: 6359191b4f684d5aa3602e4aaf394883 1f3c23a4769043ca985b8ddfed19391d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: 9643449da1da46d7861866dce490cbcb f81b43c7cb194a1cad8672129223c833 msgid "" -"And now invoke `cwltool` providing the tool description and the input " -"object on the command line:" +"And now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: 713666580a0a4466b4ba6e3eb2b54f0a a20073a8f5374eb1bc8531ff33e622b6 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: d50574c8b9694f83aa376d39b9a6fcd6 d08869beca3a4774baf1097b63e79474 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include " -"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " -"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " -"Environment][runtime] section of the CWL specification for details." +"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" +"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." +"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " +"specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: 109b773789024b2b9c063a6169c6169f msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: 959fa04f88e54d42b9b774cc95d85ee0 msgid "" -"The following are a set of recommended good practices to keep in mind " -"when writing a Common Workflow Language description for a tool or " -"workflow. These guidelines are presented for consideration on a scale of " -"usefulness: although more is better, not all are required." +"The following are a set of recommended good practices to keep in mind when " +"writing a Common Workflow Language description for a tool or workflow. These " +"guidelines are presented for consideration on a scale of usefulness: " +"although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: 64674980c3f24c45bbfbf3f957dda55e msgid "" -"No `type: string` parameters for names of input or reference " -"files/directories; use `type: File` or `type: Directory` as appropriate." +"No `type: string` parameters for names of input or reference files/" +"directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: 90f2e4265919446a902e17627f4420e2 msgid "" "A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that" -" the usual rules of software licensing apply to this document. For " -"example, if the workflow is shared publicly, licensing terms must be " -"clear so that a future user understands under what conditions they can " -"run the workflow, modify it and/or combine it with other workflows. For " -"this reason, please consider including a license field in the document. " -"The authors of this guide urge you to choose a pre-existing license " -"rather than trying to write your own (see the link below to learn more " -"about choosing a license), and our recommended practice is to choose a " -"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" -"license]." +"`Dockerfile`s) is software code. Workflow developers should be aware that " +"the usual rules of software licensing apply to this document. For example, " +"if the workflow is shared publicly, licensing terms must be clear so that a " +"future user understands under what conditions they can run the workflow, " +"modify it and/or combine it with other workflows. For this reason, please " +"consider including a license field in the document. The authors of this " +"guide urge you to choose a pre-existing license rather than trying to write " +"your own (see the link below to learn more about choosing a license), and " +"our recommended practice is to choose a license that allows for re-use by " +"anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: 6b5f91a749fd44b5acfd6071c9913342 msgid "" -"If possible, the license should be specified with its corresponding [SPDX" -" identifier][spdx]. Construct the metadata field for the license by " -"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " -"`SPDX-ID` is taken from the list of identifiers linked above. See the " -"example snippet below for guidance. For non-standard licenses without an " -"SPDX identifier, provide a URL to the license." +"If possible, the license should be specified with its corresponding [SPDX " +"identifier][spdx]. Construct the metadata field for the license by providing " +"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " +"taken from the list of identifiers linked above. See the example snippet " +"below for guidance. For non-standard licenses without an SPDX identifier, " +"provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: 5fe2962837b14f0e9989063be4a506c3 msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: 4e1bdea962ed4618884cb9d1d59d7509 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: 37eff4ca02e843259f6ffa38e4a87a04 msgid "" -"For more examples of providing metadata within CWL descriptions, see " -"[the Metadata and Authorship section of this User Guide](../topics" -"/metadata-and-authorship.md)." +"For more examples of providing metadata within CWL descriptions, see [the " +"Metadata and Authorship section of this User Guide](../topics/metadata-and-" +"authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: ae47231c203d40a98c10045038ea9b65 msgid "" -"Include [attribution information][license-example] for the author(s) of " -"the CWL tool or workflow description. Use unambiguous identifiers like " -"[ORCID][orcid]." +"Include [attribution information][license-example] for the author(s) of the " +"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" +"[orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: 018a6d5dbf1044559b365c7b9017eb3f msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: e073d8f990c44b09a73d642cfe49bebd msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in " -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" +"identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: e04fae88d9b64493ac69eaee24585098 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1377,24 +1541,26 @@ msgid "" msgstr "" #: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: b26b9c9b1c4346a297a31c9721f0172a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: b50500c3c3f54b16a535a16175a44653 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " -"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" -"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " -"types). For non-bioinformatics tools, use or build an appropriate " -"ontology/controlled vocabulary in the same way. Please edit this page to " -"let us know about it." +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" +"$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. " +"[Full IANA media type list][iana-types] (also known as MIME types). For non-" +"bioinformatics tools, use or build an appropriate ontology/controlled " +"vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: 623f3a804199449bb85e23e00c8bb507 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " @@ -1402,158 +1568,175 @@ msgid "" msgstr "" #: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: effea0b1356447c0899ca0746667ea31 msgid "" -"Each `CommandLineTool` description should focus on a single operation " -"only, even if the (sub)command is capable of more. Don't overcomplicate " -"your tool descriptions with options that you don't need or use." +"Each `CommandLineTool` description should focus on a single operation only, " +"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: 00e8ef87864c4ca2b2c1c0548b02b38d msgid "" -"Custom types should be defined with one external YAML per type definition" -" for re-use." +"Custom types should be defined with one external YAML per type definition " +"for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: 6e6f48d70b894a6c959ca30fe6bad772 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: 02fe08760a4a4ab49e96f4e51316a81d msgid "" -"If useful, include a top-level `doc` as well. This should provide a " -"longer, more detailed description than was provided in the top-level " -"`label` (see above)." +"If useful, include a top-level `doc` as well. This should provide a longer, " +"more detailed description than was provided in the top-level `label` (see " +"above)." msgstr "" #: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: 172ed7915a654964ba63f860b2d65330 msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list" -" of valid values." +"Use `type: enum` instead of `type: string` for elements with a fixed list of " +"valid values." msgstr "" #: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: 4d0a2871a7484e21b3c39c4dbaaa63fc msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. " -"One common example: manipulating `File` names and paths? Consider whether" -" one of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc., could be used instead." +"Evaluate all use of JavaScript for possible elimination or replacement. One " +"common example: manipulating `File` names and paths? Consider whether one of " +"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: 1eea9f1e284447718141f5417b6bb433 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: 509411d353fe4314b087b81b09ea960b msgid "" -"Complex workflows with individual components which can be abstracted " -"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" -" their workflow modular and allow sections of them to be easily reused." +"Complex workflows with individual components which can be abstracted should " +"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " +"workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: a54bc80bf08243bba67d98dd682ee134 msgid "" "Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics" -" software\"][containers] (also useful to other disciplines)." +"[\"Recommendations for the packaging and containerizing of bioinformatics " +"software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: 69ecdaea24ef42eebef9d86e5d716b11 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: 3cc5847468d1478bb5589dee68147189 msgid "" -"A command-line tool is a type of Process object that can be run by itself" -" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " -"`tar`, etc. The command-line tool is defined in the `baseCommand` " -"attribute of the command-line tool CWL document." +"A command-line tool is a type of Process object that can be run by itself or " +"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " +"etc. The command-line tool is defined in the `baseCommand` attribute of the " +"command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: 98c6bc409420485095ae65d6b0b9a3a0 msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The " -"following example contains a minimal example of a CWL command-line tool " -"for the `echo` Linux command, using inputs and outputs." +"A CWL command-line tool must also have `inputs` and `outputs`. The following " +"example contains a minimal example of a CWL command-line tool for the `echo` " +"Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: ebe23e5378514f888a9ec32a2adb1e98 msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: 387cfe85604f424f8d31c4a4c9c15edb msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: 7b1d65754e854693bb60289c97d3fb5d msgid "" -"The example above uses a simplified form to define inputs and outputs. " -"You will learn more about in the [Inputs](../topics/inputs.md) and in the" -" [Outputs](../topics/outputs.md) sections." +"The example above uses a simplified form to define inputs and outputs. You " +"will learn more about in the [Inputs](../topics/inputs.md) and in the " +"[Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: f440cef729c8410281432307a4da8d55 msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#: 4fbb8ceb1b59480583ac611142167049 msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network " -"access. If a command-line tool is written manually in CWL v1.1+, there is" -" a need to specify when network access is required." +"This indicates whether a process requires outgoing IPv4/IPv6 network access. " +"If a command-line tool is written manually in CWL v1.1+, there is a need to " +"specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: b87869204838415bbf694214e3680593 msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " -"Network Access automatically." +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " +"Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b 12cf5f2264504c44a2173e858bb2c283 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: 0cf51b6da6884065ae42032abc20eb0d 7694f9cabfe04308bbddd2c88ae6d9b9 msgid "" -"Sometimes you need to create a file on the fly from input parameters, " -"such as tools that expect to read their input configuration from a file " -"rather than the command line parameters, or need a small wrapper shell " -"script." +"Sometimes you need to create a file on the fly from input parameters, such " +"as tools that expect to read their input configuration from a file rather " +"than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: 2df3a3a9094d4b79b1d5dd99195f3bff b557dc4f8ef549b98f59412a918643de msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: d3f74c3b094a427fbec831afab657d50 3011eb003c084285b30cfa56a8da45b6 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: cfffc518ba6e4ed1a80762ed6f7d25df 9f9c90a2bb4b4d3b8e99b63cb0e72f76 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the " -"value at the input `message`." +"expanded by the CWL engine before creating the file. Here, insert the value " +"at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: 9454a330b9324744b89448f2694b1b03 ce78b2d147054da895beba66d0ecdab4 msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later" -" during command line tool invocation. That means that any genuine need " -"for the character `$` must be **escaped** with `\\`. For instance, " -"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " -"be evaluated by the shell script instead of the CWL engine." +"The _CWL expressions_ are independent of any _shell variables_ used later " +"during command line tool invocation. That means that any genuine need for " +"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " +"above is expanded to `${PREFIX}` in the generated file to be evaluated by " +"the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: 7f8d99a30b644457a62ac1523d0c72aa a973846ec5a946eeaff02c5b00997da9 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1562,32 +1745,33 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 #: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 +#: ca03defa3ad14cf698171cb09e3055c1 294fd83a97a64249bac38f7482159372 +#: 9e8eb1542db640ff9e300649ce50dc9d ccec7f73b9d948e79a6cdf32bc124092 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: 10d1373bb14a4a3cacd3b92a2f83382d 22948f19cb78485f8f86244686a35c09 msgid "" -"Before we run this, let us look at each step in a little more detail. The" -" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"Before we run this, let us look at each step in a little more detail. The " +"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " "command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 70e257091bdb456e8957f90a8fa90e8c 001d9579bfce438e865377fb9c2df776 msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " -"YAML array, we need a `-` on the first line of each element of the array," -" in this case we have just one element. `entryname:` can have any value, " -"but it must match what was specified in the `baseCommand`. The final part" -" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " -"means that you are using a multiline string (without it, we would need to" -" write the whole script on one line)." +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " +"array, we need a `-` on the first line of each element of the array, in this " +"case we have just one element. `entryname:` can have any value, but it must " +"match what was specified in the `baseCommand`. The final part is `entry:`, " +"this is followed by `|-` which is YAML quoting syntax, and means that you " +"are using a multiline string (without it, we would need to write the whole " +"script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: 1741804e33aa43ce88b4320c11ae5973 e62618db8995428bb3f260e03ac8f459 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1599,221 +1783,258 @@ msgstr "" #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 #: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f #: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 +#: f924d65fed0c4cb5b0a019b084a8b535 457756c4e9544f068af897113358cc89 +#: 6d5ae75431424ea788c3440606f22940 98e0548845fa447fb05a29c9fc2f17b5 +#: de5e8aad4e3046bf9bfc2ad8ccba17d0 e9801b2142cd45368a73ef9b121c1d08 msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line:" msgstr "" #: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: ee2bca9bdbb74b60a706c3118d6a17ba msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: e63ae9694f40438d872d141ae824a42d msgid "" -"Sometimes you may want to write your own custom types for use and reuse " -"in CWL descriptions. Use of such custom types can reduce redundancy " -"between multiple descriptions that all use the same type, and also allow " -"for additional customisation/configuration of a tool/analysis without the" -" need to fiddle with the CWL description directly." +"Sometimes you may want to write your own custom types for use and reuse in " +"CWL descriptions. Use of such custom types can reduce redundancy between " +"multiple descriptions that all use the same type, and also allow for " +"additional customisation/configuration of a tool/analysis without the need " +"to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: 750fdd4c270e46a09f79e867358f7414 msgid "" -"The example below is a CWL description of the [biom convert format][biom]" -" tool for converting a standard biom table file to hdf5 format." +"The example below is a CWL description of the [biom convert format][biom] " +"tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: b3f688cc82444ef7a7a0aa63dac39cac msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: 3638be18b4f64cf08053d512e590dda3 msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: 7d5b9c21739c48f18c13614ca6967f6b msgid "" -"___Note:___ To follow the example below, you need to [download the " -"example input file](https://github.com/common-workflow-" -"language/user_guide/blob/main/src/_includes/cwl/custom-" -"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " -"`wget`:" +"___Note:___ To follow the example below, you need to [download the example " +"input file](https://github.com/common-workflow-language/user_guide/blob/main/" +"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " +"*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: 8fea29993f944d8d8d3181afa29bd0a6 msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to " -"be used in the table conversion are imported as a custom object:" +"On line 29, in `inputs:table_type`, a list of allowable table options to be " +"used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: 02d0b648d70f49d7892f690be06df585 msgid "" -"The reference to a custom type is a combination of the name of the file " -"in which the object is defined (`biom-convert-table.yaml`) and the name " -"of the object within that file (`table_type`) that defines the custom " -"type. In this case the `symbols` array from the imported `biom-convert-" -"table.yaml` file define the allowable table options. For example, in " -"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" -" to create an OTU table in hdf5 format." +"The reference to a custom type is a combination of the name of the file in " +"which the object is defined (`biom-convert-table.yaml`) and the name of the " +"object within that file (`table_type`) that defines the custom type. In this " +"case the `symbols` array from the imported `biom-convert-table.yaml` file " +"define the allowable table options. For example, in `custom-types.yml`, we " +"pass `OTU table` as an `input` that tells the tool to create an OTU table in " +"hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e -msgid "The contents of the YAML file describing the custom type are given below:" +#: 0743bef42b9a42328849c8c2f9da9eed +msgid "" +"The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: 85c5d0cbbc6243a6823f5eeac0f85dd9 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: be848f30769543eb9c0be55263e3f758 msgid "" -"In order for the custom type to be used in the CWL description, it must " -"be imported. Imports are described in " -"`requirements:SchemaDefRequirement`, as below in the example `custom-" -"types.cwl` description:" +"In order for the custom type to be used in the CWL description, it must be " +"imported. Imports are described in `requirements:SchemaDefRequirement`, as " +"below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: cbff44a64ba4432cb59a82f82c2f0103 msgid "" "Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number " -"of cores required for the tool to run successfully, as well as details of" -" the version of the software that the description was written for and " -"other useful metadata. These features are discussed further in other " -"chapters of this user guide." +"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " +"cores required for the tool to run successfully, as well as details of the " +"version of the software that the description was written for and other " +"useful metadata. These features are discussed further in other chapters of " +"this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: 617f1c0084cf42d9be4c7a8fa5a48432 msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: cee79afa3c6f43c29ef05e06b7843d35 msgid "" -"Tools run in a restricted environment and do not inherit most environment" -" variables from the parent process. You can set environment variables " -"for the tool using `EnvVarRequirement`." +"Tools run in a restricted environment and do not inherit most environment " +"variables from the parent process. You can set environment variables for " +"the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: 225903b11efa417989df42de86ad2451 msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: 1a5f058290064c1cad05e63eb127fcbb msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: 74ad8d69cf294ae880dbbe28e25b3545 msgid "" -"An expression tool is a type of Process that can be run by itself or as a" -" Workflow step. It executes a pure JavaScript expression. It is meant to " -"be used as a way to isolate complex JavaScript expressions that need to " -"operate on input data and produce some result as output." +"An expression tool is a type of Process that can be run by itself or as a " +"Workflow step. It executes a pure JavaScript expression. It is meant to be " +"used as a way to isolate complex JavaScript expressions that need to operate " +"on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: 5293e8ee9b3b4f59947cfc164ef111c4 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: ffa1955c759942c68e7589429e5ea86b msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: 038bc0ba5f6a405a8255a7be76979baf msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: fae1c63de02e48c0969a98e4c49b2e06 msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains" -" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"We had to use an `InlineJavascriptRequirement` as our expression contains a " +"JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: 7093a94695524851a5463193f0701b78 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: dc8274ecb15948c29a31db89b12a58bd msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by " -"the CWL runner." +"legal you can provide a fragment of Javascript that will be evaluated by the " +"CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: cec8eef8a5aa49778ecedd4195ab9f2c msgid "" -"JavaScript expressions should only be used when absolutely necessary. " -"When manipulating file names, extensions, paths etc, consider whether one" -" of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " -"practices](best-practices.md)." +"JavaScript expressions should only be used when absolutely necessary. When " +"manipulating file names, extensions, paths etc, consider whether one of the " +"[built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc, could be used instead. See the [list of best practices](best-" +"practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: df100967597043c78112bf43b520cfab msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: 59ccf4daba39406581a6bc2d9bb1b7d2 msgid "" -"As this tool does not require any `inputs` we can run it with an (almost)" -" empty job file:" +"As this tool does not require any `inputs` we can run it with an (almost) " +"empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: 570cc75699dd4e0a987fc9aca9a01ee4 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: 9e123723048546d495ed5110d7177708 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object" -" is represented simply by a set of empty brackets." +"descriptions are contained inside curly brackets `{}`, so an empty object is " +"represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: 26543894f6e04270b89ab702451bcc89 msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: f403c1d4e43a4aa0aef8488d2b5a6262 msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: 249dffb569a944c897ce5862e5f28fad msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" #: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: 1641c96aca2f4923885fe8a509eb3a49 msgid "" "Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" -" describe the additional command line arguments." +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " +"describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: bc63405a0d964df2bd9493996abc48fe msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: 5c191d1420db4e26aca31c1b1e34cb75 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: d6a5c65e824a4bbc94578df9597d4716 msgid "" -"From " -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: 1acb064f7a4a482aa0174bdc847c6382 a7ff51fe564748229a88a0d3044dbc17 +#: c12625211cc542b68cb51365a63eef00 msgid "`arguments`" msgstr "" @@ -1824,32 +2045,39 @@ msgstr "" #: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e #: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 #: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 05c34a5a2e404a14b9d284a9d0c73bd3 +#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe +#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: e7f1993580f0425098a719e83a64cc7f msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: 17ac6d2c703b466f9720b7489209a2ff 2fd5b42cafe34d3185888de041818dff +#: c158e9ee5fbf4e868b152a0a5880092f msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 3f29e4a3087847e9af6f19166a8def9a +#: 92697d3179ec48898eaea9aba3c24dcd msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: 37392218309d4baebe62fc38bf50efe9 c0eaef93bc3743279549bcfb8b014ca3 +#: d6722e3093884ad7b62696fbb2f48fdc msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: 37c493fdc2f0410a9748f8faf09ce5b5 msgid "" -"From " -"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" #: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 @@ -1861,7 +2089,11 @@ msgstr "" #: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd #: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 #: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ed875a006df64f9e8a55fa5e9fa87404 04e3eefe4ec445cb90c2fa42344aaed5 +#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 +#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef +#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 +#: c610220d06484d589313dc29faf8222c msgid "`format`" msgstr "" @@ -1874,800 +2106,914 @@ msgstr "" #: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d #: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f #: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 +#: f760465a49d64d4c8468ad9c4fea62b1 662b36e3505f4ac3bb5070bb6e055217 +#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da +#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c +#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b +#: f71216a4b35e4157aece5ffa2602d8bf msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: a3c775a0f04b4541a9b712bfe2e4e69a msgid "" -"From " -"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: ef16c4a9a7ea415fa399297b63b9710c msgid "" -"From " -"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: 2592e429c74c4ff5b8ba68a36f060c1a msgid "" -"From " -"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: d193ce0123db4535a4f0b11405ad0322 5cca4c2ad617400eb6efad4066b1839b +#: ba1fff3ebb274dfba845b3ee20ebd71f msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 +#: d555a3d991e344a5a8e1289168d7c6d1 6914526c0a7c43a2a05438519508ee0f +#: 722d3bd7184841639b9f9a38914002da msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: e9fa9430535c424fa3e8be5d460d2ba4 737b0f9392154241ae5b56c6caa823f5 +#: 7b46d408e7e7481b91a950b2d4010c9a msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: f09e7371708b4c0685eef2a314791ccd msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff +#: b0290d1a477b48119e17cf1fed9d6dff aa6ca1def2024c98b9d5542de1a81425 +#: e9fc5f7fa4474dfc95039b94167fe894 msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: 6c37a1ff939748bf83a86c07c3d017fe msgid "" -"From " -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 +#: e1cde4aa32c041238ed2596173c6d824 3a8126b0a0334df890b2be2c693ea5d5 +#: 61744122b7d7494890cbe6b2fb72b9f7 msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 +#: c2a92d3eca7f4ee39cec649170eeea53 93cb9015dacc4b50a4ef177ce4ece2e7 +#: e0c7ccc8f8664cf794cbb7330355f3fe msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: 58a1773b1cf546d7890010fdebd47388 msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](https://www." +"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: 230f3227ed1144f7abe0f8c231bebbd5 msgid "" -"From " -"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: d0eec6969d174b258e0f010800884cc6 5c77dc9f8afe4dd88933943030e836f2 +#: c9534670f5f04769aa3749c3778eb705 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 +#: 718ceee9973240ec9c100977bbcc8921 4ec8bbac5fb14371a6a4cd53d7cd6450 +#: 7b0887a8caed41b2acccf7021bb323d3 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: c07ab08eb75d4528949c56a3d7c12b28 aceedfb558b246bc87eb3eaedea187fd +#: e5e8b8c75f0f43cbb6e160e5bf810c6e msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: b885e108dced4981a445e5fa0a044394 266dfb5fe6a842078baf66073cac9623 +#: fe3b9fb45e01490498c5a35c012b3de8 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: e9f5306ae6ea49bbb6801dcce9be2d67 85f424cbfc85460f9da310aee1ff0b82 +#: ddf82b12b12d416fb65f3ce3f51bbdf0 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: 58bf8016f5f04c26b645025f405e2288 966e88656ae5402a975022ee60646283 +#: af14fda3cca645fbb2f3c5825fe0788e msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: 7c817029d55b4700ae8e84be4d0f0ca0 09120baec1464afb8aed4edd773bf509 +#: fec70bb106ad4d95a2d55ebdcf711afc msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 #: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: 1dc4148caef748428a7d13caff37b1b1 msgid "" -"From " -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 #: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: 947b1ca132a54ed39745cd12ebcd65e1 msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 #: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 #: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 #: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: 5fa512d352d945e7a3e0d59b0987cd1b msgid "" -"From " -"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 #: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +#: 81e91df082834d2cab7ef1f62d8ba57a +msgid "" +"Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: e6bfd1dc2e324992b6c3332c11ae3445 msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" -" attribute that allows users to load external JavaScript files, or to " -"provide inline JavaScript code." +"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " +"attribute that allows users to load external JavaScript files, or to provide " +"inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: acf10261df2944ec890d754fd56c6b28 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts" -" of the CWL document." +"files or to create JavaScript functions that can be called in other parts of " +"the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: bda6b8f398554b0c946c2c7d96308a42 msgid "" -"The CWL standards (versions 1.0 through 1.2) " -"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" -" that the only version of JavaScript valid in CWL expressions is " -"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " -"that any code that you include or write in your CWL Document must be " -"compliant with ECMAScript 5.1." +"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." +"org/v1.0/CommandLineTool.html#Expressions) that the only version of " +"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" +"international.org/5.1/). This means that any code that you include or write " +"in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: 454c02c3918647039c90ae387005dea6 msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a " -"JavaScript function inline in `expressionLib`. That function can then be " -"used in other parts of the CWL document:" +"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " +"function inline in `expressionLib`. That function can then be used in other " +"parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: e1fad28bf9cb4c4c85eb74dd520ba107 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: 9835d0b399b84a0084fe5a4d9e7e6405 msgid "" -"Running this CWL workflow will invoke the JavaScript function and result " -"in the `echo` command printing the input message with capital initial " -"letters:" +"Running this CWL workflow will invoke the JavaScript function and result in " +"the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: 410ba7a5ac6349a98460c6337ee5c4fb msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: d2daf50d7f3d4de18331c8fd2c8a5786 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: 8f2015c12b2b4d5d9a800ddeaf428f25 msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: f0ff919ffc12439d89d7b40f51ade84c msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: 307a17a893fc4dafaec2a63a95704644 msgid "" -"The `custom-functions.js` file is included in the CWL document with the " -"`$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the `" +"$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: 7f393e86b114470f8dda47b2deec63aa msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: c3f459b87b96435583637b3f1573e658 msgid "" -"Finally, note that you can have both inline and external JavaScript code " -"in your CWL document. In this final example we have added another entry " -"to the `expressionLib` attribute with the new function " -"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" -" the external file `custom-functions.js`." +"Finally, note that you can have both inline and external JavaScript code in " +"your CWL document. In this final example we have added another entry to the " +"`expressionLib` attribute with the new function `createHelloWorldMessage`, " +"that calls the `capitalizeWords` function from the external file `custom-" +"functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: 9f676022eb2744839ca2109920250cb6 msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: ede7285f77864fb0aee6cfecc2c97fa0 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: c55fb184bc614ee2b6e5e64611e5df9b msgid "" -"The `$include` statement can be used to include a file from the local " -"disk or from a remote location. It works with both relative and absolute " -"paths. Read the [text about " -"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " -"the CWL specification to learn more about it." +"The `$include` statement can be used to include a file from the local disk " +"or from a remote location. It works with both relative and absolute paths. " +"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: 66b522f46ce242149386e79f63b32cf8 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: 64a20285785d48ca86227a0cf6353ad4 msgid "" "Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This " -"helps document for others how to use your tool while allowing you to do " -"some simple type-checking when creating parameter files." +"output. We also recommend indicating the format for `File` types. This helps " +"document for others how to use your tool while allowing you to do some " +"simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: 5f71bbe2c74e4260b79d4d9230d35397 msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM" -" in our example), reference a local ontology for your institution, or do " -"not add a file format initially for quick development before sharing your" -" tool with others. You can browse existing [IANA file format " -"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +"For file formats, we recommend referencing existing ontologies (like EDAM in " +"our example), reference a local ontology for your institution, or do not add " +"a file format initially for quick development before sharing your tool with " +"others. You can browse existing [IANA file format listings][IANA] and [EDAM " +"file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: 63bfff437e3348428f7e33ece7ec55e7 msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` " -"section of the document in greater detail, so don't worry about these for" -" now." +"In the next tutorial, we explain the `$namespaces` and `$schemas` section " +"of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: 6ce83d9c06e4436881aa47d94ef41e0b msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: 55006c594abf4e70a38e979568fadcf4 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 #: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: 1a1905ff2d624eca952c8a53b3bee678 msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: 368ff92476b14f5c8331260eafc5acb5 msgid "" -"Below is an example of a parameter file for the example above. We " -"encourage checking in working examples of parameter files for your tool. " -"This allows others to quickly work with your tool, starting from a " -"\"known good\" parameterization." +"Below is an example of a parameter file for the example above. We encourage " +"checking in working examples of parameter files for your tool. This allows " +"others to quickly work with your tool, starting from a \"known good\" " +"parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: 5d530afa23f349a79f54d51d40724747 msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: 16f965f86712483aa7f95dfa3f944a17 msgid "" -"___Note:___ To follow the example below, you need to download the example" -" input file, *file-formats.bam*. The file is available from " -" and can be downloaded e.g. via `wget`:" +"___Note:___ To follow the example below, you need to download the example " +"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: dc629e2c90ed458b96107a6994676434 msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: cf2f077cf8044079a7005e6e508dcd8c msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: 129e1d2a71894d28b009f4846754a75d msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: d6791bbe575042b9a7282c69407dd907 msgid "" -"The `inputs` of a tool is a list of input parameters that control how to " -"run the tool. Each parameter has an `id` for the name of parameter, and " -"`type` describing what types of values are valid for that parameter." +"The `inputs` of a tool is a list of input parameters that control how to run " +"the tool. Each parameter has an `id` for the name of parameter, and `type` " +"describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: e8da87f8bb664334adf831995601f462 msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*," -" and *null*; complex types are *array* and *record*; in addition there " -"are special types *File*, *Directory* and *Any*." +"Available primitive types are *string*, *int*, *long*, *float*, *double*, " +"and *null*; complex types are *array* and *record*; in addition there are " +"special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: de6c322618304207b6d1364d1ec2dc13 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: 43bdcf6dc1b14030bff27fa53289c02c msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: 056510b42ea64717996ab49c307bda86 msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: 6852f5dbd9094c99bb68f2a88f76c9bc msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: f33b6800367248b7927d97ad7b4be5b5 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: 8ad812d7e88f4cbba83228ffb1711576 msgid "" -"You can use `cwltool` to create a template input object. That saves you " -"from having to type all the input parameters in a input object file:" +"You can use `cwltool` to create a template input object. That saves you from " +"having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: cc680bbf091a46f8b4b3dbe6324c040a msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template " -"inp.cwl > inp-job.yml`, and then modify the default values with your " -"desired input values." +"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " +"> inp-job.yml`, and then modify the default values with your desired input " +"values." msgstr "" #: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: 446ac81f078d46289a18f494748f482c msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: 3d6d958d111943f3a2139b4dbb7810db msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" -" command line." +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " +"command line." msgstr "" #: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: ba0ec9157709430c822f4e91459288e2 msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " -"following boxed text describes these two commands and the expected output" -" from the command line:" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " +"boxed text describes these two commands and the expected output from the " +"command line:" msgstr "" #: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: 2565f8fd4a15429e887aeb71eacdff1e msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not " -"explicitly specified" +"that the tools aren't accidentally accessing files that were not explicitly " +"specified" msgstr "" #: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: 659ed5c64fb546399b741553a347b8e8 msgid "" -"The field `inputBinding` is optional and indicates whether and how the " -"input parameter should appear on the tool's command line. If " -"`inputBinding` is missing, the parameter does not appear on the command " -"line. Let's look at each example in detail." +"The field `inputBinding` is optional and indicates whether and how the input " +"parameter should appear on the tool's command line. If `inputBinding` is " +"missing, the parameter does not appear on the command line. Let's look at " +"each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: 3d87e69d41374fbab23b26d36c1aee03 msgid "" -"Boolean types are treated as a flag. If the input parameter " -"\"example_flag\" is \"true\", then `prefix` will be added to the command " -"line. If false, no flag is added." +"Boolean types are treated as a flag. If the input parameter \"example_flag" +"\" is \"true\", then `prefix` will be added to the command line. If false, " +"no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: 07bc81683e2c4ac68b379462bae95207 msgid "" -"String types appear on the command line as literal values. The `prefix` " -"is optional, if provided, it appears as a separate argument on the " -"command line before the parameter . In the example above, this is " -"rendered as `--example-string hello`." +"String types appear on the command line as literal values. The `prefix` is " +"optional, if provided, it appears as a separate argument on the command line " +"before the parameter . In the example above, this is rendered as `--example-" +"string hello`." msgstr "" #: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: 3e304da2150f448d9e39715ac5f5deaa msgid "" -"Integer (and floating point) types appear on the command line with " -"decimal text representation. When the option `separate` is false (the " -"default value is true), the prefix and value are combined into a single " -"argument. In the example above, this is rendered as `-i42`." +"Integer (and floating point) types appear on the command line with decimal " +"text representation. When the option `separate` is false (the default value " +"is true), the prefix and value are combined into a single argument. In the " +"example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: fd8a98686e3c4c609f79ae427f1558d3 msgid "" "File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the " -"parameter is optional. In the example above, this is rendered as " -"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " -"parameter were not provided in the input, nothing would appear on the " -"command line." +"parameter type ends with a question mark `?` it indicates that the parameter " +"is optional. In the example above, this is rendered as `--file=/tmp/random/" +"path/whale.txt`. However, if the \"example_file\" parameter were not " +"provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: f1a2e1bbb1104a4fab5a7f04cac845c7 msgid "" -"Input files are read-only. If you wish to update an input file, you must" -" [first copy it to the output directory](staging-input-files.md)." +"Input files are read-only. If you wish to update an input file, you must " +"[first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: 6a7f0ccd227e4f90a8c8ca96744bda68 msgid "" -"The value of `position` is used to determine where parameter should " -"appear on the command line. Positions are relative to one another, not " -"absolute. As a result, positions do not have to be sequential, three " -"parameters with positions 1, 3, 5 will result in the same command line as" -" 1, 2, 3. More than one parameter can have the same position (ties are " -"broken using the parameter name), and the position field itself is " -"optional. The default position is 0." +"The value of `position` is used to determine where parameter should appear " +"on the command line. Positions are relative to one another, not absolute. " +"As a result, positions do not have to be sequential, three parameters with " +"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " +"than one parameter can have the same position (ties are broken using the " +"parameter name), and the position field itself is optional. The default " +"position is 0." msgstr "" #: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: 1f79d115d8a145189638c68c3095396c msgid "" -"The `baseCommand` field will always appear in the final command line " -"before the parameters." +"The `baseCommand` field will always appear in the final command line before " +"the parameters." msgstr "" #: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: 6e1b3e2d90184e34925891099d2b5cc1 msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: 4f6df7f13e42448eb4a53f03bc477b56 msgid "" "It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to " -"provide `type` field with `type: array` and `items` defining the valid " -"data types that may appear in the array. Alternatively, brackets `[]` may" -" be added after the type name to indicate that input parameter is array " -"of that type." +"line. There are two ways to specify an array parameter. First is to provide " +"`type` field with `type: array` and `items` defining the valid data types " +"that may appear in the array. Alternatively, brackets `[]` may be added " +"after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: dbc0b52627514ad0908969d0b4ddfdf4 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: f173dd96ad124470a53573c86a8df203 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 #: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +#: af25945b530048b685891b1de4e35e72 cb07caa4ff0149b3ae832be53f8d76f6 +#: e0098a77080d4349b05ceb7735a5fdf5 msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" +"Now invoke `cwltool` providing the tool description and the input object on " +"the command line:" msgstr "" #: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: 2445d2c7c2794fd3ad8b6ed8b4a9440b msgid "" -"The `inputBinding` can appear either on the outer array parameter " -"definition or the inner array element definition, and these produce " -"different behavior when constructing the command line, as shown above. In" -" addition, the `itemSeparator` field, if provided, specifies that array " -"values should be concatenated into a single argument separated by the " -"item separator string." +"The `inputBinding` can appear either on the outer array parameter definition " +"or the inner array element definition, and these produce different behavior " +"when constructing the command line, as shown above. In addition, the " +"`itemSeparator` field, if provided, specifies that array values should be " +"concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: 4459819ba75647d185986a3386939494 msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` " -"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " -"lines, where array values that are not defined with an associated key are" -" marked by a leading `-`. This will be demonstrated in the next lesson " -"and is discussed in more detail in the [YAML Guide](yaml-" -"guide.md#arrays). You can specify arrays of arrays, arrays of records, " -"and other complex types." +"Note that the arrays of inputs are specified inside square brackets `[]` in " +"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " +"where array values that are not defined with an associated key are marked by " +"a leading `-`. This will be demonstrated in the next lesson and is discussed " +"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " +"arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: 8f163bd34ded4785b6e28c8e2147e0dd msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: 1799e11a7b9c4929a3d1379d7ea45d03 msgid "" "Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be " -"provided together (they are exclusive). You can use records and type " -"unions to group parameters together to describe these two conditions." +"together (they are dependent) or several arguments that cannot be provided " +"together (they are exclusive). You can use records and type unions to group " +"parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: 9510c0b431a44b5e84e0b583de7c5446 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: efb4eb6f5e994b50a52fa2c707dad1ce msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: 34599c6f10ce4104be2359a1b37f91cb msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" #: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: 0663ea7918994d3f9c45c652a3ed12db msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: a98dda6ca4b14edba467de638bba28fc msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the " -"first matching item (`itemC`) is added to the command line and remaining " -"item (`itemD`) is ignored." +"In the second example, `itemC` and `itemD` are exclusive, so only the first " +"matching item (`itemC`) is added to the command line and remaining item " +"(`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: 10d0e9f8df8c47788703073b17529bc8 msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: 9a0e1a130fba4d24a9168ca3e455cd23 msgid "" -"In the third example, only `itemD` is provided, so it appears on the " -"command line." +"In the third example, only `itemD` is provided, so it appears on the command " +"line." msgstr "" #: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: 992a8c801ceb4233acf56b6bff315188 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: 9027d23fa7074b789c3b86ca5ea17fa4 msgid "" -"If you use exclusive input parameters combined with expressions, you need" -" to be aware that the `inputs` JavaScript object will contain one of the " +"If you use exclusive input parameters combined with expressions, you need to " +"be aware that the `inputs` JavaScript object will contain one of the " "exclusive input values. This means that you might need to use an **or** " "boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: 68b47710a8ea4b978428b42c627944e9 msgid "" "Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from" -" an enum." +"parameter that accepts `null` (i.e. no value provided), or any value from an " +"enum." msgstr "" #: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: d33e4cac65d14111a89c838c4d1759b9 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: 24cea1cf7d774b6ab56959f289cab39d msgid "" "Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you " -"provide a valid value, such as “fasta” (one of the values of the enum), " -"your command should execute successfully:" +"parameter without taking into consideration a `null` value. If you provide a " +"valid value, such as “fasta” (one of the values of the enum), your command " +"should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: b866867d6f8e4d3999b62a85e6884ebc msgid "" -"However, if you do not provide any input value, then `file_format` will " -"be evaluated to a `null` value, which does not match the expected type " -"for the output field (a `string`), resulting in failure when running your" -" workflow." +"However, if you do not provide any input value, then `file_format` will be " +"evaluated to a `null` value, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: 80c49ed168b14d25b2f09b3b0186b44f msgid "" -"To correct it, you must remember to use an or operator in your JavaScript" -" expression when using exclusive parameters, or any parameter that allows" -" `null`. For example, the expression could be changed to " -"`$(inputs.file_format || 'auto')`, to have a default value if none was " -"provided in the command line or job input file." +"To correct it, you must remember to use an or operator in your JavaScript " +"expression when using exclusive parameters, or any parameter that allows " +"`null`. For example, the expression could be changed to `$(inputs." +"file_format || 'auto')`, to have a default value if none was provided in the " +"command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: d33aa2353ad44fb885d3a1ee48263dc4 71628ebe908b4cd28dd1fa17e3d2e2fb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: cd64d2d828834cbbb24ea5358caf5405 f123ca244c23413c91405a4b84887525 msgid "" -"Implementation extensions not required for correct execution (for " -"example, fields related to GUI presentation) and metadata about the tool " -"or workflow itself (for example, authorship for use in citations) may be " -"provided as additional fields on any object. Such extensions fields (e.g." -" `format: edam:format_2572`) can use a namespace prefix listed in the " -"`$namespaces` section of the document (e.g. edam: " -"http://edamontology.org/) as described in the [Schema Salad specification" -"][schema-salad]. Once you add the namespace prefix, you can access it " -"anywhere in the document as shown below. Otherwise, one must use full " -"URLs: `format: http://edamontology.org/format_2572`." +"Implementation extensions not required for correct execution (for example, " +"fields related to GUI presentation) and metadata about the tool or workflow " +"itself (for example, authorship for use in citations) may be provided as " +"additional fields on any object. Such extensions fields (e.g. `format: edam:" +"format_2572`) can use a namespace prefix listed in the `$namespaces` section " +"of the document (e.g. edam: http://edamontology.org/) as described in the " +"[Schema Salad specification][schema-salad]. Once you add the namespace " +"prefix, you can access it anywhere in the document as shown below. " +"Otherwise, one must use full URLs: `format: http://edamontology.org/" +"format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 80af387fe3ff4e2da999903385bd602b 23299ae1bec94b00a32a8af7eeac350f msgid "" "For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to " -"cite your tool." +"tool and workflows. This example includes metadata allowing others to cite " +"your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 2495a9f2032a47c188338cb81ba429eb msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: d402bf528c7f4eb69aaaa275be2bf1d4 3fd2f3cf7bdf44089df2ce3122534801 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 d5a5b8b490b640439db92da949266e4e msgid "" -"For those that are highly motivated, it is also possible to annotate your" -" tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints" -" at hardware requirements in order to use the tool, and a few more " -"metadata fields." +"For those that are highly motivated, it is also possible to annotate your " +"tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints at " +"hardware requirements in order to use the tool, and a few more metadata " +"fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 2dfbd4d580044ed083992f3ceb1bc64e 5935ed94331d4b2f8ce597f31edea843 msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: 5feb559552194ba58da7206c601292fe msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: b7124ba4df9042baadc1641ee09545d6 msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-" -"line tool, or an expression tool. It is a step of a workflow that " -"specifies inputs and outputs, but it does not provide enough information " -"to be executed." +"An Operation is a type of CWL process, just like a workflow, a command-line " +"tool, or an expression tool. It is a step of a workflow that specifies " +"inputs and outputs, but it does not provide enough information to be " +"executed." msgstr "" #: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: d34b698c62114041a64e0abce25ca935 msgid "" -"You can create operations to visualize a workflow during development, " -"before you are ready to submit the workflow to a CWL runner:" +"You can create operations to visualize a workflow during development, before " +"you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: cba2c31262bd450cbafc7ca77f4fb8fa msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: b01be5f632104096b5af6193aab34d90 msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like" -" a command line tool or an expression. You can also plot it with the CWL " -"Viewer or `cwltool`:" +"The `uppercase` step of the workflow is an operation. It can be used like a " +"command line tool or an expression. You can also plot it with the CWL Viewer " +"or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: 60a6a02c1367403db6df3ec10f75eb69 msgid "" -"The output of the command above can be rendered with a Graphviz renderer." -" The following image is rendered with the Sphinx Graphviz directive (this" -" user guide is built with Sphinx):" +"The output of the command above can be rendered with a Graphviz renderer. " +"The following image is rendered with the Sphinx Graphviz directive (this " +"user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: 314ea7bc35154f41b2af5fa6683ca389 msgid "" -"If you try running it with `cwltool`, the command will fail since " -"`cwltool` does not have enough information to know how to execute it:" +"If you try running it with `cwltool`, the command will fail since `cwltool` " +"does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: d81e679b13474f74bc5e1ce1e31c2bc6 msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: d7fb27131ee44bfc82f698ee44b2bae0 msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A" -" CWL runner could, for instance, use abstract operations with ID's that " +"CWL runners may come up with ways to bind operations to concrete steps. A " +"CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: b8ef11eafd1d46e088f1277f4ac372bc msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: d2382ed1f644459594655d5b5b4d838a msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: 6651632d977b44479b721174fffeda2d msgid "" "The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name" -" of parameter, and `type` describing what types of values are valid for " -"that parameter." +"returned after running the tool. Each parameter has an `id` for the name of " +"parameter, and `type` describing what types of values are valid for that " +"parameter." msgstr "" #: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: bee5f532554241088764ac9e56abbe85 msgid "" -"When a tool runs under CWL, the starting working directory is the " -"designated output directory. The underlying tool or script must record " -"its results in the form of files created in the output directory. The " -"output parameters returned by the CWL tool are either the output files " -"themselves, or come from examining the content of those files." +"When a tool runs under CWL, the starting working directory is the designated " +"output directory. The underlying tool or script must record its results in " +"the form of files created in the output directory. The output parameters " +"returned by the CWL tool are either the output files themselves, or come " +"from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: 0c7c506f38be421399073871f64e99b0 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: 8b60286e56cc42a8ab5f751a97adf771 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: fa0ad674f15348339a1eee771a6ba9e2 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2676,464 +3022,520 @@ msgid "" msgstr "" #: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: 177b5f1b95a34fb9b2eb42f733d79ac8 msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: a08a6d8aca8e490482e127a8fd5e650e msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: c2c60f68b1e045f88844076e191fda9b msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: 6d939f62526e4e6d95acb57d72f60a84 msgid "" -"And now invoke `cwltool` with the tool description and the input object " -"on the command line:" +"And now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "" #: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: c48edd9034364b81ad42540a98b51d91 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" #: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: 9ebe0186a7124dfaa30e558e8f59653a msgid "" -"The `glob` field consists of the name of a file in the output directory. " -"If you don't know name of the file in advance, you can use a wildcard " -"pattern like `glob: '*.txt'`." +"The `glob` field consists of the name of a file in the output directory. If " +"you don't know name of the file in advance, you can use a wildcard pattern " +"like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: 9381b7d7c9904df0a5e16dac29c2e08f msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: 2aa9c6916e3546b7b92fa64bb83275d1 msgid "" -"To capture a tool's standard output stream, add the `stdout` field with " -"the name of the file where the output stream should go. Then add `type: " -"stdout` on the corresponding output parameter." +"To capture a tool's standard output stream, add the `stdout` field with the " +"name of the file where the output stream should go. Then add `type: stdout` " +"on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: 63afb7a597fc4e459b6a7dbd40bbf6ff msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: 7418915470f041c9af5bd39ea652de36 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: f82db001b58c4969b2d8bc1dcbd7cf8a msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" #: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: 26d9f0b28d384617a8e490c1f8e26e52 msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: cf46c971b31b4e10bf0fefb4cd028c2f msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: a4347983fb9945a4a2773af88e426dc9 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions" -" to mark entries in arrays, as demonstrated in several of the upcoming " -"sections." +"marked by a leading `-`. This format can also be used in CWL descriptions to " +"mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: c5489e0633114372b273098ee2c9ffd9 msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: 75de9fd63393429daf1ca10a85339aa7 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file " -"we were interested in was called \"hello.txt\", and this was written into" -" the `.cwl` file. This is not the best way to do this, as the " -"\"hello.txt\" filename may vary or be dependent on the input file(s) " -"used. To avoid this we can specify the name of the file we want in the " -"job parameters file (`.yml`). In this example, you will see how to " -"reference the value of input parameters dynamically from other fields, " -"which will allow us to then specify the name of the file to extract." +"However, that example was very limited because it assumed that the file we " +"were interested in was called \"hello.txt\", and this was written into the `." +"cwl` file. This is not the best way to do this, as the \"hello.txt\" " +"filename may vary or be dependent on the input file(s) used. To avoid this " +"we can specify the name of the file we want in the job parameters file (`." +"yml`). In this example, you will see how to reference the value of input " +"parameters dynamically from other fields, which will allow us to then " +"specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: 8b5d0ada32d645be9359f43a431f5f91 msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: 2ed93dc8778e44209194f41b9ad193d5 msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: a80dd6d9920540e9880514e04035af86 msgid "" -"Create your input files and invoke `cwltool` with the tool description " -"and the input object on the command line:" +"Create your input files and invoke `cwltool` with the tool description and " +"the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: 9de300f7b9da49f59d1c9fd96dec4a8b msgid "" -"Certain fields permit parameter references which are enclosed in " -"`$(...)`. These are evaluated and replaced with value being referenced." +"Certain fields permit parameter references which are enclosed in `$(...)`. " +"These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: a61f52d3c1024c3692899e05fcea4bee msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " -"`$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" +"$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: dafc9ba578c14fd79d075160e6b7bd6b msgid "" -"The value of the \"inputs\" variable is the input object provided when " -"the CWL tool was invoked." +"The value of the \"inputs\" variable is the input object provided when the " +"CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: 28ca6cae42904559bcec98fb9d2b07cb msgid "" -"Note that because `File` parameters are objects, to get the path to an " -"input file you must reference the path field on a file object; to " -"reference the path to the tar file in the above example you would write " -"`$(inputs.tarfile.path)`." +"Note that because `File` parameters are objects, to get the path to an input " +"file you must reference the path field on a file object; to reference the " +"path to the tar file in the above example you would write `$(inputs.tarfile." +"path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: 616c9ff9fcae489285f0bbbc67f07d29 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: ac17acd83ddb43dc9fb7a5e595ab1153 msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: 156573324cde41ee8b3c47deabf43db8 msgid "" -"From " -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: c9725be01e8a401fb3ad9ff01339f81e msgid "" -"From " -"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: 6797335256e2412cbbe7636507931455 msgid "" -"From " -"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: 05a5f0fcb7454cb697e3d810d55fac26 msgid "" -"From " -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: 406e68280b5c4ee494632f94b635b7ad msgid "" -"From " -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: 2d6e2a4ff391494591bbdf8dbcc4a6ae msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: e71a974b29624210a107fc2d097d4196 msgid "" -"From " -"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: b59df98754e24654bfef0b1fe1d91660 msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: d2bccbff1ce646348fe38c776ad183e1 msgid "" -"From " -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 5d8bed66282c408695292ea92a03b2c4 943ba46512ce48fe8c5b62327734c503 msgid "" -"From " -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: 958178d1fa8843aaa0541e2bb115cfd4 bbcd43d5af7d44108aeb65075a6bd2be msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 834295755af841a78e466eea43864861 msgid "" -"From " -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: aac74f957774479a83aab4c6ff1390ae a6b626489bfa468e8f059ab3aa669201 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: b75d29d1d55d44488338f9689f156855 e1dbea105aa845c38cb1f90b43847271 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: 574d93d1d592458a985f259519c036cb e9640f47d40e45bca184eb30700df648 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may " -"also help to avoid confusion about which version of a tool the " -"description was written for." +"include a `SoftwareRequirement` field in the `hints` section. This may also " +"help to avoid confusion about which version of a tool the description was " +"written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 82e48b3e3c3f451480cc0b6a529271f6 0456efb3718b4356ad2b277ee16de967 msgid "" -"In this example, the software requirement being described is InterProScan" -" version 5.21-60." +"In this example, the software requirement being described is InterProScan " +"version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: 02e40154eac74ecc98d0447d03475b44 f7e97f926505407f8f8e9a427e055e43 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the " -"[dependency resolvers configuration][dependencies]." +"enable these checks with the reference implementation, use the [dependency " +"resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the " -"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" -" looked up in the [SciCrunch][scicrunch] registry, which provides a " -"portal for finding, tracking, and referring to scientific resources " -"consistently. If you want to specify a tool as a `SoftwareRequirement`, " -"search for the tool on SciCrunch and use the RRID that it has been " -"assigned in the registry. (Follow this [Adding a Resource Tutorial" -"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " -"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " -"field of your requirement description. Other good choices, in order of " -"preference, are to include the DOI for the main tool citation and the URL" -" to the tool." +#: 8cb1c5d9b1a54c40924099494eb766c6 ec597ff8f6ee47bc815b069335869f1f +msgid "" +"As well as a version number, a unique resource identifier (URI) for the tool " +"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " +"up in the [SciCrunch][scicrunch] registry, which provides a portal for " +"finding, tracking, and referring to scientific resources consistently. If " +"you want to specify a tool as a `SoftwareRequirement`, search for the tool " +"on SciCrunch and use the RRID that it has been assigned in the registry. " +"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " +"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." +"org][identifiers]) in the `specs` field of your requirement description. " +"Other good choices, in order of preference, are to include the DOI for the " +"main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: 7467a7f6f26a459ba4ce83e4e6dfcc2b msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 msgid "" -"Normally, input files are located in a read-only directory separate from " -"the output directory. This causes problems if the underlying tool " -"expects to write its output files alongside the input file in the same " -"directory. You use `InitialWorkDirRequirement` to stage input files into" -" the output directory. In this example, we use a JavaScript expression to" -" extract the base name of the input file from its leading directory path." +"Normally, input files are located in a read-only directory separate from the " +"output directory. This causes problems if the underlying tool expects to " +"write its output files alongside the input file in the same directory. You " +"use `InitialWorkDirRequirement` to stage input files into the output " +"directory. In this example, we use a JavaScript expression to extract the " +"base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: a03372581fa44f9b8e3e088a4099cdd9 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: 36e082be73464be0ad5d0b681cc510da msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: 4464455b51ad4873ac13c4a63ee5fb54 msgid "" -"In this section you will find ways to troubleshoot when you have problems" -" executing CWL. We focus on `cwltool` here but some of these techniques " -"may apply to other CWL Runners." +"In this section you will find ways to troubleshoot when you have problems " +"executing CWL. We focus on `cwltool` here but some of these techniques may " +"apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: ed7ff0753d1743a995f4cfedd6e5dcc2 msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: 4c2dd10dd66446058477a52fb8d2c602 msgid "" "You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor " -"output files, but created while your workflow is running). By default, " -"these files are created in a temporary directory but writing them to a " -"separate directory makes accessing them easier." +"`cwltool` to cache intermediate files (files that are not input nor output " +"files, but created while your workflow is running). By default, these files " +"are created in a temporary directory but writing them to a separate " +"directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: 978b6a5fd5fa425fa9a18d9f0e8788da msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " -"World\" | rev`, which would print the message \"Hello World\" reversed, " -"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," -" where instead of executing the `rev` command it tries to execute `revv`," -" which fails." +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " +"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " +"olleH\". However, the second step, `step_b`, **has a typo**, where instead " +"of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: 000c0d6ae8bf414d9293b9f13fd2e448 msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: 7e91b8811be14f8e80df39ac4c5bd316 msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " -"value (`cwltool` will create the directory for you if it does not exist " -"already):" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " +"(`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: d42799cc5bd4484bb6beb309a61e103e msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. " -"You can inspect the intermediate files created:" +"successfully and its output has been cached in your `cachedir` location. You " +"can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: 48bb0f6666ac48648c7d969608b3bd48 msgid "" -"Each workflow step has received a unique ID (the long value that looks " -"like a hash). The `${HASH}.status` files display the status of each step " -"executed by the workflow. And the `step_a` output file `stdout.txt` is " -"visible in the output of the command above." +"Each workflow step has received a unique ID (the long value that looks like " +"a hash). The `${HASH}.status` files display the status of each step executed " +"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " +"output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: f8876044db184cbaaca56579d0c773df msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" -" in the `step_b`). After fixing the typo, when you execute `cwltool` with" -" the same arguments as the previous time, note that now `cwltool` output " -"contains information about pre-cached outputs for `step_a`, and about a " -"new cache entry for the output of `step_b`. Also note that the status of " -"`step_b` is now of success." +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " +"the `step_b`). After fixing the typo, when you execute `cwltool` with the " +"same arguments as the previous time, note that now `cwltool` output contains " +"information about pre-cached outputs for `step_a`, and about a new cache " +"entry for the output of `step_b`. Also note that the status of `step_b` is " +"now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: a5a3d408dbe34cfda4dd0b2abe67e7d7 msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had" -" been cached, and there was no change in its execution or output. " +"In this example the workflow step `step_a` was not re-evaluated as it had " +"been cached, and there was no change in its execution or output. " "Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for" -" troubleshooting your CWL documents and also as a way to prevent " -"`cwltool` to re-evaluate steps unnecessarily." +"`step_b` after we fixed the executable name. This technique is useful for " +"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " +"re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: 4c240a18c4e6441189489011242c1efd msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: e37e76ef376a4ee695e600998906ec1c msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: 51a307b0ba7c4c1d89309ba8d2250471 msgid "" -"[Docker][docker] containers simplify software installation by providing a" -" complete known-good runtime for software and its dependencies. However," -" containers are also purposefully isolated from the host system, so in " -"order to run a tool inside a Docker container there is additional work to" -" ensure that input files are available inside the container and output " -"files can be recovered from the container. A CWL runner can perform this" -" work automatically, allowing you to use Docker to simplify your software" -" management while avoiding the complexity of invoking and managing Docker" -" containers." +"[Docker][docker] containers simplify software installation by providing a " +"complete known-good runtime for software and its dependencies. However, " +"containers are also purposefully isolated from the host system, so in order " +"to run a tool inside a Docker container there is additional work to ensure " +"that input files are available inside the container and output files can be " +"recovered from the container. A CWL runner can perform this work " +"automatically, allowing you to use Docker to simplify your software " +"management while avoiding the complexity of invoking and managing Docker " +"containers." msgstr "" #: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: 13cc38d72d34468fa4eb6d91f23ff105 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the " -"container." +"input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: 42a48398d3ef4b03bd7395120f2cfb42 msgid "" -"This example runs a simple Node.js script inside a Docker container which" -" will then print \"Hello World\" to the standard output." +"This example runs a simple Node.js script inside a Docker container which " +"will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: d59387b433bc4ecfaf7e72026624db02 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: d963418ccc0b4803bbc758d718ccb5aa msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: a224d1510c9e46aab23d8bdc03c349dd msgid "" "Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that " -"is really new is the `dockerRequirement` section." +"Most of this has been explained in previous sections, the only part that is " +"really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: 0a82f8a45b0546aaac4c976dcc98014a msgid "" -"`baseCommand: node` tells CWL that we will be running this command using " -"the Node Js runtime that is meant for Javascript files. We then need to " -"specify some `hints` for how to find the container we want. In this case" -" we list just our requirements for the docker container in " -"`DockerRequirements`. The `dockerPull:` parameter takes the same value " -"that you would pass to a `docker pull` command. That is, the name of the " -"container image (you can even specify the tag, which is good idea for " -"best practices when using containers for reproducible research). In this " -"case we have used a container called `node:slim`." +"`baseCommand: node` tells CWL that we will be running this command using the " +"Node Js runtime that is meant for Javascript files. We then need to specify " +"some `hints` for how to find the container we want. In this case we list " +"just our requirements for the docker container in `DockerRequirements`. The " +"`dockerPull:` parameter takes the same value that you would pass to a " +"`docker pull` command. That is, the name of the container image (you can " +"even specify the tag, which is good idea for best practices when using " +"containers for reproducible research). In this case we have used a container " +"called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: bc418a2a535e49359c4cd44b373bbe02 msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` " -"providing the tool description and the input object on the command line:" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " +"the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: a799fba2322944cea00e413c08066536 msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: 35379c6b972940bd8451f10b74dd793e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" #: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: 2d5265525ad544a0b64ad2cf07aacc26 msgid "" -"In this example, the path to the script `hello.js` is " -"`/home/me/cwl/user_guide/hello.js` outside the container but " -"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " -"reflected in the invocation of the `node` command." +"In this example, the path to the script `hello.js` is `/home/me/cwl/" +"user_guide/hello.js` outside the container but `/var/lib/cwl/" +"job369354770_examples/hello.js` inside the container, as reflected in the " +"invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: e2521b89596d42f8a87a3207fd6c32f2 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: 3676f23b63e142cb8e5715ae07216a47 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " @@ -3141,239 +3543,265 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: 00725aed13a440ca8b3c4f9155fbee99 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: 2e38a4f9072b4ad9bbb74f943d22084d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier " -"examples." +"command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: 2b9f4035ea864b6db50c861a1819289d msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: 28e9064780e7418a8e02a22f92e34404 msgid "" -"A command-line tool or expression tool can also be written directly in " -"the same CWL document as the workflow. For example, we can rewrite the " -"`echo-uppercase.cwl` workflow as a single file:" +"A command-line tool or expression tool can also be written directly in the " +"same CWL document as the workflow. For example, we can rewrite the `echo-" +"uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: 66ce14a10d2d4dc497d3ed71e11ed8b8 msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: 8dc00528c3d2426c8a3492a8191f1d81 msgid "" -"Having separate files helps with modularity and code organization. But it" -" can be helpful writing everything in a single file for development. " -"There are other ways to combine multiple files into a single file (e.g. " -"`cwltool --pack`) discussed further in other sections of this user guide." +"Having separate files helps with modularity and code organization. But it " +"can be helpful writing everything in a single file for development. There " +"are other ways to combine multiple files into a single file (e.g. `cwltool --" +"pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: f9ef5e258f7c4971a8543d1dfed711a8 msgid "" "For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this" -" user guide in more detail." +"`SubworkflowFeatureRequirement`. It is covered in another section of this " +"user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: 324bc51071d743ea80124c23880ddc0a msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: d8c13e01976b43a1af34c11a7bc36897 msgid "" -"This workflow extracts a java source file from a tar file and then " -"compiles it." +"This workflow extracts a java source file from a tar file and then compiles " +"it." msgstr "" #: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: 43910a8ab4484e529a17df418b1aedbb msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 #: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: 7ad12d67e815400c94080804b9285629 msgid "" -"[![Visualization of 1st-" -"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" +"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" "workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" +"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" +"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: 457d5a31c79143acae2683d95d27f7a3 msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a" -" run:" +"Use a YAML or a JSON object in a separate file to describe the input of a " +"run:" msgstr "" #: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: a2a73901bf634547900d08b9a1ac8889 msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: f347d80e62384b14acf6423675e5359a msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: 2a845a4f3f98428fb82f3ca7ce038a6e msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: e2007c74d5f449a882809d6b91c010bf msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a " -"workflow." +"document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: 7f5e53ee7cf94be2bff45ef64db28a24 msgid "" -"The `inputs` section describes the inputs of the workflow. This is a " -"list of input parameters where each parameter consists of an identifier " -"and a data type. These parameters can be used as sources for input to " -"specific workflows steps." +"The `inputs` section describes the inputs of the workflow. This is a list " +"of input parameters where each parameter consists of an identifier and a " +"data type. These parameters can be used as sources for input to specific " +"workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: a0d076b7b8b048478580c99ef0c8429f msgid "" -"The `outputs` section describes the outputs of the workflow. This is a " -"list of output parameters where each parameter consists of an identifier " -"and a data type. The `outputSource` connects the output parameter " -"`classfile` of the `compile` step to the workflow output parameter " -"`compiled_class`." +"The `outputs` section describes the outputs of the workflow. This is a list " +"of output parameters where each parameter consists of an identifier and a " +"data type. The `outputSource` connects the output parameter `classfile` of " +"the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: 7fd926c18ad548e98845e9b5134dd6f2 msgid "" "The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second " -"step compiles the file from the first step using the java compiler. " -"Workflow steps are not necessarily run in the order they are listed, " -"instead the order is determined by the dependencies between steps (using " -"`source`). In addition, workflow steps which do not depend on one " -"another may run in parallel." +"example, the first step extracts a file from a tar file, and the second step " +"compiles the file from the first step using the java compiler. Workflow " +"steps are not necessarily run in the order they are listed, instead the " +"order is determined by the dependencies between steps (using `source`). In " +"addition, workflow steps which do not depend on one another may run in " +"parallel." msgstr "" #: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: 789fbd47f8564cceb430ef3c0bc90e9b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input" -" parameters, `tarfile` and `extractfile` and one output parameter " +"[Parameter References](parameter-references.md)). This tool has two input " +"parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: 45c4d0492d6143ca9cebe81e9b2cf3ae msgid "" -"The ``in`` section of the workflow step connects these two input " -"parameters to the inputs of the workflow, `tarball` and " -"`name_of_file_to_extract` using `source`. This means that when the " -"workflow step is executed, the values assigned to `tarball` and " -"`name_of_file_to_extract` will be used for the parameters `tarfile` and " -"`extractfile` in order to run the tool." +"The ``in`` section of the workflow step connects these two input parameters " +"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " +"`source`. This means that when the workflow step is executed, the values " +"assigned to `tarball` and `name_of_file_to_extract` will be used for the " +"parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: 73bd3da2af8545928d5ea71d0f7454f6 msgid "" -"The `out` section of the workflow step lists the output parameters that " -"are expected from the tool." +"The `out` section of the workflow step lists the output parameters that are " +"expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: 15ce3d2700424f0fbb280d602ccebcf6 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described " -"previously in [Additional Arguments and Parameters](additional-arguments-" -"and-parameters.md)). The output of this step `classfile` is connected to " -"the `outputs` section for the Workflow, described above." +"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " +"in [Additional Arguments and Parameters](additional-arguments-and-parameters." +"md)). The output of this step `classfile` is connected to the `outputs` " +"section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: af4268f19202436eb0a7e8c6bed5e386 msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: 94a4eadca6b949d79de2990a0150eee8 msgid "" -"Workflows are ways to combine multiple tools to perform a larger " -"operations. We can also think of a workflow as being a tool itself; a CWL" -" workflow can be used as a step in another CWL workflow, if the workflow " -"engine supports the `SubworkflowFeatureRequirement`:" +"Workflows are ways to combine multiple tools to perform a larger operations. " +"We can also think of a workflow as being a tool itself; a CWL workflow can " +"be used as a step in another CWL workflow, if the workflow engine supports " +"the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: 09c1619e8cbd4febbb637f7e99ad5890 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" #: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: 677ea7a27eb64568ab3689142d6efe70 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: 097e6d47f9394e62b80110700492783a msgid "" -"This two-step workflow starts with the `create-tar` step which is " -"connected to the `compile` step in orange; `compile` is another workflow," -" diagrammed on the right. In purple we see the fixed string " -"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +"This two-step workflow starts with the `create-tar` step which is connected " +"to the `compile` step in orange; `compile` is another workflow, diagrammed " +"on the right. In purple we see the fixed string `\"Hello.java\"` being " +"supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: e93affce8c104bf6977182047c1f1077 msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows.cwl" +"\"> \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: 06c9e04ba890473b851240a0fa9c3b12 msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " -"its CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " -"mapped to become the step's input/outputs." +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " +"CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " +"to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: 0380dc1fe3aa48e4b62283b7b2a611d8 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and " -"`*.java` filename. This is generally best-practice, as it means it can be" -" reused in multiple parent workflows, or even in multiple steps within " -"the same workflow." +"running it we had to provide a job file to denote the tar file and `*.java` " +"filename. This is generally best-practice, as it means it can be reused in " +"multiple parent workflows, or even in multiple steps within the same " +"workflow." msgstr "" #: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: 49b251f7a313492ea60504b00109e526 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar" -" file at `tarball`, which we will prepare in the `create-tar` step. At " -"this point it is probably a good idea to refactor `1st-workflow.cwl` to " -"have more specific input/output names, as those also appear in its usage " -"as a tool." +"`name_of_file_to_extract` input, however our workflow also requires a tar " +"file at `tarball`, which we will prepare in the `create-tar` step. At this " +"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " +"specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: 7ee55702d7dd4679a24ff052f6f0cbeb msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3382,186 +3810,212 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: 85d7e2e270874aa6b9f477cec0f48154 msgid "" -"In this case our step can assume `Hello.java` rather than be " -"parameterized, so we can use hardcoded values `hello.tar` and " -"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +"In this case our step can assume `Hello.java` rather than be parameterized, " +"so we can use hardcoded values `hello.tar` and `Hello.java` in a " +"`baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: 570e94513c984c09ad6aa255f534216d msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This " -"is generally not best practice, as the tool then can't be reused. The " -"reason for doing it in this case is because the command line is hard-" -"coded with filenames that only make sense within this workflow." +"separate file, but rather embedded it within the CWL Workflow file? This is " +"generally not best practice, as the tool then can't be reused. The reason " +"for doing it in this case is because the command line is hard-coded with " +"filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: a107258662fb4bd4a9a3d8754e34d1e9 msgid "" -"In this example we had to prepare a tar file outside, but only because " -"our inner workflow was designed to take that as an input. A better " -"refactoring of the inner workflow would be to take a list of Java files " -"to compile, which would simplify its usage as a tool step in other " -"workflows." +"In this example we had to prepare a tar file outside, but only because our " +"inner workflow was designed to take that as an input. A better refactoring " +"of the inner workflow would be to take a list of Java files to compile, " +"which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: fc1a6502d831458ab8371a575cea47e2 msgid "" "Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL" -" Tool description, care must be taken to improve its usability in " -"multiple workflows." +"functional and reusable workflow units - but just like for creating a CWL " +"Tool description, care must be taken to improve its usability in multiple " +"workflows." msgstr "" #: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: 2d10806bf1ce4e26b92adda61efc0862 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: 046c5e134de94b629cc22d416f3c9182 msgid "" "Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish " -"to run a tool or workflow multiple times over a list of inputs. The " -"workflow then takes the input(s) as an array and will run the specified " -"step(s) on each element of the array as if it were a single input. This " -"allows you to run the same workflow on multiple inputs without having to " -"generate many different commands or input yaml files." +"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " +"run a tool or workflow multiple times over a list of inputs. The workflow " +"then takes the input(s) as an array and will run the specified step(s) on " +"each element of the array as if it were a single input. This allows you to " +"run the same workflow on multiple inputs without having to generate many " +"different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: 52fa22d3277940049fbb589a3ea73433 msgid "" -"The most common reason a new user might want to use scatter is to perform" -" the same analysis on different samples. Let's start with a simple " -"workflow that calls our first example (`hello_world.cwl`) and takes an " -"array of strings as input to the workflow:" +"The most common reason a new user might want to use scatter is to perform " +"the same analysis on different samples. Let's start with a simple workflow " +"that calls our first example (`hello_world.cwl`) and takes an array of " +"strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: 6043beb96c2c49648011ec556aa9e986 msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: 5ac4310515124e2986724425bed5651f msgid "" -"Aside from the `requirements` section including " -"`ScatterFeatureRequirement`, what is going on here?" +"Aside from the `requirements` section including `ScatterFeatureRequirement`, " +"what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: 7958e91d5c2f4046aa9d2070a900f9ae msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" #: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: 2db234d776fe4fd38bab07245dcb783a msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This " -"field tells the runner that we'd like to scatter over this input for this" -" particular step. Note that the input name listed after scatter is the " -"one of the step's input, not a workflow level input." +"Here we've added a new field to the step `echo` called `scatter`. This field " +"tells the runner that we'd like to scatter over this input for this " +"particular step. Note that the input name listed after scatter is the one of " +"the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: 7cfb17230e284ee7b6e2a00efe8eeb74 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if " -"you expect that the final output of your workflow will now have multiple " -"outputs to collect, be sure to update that to an array type as well!" +"collect any outputs, we still use `outputs: []` in our workflow, but if you " +"expect that the final output of your workflow will now have multiple outputs " +"to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: 4311ac98544e4fb0b2f4b24985710a01 msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: 780f9c72e6c34c39918642c7e2477355 msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: cc4a7316db644b438cbaa181ad9ef2d3 msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" -" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " +"calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: dfc461a03fe8487794837904febb8b63 msgid "" -"You can see that the workflow calls echo multiple times on each element " -"of our `message_array`. Ok, so how about if we want to scatter over two " -"steps in a workflow?" +"You can see that the workflow calls echo multiple times on each element of " +"our `message_array`. Ok, so how about if we want to scatter over two steps " +"in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: 1e83485b00b64dfaba897bd8d772e0f0 msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding " -"the following lines instead of `outputs: []`" +"Let's perform a simple echo like above, but capturing `stdout` by adding the " +"following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: d0321d6805ec4d3abf3877d02a0a417f msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: d7d77e807b3048c7bdf89558f76804cb msgid "" -"And add a second step that uses `wc` to count the characters in each " -"file. See the tool below:" +"And add a second step that uses `wc` to count the characters in each file. " +"See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: 8d9b8be147fc4a71922dde858842e543 msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: 34b7705416a745a6a42e6d402c0757ed msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under " -"each step:" +"Now, how do we incorporate scatter? Remember the scatter field is under each " +"step:" msgstr "" #: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: 257adcee9da64d5c987f3b64efd20ab0 msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 -msgid "" -"Here we have placed the scatter field under each step. This is fine for " -"this example since it runs quickly, but if you're running many samples " -"for a more complex workflow, you may wish to consider an alternative. " -"Here we are running scatter on each step independently, but since the " -"second step is not dependent on the first step completing all languages, " -"we aren't using the scatter functionality efficiently. The second step " -"expects an array as input from the first step, so it will wait until " -"everything in step one is finished before doing anything. Pretend that " -"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " -"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " -"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " -"could finish in 4 minutes, it will actually finish in 8 minutes because " -"the first step must wait on `echo Hallo welt!`. You can see how this " -"might not scale well." +#: fa6ed5d0c14f42f4aa3c5144648db22c +msgid "" +"Here we have placed the scatter field under each step. This is fine for this " +"example since it runs quickly, but if you're running many samples for a more " +"complex workflow, you may wish to consider an alternative. Here we are " +"running scatter on each step independently, but since the second step is not " +"dependent on the first step completing all languages, we aren't using the " +"scatter functionality efficiently. The second step expects an array as input " +"from the first step, so it will wait until everything in step one is " +"finished before doing anything. Pretend that `echo Hello World!` takes 1 " +"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " +"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " +"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " +"actually finish in 8 minutes because the first step must wait on `echo Hallo " +"welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: 333e8ce458d54de394526769f96d12d2 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can" -" make an entire workflow a single step in another workflow! Convert our " -"two-step workflow to a single step subworkflow:" +"samples? Remember from [Nested Workflows](#nested-workflows), that we can " +"make an entire workflow a single step in another workflow! Convert our two-" +"step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: b819e8a5df6e4fa495924095709669ef msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: f1955468a1364d44a930db77c9c4b495 msgid "" -"Now the scatter acts on a single step, but that step consists of two " -"steps so each step is performed in parallel." +"Now the scatter acts on a single step, but that step consists of two steps " +"so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: 8c3b9b645a204d02b2c73a205e8ec296 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: 4d88b9c186cd4502adbf752e8a70b6ce msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " @@ -3569,252 +4023,357 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: 9927673564024ba5833b5ac271737857 msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: 84f4ed7ce2004742b8db9087104a469a msgid "" -"The first thing you'll notice is that this workflow is only compatible " -"for version 1.2 or greater of the CWL standards." +"The first thing you'll notice is that this workflow is only compatible for " +"version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: 2b5f9757adca4490a149c7f45e14fcb5 msgid "" "The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when`" -" is where the condition validation takes place. In this case only when " -"`in1` from the workflow contains a value `< 1` this step will be " -"executed." +"will execute foo.cwl when the conditions are met. The new property `when` is " +"where the condition validation takes place. In this case only when `in1` " +"from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: 0418de720813442f81ecff293c9448b5 msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" -" will pass the first conditional step and will therefore be executed and " -"is shown in the log by `INFO [step step1] start` whereas the second step " -"is skipped as indicated by `INFO [step step2] will be skipped`." +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " +"will pass the first conditional step and will therefore be executed and is " +"shown in the log by `INFO [step step1] start` whereas the second step is " +"skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: 524eec63be8248ae982939c975ef50a2 msgid "" -"When a value of 3 is given the first conditional step will not be " -"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +"When a value of 3 is given the first conditional step will not be executed " +"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: 5e99f9912cc549a7890e2934425eb943 msgid "" -"If no conditions are met for example when using `--val 2` the workflow " -"will raise a permanentFail." +"If no conditions are met for example when using `--val 2` the workflow will " +"raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: b0121ee087d6424fbb0ea5957a7b0b8c msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: 49e9f6b3a06840289decf3f557860f87 msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers " -"and humans. This guide introduces the features of YAML that are relevant " -"when writing CWL descriptions and input parameter files." +"[YAML][yaml] is a file format designed to be readable by both computers and " +"humans. This guide introduces the features of YAML that are relevant when " +"writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: ed9eebec0b3d4b72ba65507d37757a37 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: bf9b255a24a84f3ba989a223492b8f41 msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: e79fa0b7f8b14810a3a20908ef92bc55 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: 290e2035f903417cbecb5dc5f09d6ebe msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: d420730151534f1a89076588a3358f09 msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: a6b5378bbe1e4bee9e37a765bddf75f7 msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: 6e4d9465dc2b454d96b02d7ad1817795 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: a649d4af5f434dac9395e013ec4836bb msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: 446190a298834b73bda068286e8490cf msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the " -"`:` is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have " -"special meaning in the CWL specification and underscored key names " -"otherwise. For example:" +"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " +"is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have special " +"meaning in the CWL specification and underscored key names otherwise. For " +"example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#: 2f35c012ff174721bffe66a3f58a804f msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, " -"`age_years`, and `home` - with their four respective values. Values can " -"be character strings, numeric (integer, floating point, or scientific " -"representation), Boolean (`true` or `false`), or more complex nested " -"types (see below)." +"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " +"and `home` - with their four respective values. Values can be character " +"strings, numeric (integer, floating point, or scientific representation), " +"Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#: 43127c98c9d94aedac61cee67929c1a6 msgid "" -"Values may be wrapped in quotation marks, but be aware that this may " -"change the way that they are interpreted i.e. `\"1234\"` will be treated " -"as a character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a" -" command: in CWL all parts of `baseCommand` must be strings so, if you " -"want to specify a fixed numeric value to a command, make sure that you " -"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +"Values may be wrapped in quotation marks, but be aware that this may change " +"the way that they are interpreted i.e. `\"1234\"` will be treated as a " +"character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a " +"command: in CWL all parts of `baseCommand` must be strings so, if you want " +"to specify a fixed numeric value to a command, make sure that you wrap that " +"numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: dc4fe561203c4c38a9caea5bd6eff2cd msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: f924e4896db2424d99ce8c9da14c599a msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program " -"interpreting the YAML. For example:" +"characters to the right of ` #` will be ignored by the program interpreting " +"the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: bf7646f5f925485c842a6d34140e40b8 msgid "" -"If there is anything on the line before the comment, be sure to add at " -"least one space before the `#`!" +"If there is anything on the line before the comment, be sure to add at least " +"one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: c483e61dec8949fa96bb893d422888a0 msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: 85fcb523d0e34a499eae04d304887f7b msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, " -"these hierarchical structures are described in YAML by providing " -"additional key-value pairs as the value of any key. These pairs " -"(sometimes referred to as \"children\") are written on new lines under " -"the key to which they belong (the \"parent\"), and should be indented " -"with two spaces (⇥tab characters are not allowed). For example:" +"construct more complex, nested representations. Referred to as _maps_, these " +"hierarchical structures are described in YAML by providing additional key-" +"value pairs as the value of any key. These pairs (sometimes referred to as " +"\"children\") are written on new lines under the key to which they belong " +"(the \"parent\"), and should be indented with two spaces (⇥tab characters " +"are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: 83d47c8736a34f3cbf09e3997845e4f4 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and " -"`inputBinding`, while one of these children, `inputBinding`, contains a " -"further two key-value pairs (`position` and `prefix`). See the " -"[Arrays](#arrays) section below for more information about providing " -"multiple values/key-value pairs for a single key. For comparison with the" -" example YAML above, here is a graphical representation of the `inputs` " -"object it describes." +"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " +"while one of these children, `inputBinding`, contains a further two key-" +"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " +"below for more information about providing multiple values/key-value pairs " +"for a single key. For comparison with the example YAML above, here is a " +"graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: c698fb3d37bc403e9aeb679b8fc0e15e msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ae8af2f0eeda4aec97201211dfa965c7 msgid "" "In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) " -"section above, more than one key-value pair can be mapped to a single " -"key. However, it is also possible to define multiple values for a key " -"without having to provide a unique key for each value. We can achieve " -"this with an _array_, where each value is defined on its own line and " -"preceded by `-`. For example:" +"objects for a single key. As we've already seen in the [Maps](#maps) section " +"above, more than one key-value pair can be mapped to a single key. However, " +"it is also possible to define multiple values for a key without having to " +"provide a unique key for each value. We can achieve this with an _array_, " +"where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: 2ee87aa465cd41fda16a61e242f8c9d0 msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: 0a6fd4469ff24b61b3ad001b09eead18 msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: b96ba19bce9341d39c46054e1f10fe8f msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " -"arrays can also be defined in YAML using the native JSON syntax. For " -"example:" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " +"can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: 903f30af3d0c45cfb61063936a8097a7 msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: ede8db7c0a58432e8a1c416e937a06d2 msgid "" -"Native JSON can be useful in indicating where a field is intentionally " -"left empty (such as `[]` for an empty array), as well as where it makes " -"more sense for the values to be located on the same line (For example, " -"when providing option flags and their values in a shell command). " -"However, as the second example above shows, it can severely affect the " -"readability of a YAML file, and should be used sparingly." +"Native JSON can be useful in indicating where a field is intentionally left " +"empty (such as `[]` for an empty array), as well as where it makes more " +"sense for the values to be located on the same line (For example, when " +"providing option flags and their values in a shell command). However, as the " +"second example above shows, it can severely affect the readability of a YAML " +"file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: c8b53615476a4a1fbef2420d93bac94e msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: ea03cb5525cc491f9feb5c4780b38fee msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" -" us while we wrote this guide, though it also covers features that are " -"not valid in CWL." +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " +"while we wrote this guide, though it also covers features that are not valid " +"in CWL." msgstr "" #: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: 92fd3a5e31714eab859dd630af2e78cf msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: de660ecdb5b44c97a0e519d00b232497 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to " -"the list." +"this page` link in the menu if you would like to add another tutorial to the " +"list." msgstr "" #: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: 5afc1e1288e74ed0985e61e5164479c7 msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: 862dc7ac81e54b1fb3d4c2f961b8810e msgid "" -"[Introduction to Workflows with Common Workflow Language: For " -"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" -"tutorial/)" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: e2c94c0e1c7048d38cd7aa2c465a859d msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: b63253780f51467a95207d820d13ac39 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: 6d06ca7ed5df4560aaed286f4fe33928 msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: 5448df4a6a8f431d80e269bcd480e19e msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" +#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee +msgid "" +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the `Creative Commons " +"Attribution license `_. The following is a human-readable " +"summary of (and not a substitute for) the `full legal text of the CC BY 4.0 " +"license `_." +msgstr "" +"Todo o material instrucional do projeto Common Workflow Language e " +"alterações na estrutura também são disponibilizados sob a `licença Creative " +"Commons Attribution `_. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o `texto legal completo da licença CC " +"BY 4.0 `_." + +#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 +msgid "to **Share**—copy and redistribute the material in any medium or format" +msgstr "" +"**Compartilhar**—copiar e redistribuir o material em qualquer suporte ou " +"formato" + +#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 +msgid "to **Adapt**—remix, transform, and build upon the material" +msgstr "**Adaptar**—remixar, transformar, e criar a partir do material" + +#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 +msgid "" +"**Attribution**—You must give appropriate credit (mentioning that your work " +"is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a `link to the license `_, and indicate if changes " +"were made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." +msgstr "" +"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " +"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um `link para a licença `_, e " +"indicar se foram feitas alterações. Você pode fazê-lo de qualquer forma " +"razoável, mas não de uma forma que sugira que o licenciante o apoia ou " +"aprova o seu uso." + +#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 +msgid "" +"**No additional restrictions**—You may not apply legal terms or " +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" +msgstr "" +"**Sem restrições adicionais**—Você não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " +"algo que a licença permita. Com o entendimento de que:" + +#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the " +"`OSI`_-approved `Apache 2.0 license `_." +msgstr "" +"Salvo indicação em contrário, os programas de exemplo e outro software " +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " +"`licença Apache 2.0 `_ aprovada pela `OSI`_." + +#: ../../LICENSE.rst:50 9c4d58a1129a4d4eb4db1bfabbeddb6e +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." +msgstr "" From 761ad42bf4a9d7747a9170a77e764711bd1f1494 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 16:14:13 +0100 Subject: [PATCH 48/49] remove obsolete .rst translations --- Makefile | 2 +- locales/es/LC_MESSAGES/user_guide.po | 1935 +++++++++----------------- locales/pt/LC_MESSAGES/user_guide.po | 1930 +++++++++---------------- 3 files changed, 1323 insertions(+), 2544 deletions(-) diff --git a/Makefile b/Makefile index 83ba9e13..c549b172 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS = "" # was "-W" (turn warnings into errors) +#SPHINXOPTS = # was "-W" (turn warnings into errors) SPHINXBUILD = sphinx-build SOURCEDIR = src BUILDDIR = _build diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index b1952aae..ca09ccab 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -8,30 +8,27 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"POT-Creation-Date: 2023-01-27 16:02+0100\n" "PO-Revision-Date: 2023-01-27 14:27+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Spanish \n" "Language: es\n" +"Language-Team: Spanish \n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n != 1;\n" -"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 ../../LICENSE.rst:2 -#: dcdc2e8da0ec4d9e9453601fdd83bac5 +#: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 msgid "Licenses" msgstr "Licencias" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 ../../LICENSE.rst:5 -#: 3e165520ca56481b8f8d494a8d471de3 +#: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 msgid "Instructional Material" msgstr "Material didáctico" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +#: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c msgid "" "All Common Workflow Language project instructional material and changes to " "the structure are also made available under the [Creative Commons " @@ -45,29 +42,26 @@ msgstr "" "legible por humanos (y no un sustituto) del [texto legal completo de la " "licencia CC BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 ../../LICENSE.rst:12 -#: b7a7a0fb40344fe087c1cc3ec19308aa +#: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 msgid "You are free:" msgstr "Usted es libre de:" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +#: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 msgid "" "to **Share**---copy and redistribute the material in any medium or format" msgstr "" "**Compartir**---copiar y redistribuir el material en cualquier medio o " "formato" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 d66dcbf95ccc41aaa53be523487ec913 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 ../../LICENSE.rst:18 -#: 430ff4de74924bc3a3b2c7e809ea4456 +#: ../../LICENSE.md:17 ca1c299a1b834b868bcdd4ca9f244696 msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e ../../LICENSE.rst:20 -#: 8bc6672f4a33428296226112a1be6fbe +#: ../../LICENSE.md:19 6133f79f93be4991a6f5290f72d1a63d msgid "" "The licensor cannot revoke these freedoms as long as you follow the license " "terms:" @@ -75,7 +69,7 @@ msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia:" -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +#: ../../LICENSE.md:24 2d6ce81add1043629b676187f890288c msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " "work is derived from work that is Copyright © the Common Workflow Language " @@ -86,13 +80,13 @@ msgid "" msgstr "" "**Atribución**---Usted debe dar crédito de manera adecuada(mencionando que " "su trabajo se deriva de un trabajo que tiene «Copyright © The Common " -"Workflow Language Project» y, cuando sea práctico, con un enlace a " -"https://www.commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], " -"e indicar si se han realizado cambios. Puede hacerlo en cualquier forma " +"Workflow Language Project» y, cuando sea práctico, con un enlace a https://" +"www.commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e " +"indicar si se han realizado cambios. Puede hacerlo en cualquier forma " "razonable, pero no de forma tal que sugiera que usted o su uso tienen el " "apoyo de la licenciante." -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +#: ../../LICENSE.md:32 f3f22597b6f845208a0cce3b3b2c8f5d msgid "" "**No additional restrictions**---You may not apply legal terms or " "technological measures that legally restrict others from doing anything the " @@ -102,8 +96,7 @@ msgstr "" "medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " "permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 ../../LICENSE.rst:35 -#: 1798d65c10104040923c2fea2199bab2 +#: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef msgid "" "You do not have to comply with the license for elements of the material in " "the public domain or where your use is permitted by an applicable exception " @@ -113,8 +106,7 @@ msgstr "" "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 ../../LICENSE.rst:38 -#: c65198b804f8436ba783643d51bc72d9 +#: ../../LICENSE.md:39 c836a570faaf449d9716da5f75556627 msgid "" "No warranties are given. The license may not give you all of the permissions " "necessary for your intended use. For example, other rights such as " @@ -125,12 +117,11 @@ msgstr "" "publicidad, privacidad, o derechos morales pueden limitar la forma en que " "utilice el material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea ../../LICENSE.rst:44 -#: 3d7ca3f2cede4d5f998bf014bd970748 +#: ../../LICENSE.md:44 896f9966e5014e8a88b060be3063fe09 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +#: ../../LICENSE.md:46 007f8613dc234c3fa8d5d92b18af0eb1 msgid "" "Except where otherwise noted, the example programs and other software " "provided by Common Workflow Language project are made available under the " @@ -141,7 +132,7 @@ msgstr "" "disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " "la [OSI][osi]." -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +#: ../../LICENSE.md:51 227bc635a06f49dbb771fd9b62157d00 msgid "" "Unless required by applicable law or agreed to in writing, software " "distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " @@ -156,9 +147,8 @@ msgstr "" "under the License." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 271049c39d294b11b9bd94cb6be2857f -#: 61af90891e2d4542b5f45fb3ec6480af bf309fa01bed4355bf052ae4afbf9a67 +#: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd +#: d6055d3f15604ce6940770c7b561d4c5 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece of " @@ -167,36 +157,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f -#: 055f0e960450410585b59760ef3ad284 6294af2e32e04207a87399c7f0780011 +#: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 -#: 6428125fc43c43bba8518ece2f5d150f +#: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 -#: ce8fade1e88e4b03ac0d3fc71d16f844 +#: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 -#: 9e7483b53a984b689964c69afcaa7123 +#: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 -#: 8c5a89257ef248cd99cba303713e5082 +#: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 -#: 9e80d8eeefcf4a9d95fd5fe9d9fa124a +#: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 msgid "" "This example demonstrates how to change the name of an input file as part of " "a tool description. This could be useful when you are taking files produced " @@ -204,139 +188,117 @@ msgid "" "names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f -#: c2e5f62490f940aab19166403a840597 +#: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 -#: ffcffabdf25a4c398e8e53bc817ea769 +#: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 msgid "" "This example demonstrates how to change the name of an output file from the " "default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 -#: c8a6b85cfca542ccb042a0269294e5e3 +#: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 -#: 98f583e5e36941c1856d719a16e58e4a +#: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb -#: fb9cac0954474b5284793330b7424949 +#: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 msgid "" "The first method involves adding the folder containing your scripts to the " "`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 -#: cc45d609de1f423db86d58eea933e132 +#: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 -#: 27ee63895cb14321a1814f4372d3180f +#: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc msgid "" "After that, make the script executable with the command `chmod +x scriptname." "sh`" msgstr "" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 -#: f1c841980f3d4364a2158a4eb2f0d257 +#: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be -#: 6d53d38ddcf244fb997db37eae7fcf90 +#: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa msgid "" "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 -#: b6d60d66f3744ab3aea1b175ecb23d4a +#: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 -#: cf4fa3ae602841d393b4143e9f6f5e82 +#: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 msgid "" "The second method involves including an input of `type: File` in the script " "itself:" msgstr "" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 -#: 41a3c9aa55c5406f9b52af2243c79ccc +#: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 -#: 3b8eb247425a4a708f51c08cf258e30a +#: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c -#: 388a6e091a054dc48afc928f46dac7b7 +#: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their input " "binding makes use of `self`. Below is an example workaround for this, " "pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 -#: 28c59d12156e44ea833822fd3ecaf824 +#: ../../src/faq.md:165 60f009e3714c405695da069204b196ea msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 -#: 8267843ff5c940c590b10047455f2102 +#: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 msgid "" "Below is an example showing how to specify different strings to be added to " "a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c -#: 6e6f55bc915e4cceb8e360544d6b4ae5 +#: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d -#: 1bc80953bd60405082a10a7798c1413d +#: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a msgid "" "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" "Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 -#: a6cd4bf4dc314e66a951f7f1227c7bb7 +#: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 -#: 7ab2440a92aa44b09e8a324cd67ca728 +#: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 msgid "" "The input must be an array consisting of exactly one entry for each input " "link. If \"merge_nested\" is specified with a single link, the value from " "the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 -#: 152a529dfa2c42c1b6f0083589fa5aeb +#: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 -#: b278c137167d4b958c099c0509edb79c +#: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -345,61 +307,51 @@ msgid "" "destination step." msgstr "" -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd -#: f0b38723838f479d9db8eb5142d28a1e +#: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 -#: fc1e4a808e85422cbb4d128c5a1f4d0c +#: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 -#: d74964c9d19241848f4dd92a201e201f +#: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 msgid "" msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c -#: 859b8e18e05a4c3285fb20bbb44c1ed4 +#: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 -#: eb6e932924a54afd9114c629b2d0e93b +#: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 msgid "" "For command line flags that require a specific input as the argument an enum " "type can be declared in CWL. **Specifying null here is known as long form " "style. It does the same thing as the question mark on the other inputs.**" msgstr "" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd -#: 31d70b41ddf042f6aa530b7bd6daae73 +#: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 msgid "" msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 -#: 9aa3ff8c957b42c8a30f37167a8177fd +#: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c -#: 777ac7f6bde2470b981efc91feb01c81 +#: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 -#: 8647071efc0548a1807c03fe8a4ee54c +#: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 -#: 4404233183124085990c44793a6b25f6 +#: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c msgid "" "To properly set fields in a record input type, you need to pass a dictionary " "to the input to properly set the parameters. This is done by using inline " @@ -408,93 +360,76 @@ msgid "" "be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 -#: c5eecacfa07f47649f07ef9d888f4c5e +#: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 -#: 1efef04061fd48f1ab39a99508b5bc0b +#: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 -#: 57e8ace8e8d64e7a90510e1ccea69612 +#: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 -#: 138606e8d7be40bb960f278977f9107f +#: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c -#: d0f668dc78464469a9f2bfc61a90aa76 +#: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 -#: f2a49a7663e1456cac6b2eac0c46c662 +#: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a -#: eefe4adebdba4063af0cac3ab5d46442 +#: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a msgid "" "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde -#: 526f2816123a43ecbcf09c46904b4b5f +#: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 -#: 0ecf267c5f4d4557ad0d7ddef2f4b5e6 +#: ../../src/faq.md:373 857024702f624885be706c405b7a088e msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 -#: 935a253376854d12928f00c2870ed4c0 +#: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 -#: bc6c0bf679ae48e7822add7ab2cda220 +#: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 -#: a63643806a2a4eee8ebd3502fd6ce2b5 +#: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 -#: fc54964adcd648948d7baff02f47598e +#: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 -#: aabc495306a149fdb15835ae1df93c42 +#: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d -#: 2930faead8be45a6b9adbf51dcdfef6e +#: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 msgid "" "If it is not possible to change the input identifier, then you can use an " "alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 -#: f885e4716a8d4de0b25d2d3356789672 +#: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e -#: 6487ff3c19c944eb8257b2cf60d0aac7 +#: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 msgid "" "The CWL standards are built around (optional) Docker format containers. The " "reference runner and several other CWL implementations support running those " @@ -502,13 +437,11 @@ msgid "" "Singularity format container is not part of the CWL standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 -#: 4cbacce539ce4f6cb5bb8ccf1574640c +#: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 -#: 27321576de714cd5b82c67f59b2e3e6f +#: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d msgid "" "You can use the --js-console option of cwltool, or " "you can try creating a JavaScript or TypeScript project for your code, and " @@ -519,26 +452,22 @@ msgid "" "dd>" msgstr "" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e -#: 6afded7ba21247099c9bfcedf40c9171 +#: ../../src/index.md:1 1506b4e7ee014a01bfdb067489501a9e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab -#: 17c386e7cd25496784207140f9876b90 +#: ../../src/index.md:3 0ce058b5210d46a0b78eb78dbca07a9f msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 -#: 3bfd9bcf826a4400935dfad338612b12 +#: ../../src/index.md:7 3404c064950d453d8af446e8b6554cb6 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 -#: 4b38f1439da44ebb967b5b1e3df8f78a +#: ../../src/index.md:9 1e239cad669648e48694eaf91284766a msgid "" "If you find that something is missing from this guide, or if you would like " "to provide other feedback, file an Issue on the [project repository for this " @@ -546,13 +475,11 @@ msgid "" "clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f -#: a4a60a8d010448b0b8ad1e05cbc78f2b +#: ../../src/index.md:16 9dba2e06f1be4a50b1fabaaf216d02b4 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 -#: e23e00e89c81410ba8381fd81bc73b3c +#: ../../src/index.md:18 ba4074bbb69e4096a808001afaf2e0dc msgid "" "If you are a beginner user get started with the [Introduction](/introduction/" "index.md) section. For advanced users the subsections of the [Topics](/" @@ -560,8 +487,7 @@ msgid "" "CWL." msgstr "" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 -#: 7274d92e678a440eb0d3ae3109f4157a +#: ../../src/index.md:23 ad34a37bf4ec488bb825a34456f4fe8d msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -569,18 +495,15 @@ msgid "" "and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c -#: 6ad5f2d254a24ac1b3faf382d08b58aa +#: ../../src/index.md:28 2bd8eb5957ed40f4a72a6b7408044c78 msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 -#: 7208cbccb84d45d58c7d5becec74b7d3 +#: ../../src/introduction/basic-concepts.md:1 8bb0df5531474301a185f1ba375320df msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 -#: 8b9809abb49840b195a89943ba15f78a +#: ../../src/introduction/basic-concepts.md:3 653373e1f11e4f81ad561378854a71fc msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are expected " @@ -591,21 +514,18 @@ msgid "" "this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 -#: 9a934bf0848b438aaef7c4f00e0f2901 +#: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf -#: 5a299600dc304fd886b7153de1a706f7 +#: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered in " "this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 -#: 55f7696f07d64277ad1b39d283175b37 +#: ../../src/introduction/basic-concepts.md:25 74e92eb0a4e64098b5aaf08d043e0641 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -615,20 +535,17 @@ msgid "" "and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d -#: b854ca0af98347d2b66e74754eb92a50 +#: ../../src/introduction/basic-concepts.md:33 baa40b445f3c409b9a3e10a85fa38bfd msgid "" "The model used for the specification version is called Semantic Versioning. " "See the end of this section to [learn more](#learn-more) about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d -#: d9785269c51e4902bf3a70e917d33238 +#: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 -#: b57a31b8d26545d1823fcd1fa2c83316 +#: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a msgid "" "An implementation of the CWL specification is any software written following " "what is defined in a version of the specification document. However, " @@ -636,26 +553,24 @@ msgid "" "implementations are licensed under both Open Source and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 -#: 4e264b1a40bd4935abb5bdeb75fa5c64 +#: ../../src/introduction/basic-concepts.md:44 b1c864d6775048cab01eb3de641f6475 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud " "and high performance computing environments where tasks are scheduled in " "parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf -#: 791b02bb1ee6459d8d8332fc2dee353c +#: ../../src/introduction/basic-concepts.md:51 a05d24121e534d65947eb26e4dada5b7 msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 17300bbe695044e7b8917d23bd0aa597 +#: ace0388fd04845e79d31ec99a48a8a3f msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 526614f195614818a614fc9a576e7cb5 +#: 70ecd37237e14ae19539f2bf692882ed msgid "" "A process is a computing unit that takes inputs and produces outputs. The " "behavior of a process can be affected by the inputs, requirements, and " @@ -664,39 +579,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f 7b47991653054f2d9f49a91720754abf +#: 38121b4b00324bebb6499184b3dcb5c1 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b aa8838c0ee0a4b4285cb1b5dc6eb5d31 +#: e0c278f52e824673ac708885d985b7d2 msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 457c73a37cb143d98005ebf6e67f5bf1 +#: 6b4d0f0651cc46f5abf195b281967913 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f c28057f3b7814f8395dbc3ad54d5f6f9 +#: 88bdc9e046e4487cb0eee3f1d4819e57 msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 83afed0785cd4b0bb86863c2841ce982 +#: 12eed3ef7d444585b150bbdab0665bc8 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a f332864bcc1e49d582a82f3d721ff3cf +#: dfc85226313d46f9868dc4de53546a69 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 3005c6d669de412ab7f8e30d00752a20 +#: f636b10c47734e589291de95443d8115 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be used " "to simplify workflows and command-line tools, moving common parts of a " @@ -705,7 +620,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef 2e4041cb402e4054a53ea5890b938ac1 +#: bb51025d04444dd5b16000d5d6a3f41a msgid "" "Operation is an abstract process that also takes inputs, produces outputs, " "and can be used in a workflow. But it is a special operation not so commonly " @@ -714,7 +629,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 972f9a1e64394a63be3258d3af0b1d79 +#: 93dbaa0aa2c6493ab22a937c6861fac4 msgid "" "The workflow is a process that contains steps. Steps can be other workflows " "(nested workflows), command-line tools, or expression tools. The inputs of a " @@ -723,7 +638,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 a572f0789084402fb2d216ac845bbfdb +#: fcde5ef65ebf45a3b4b67eec993a1729 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through *requirements*. " @@ -731,23 +646,23 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 c7c5c9a1e98e47c0a5a6dfa69e96f921 +#: c8ff34ff5d3b4a508e8c291196d08067 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 357d42768e794286bf5463ca5850a7ed +#: fe25f15fc11c49ab827b884d081c3df0 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 61966aab989744c1b9b93f7751f35ebc +#: 2b93b6219142431ca748a404a56ced5d msgid "" "`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee e14a2082d2c44f3690a07d3cee5b13d1 +#: 0094b13b26014ba3be61769b422802f5 msgid "" "Some CWL runners may provide requirements that are not in the specification. " "For example, GPU requirements are supported in `cwltool` through the " @@ -757,7 +672,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e c128a76992e04d20bcc3edae8b6c0bc0 +#: 576a0778d3dd44f68cb241346f441660 msgid "" "Hints are similar to requirements, but while requirements list features that " "are required, hints list optional features. Requirements are explained in " @@ -765,12 +680,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 42953a3d591c48c6b4e80e9ea4b97bb3 +#: 7d98949fe97744158fad81f41d780de9 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 e3762a763ba24571a9627efafe172441 +#: fc142b791aa1434aa75b0782248de988 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -783,7 +698,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a be8e01a012ed45d6b7e4e6aab1afcc32 +#: c3fc91ae3bae4e3db60e8271e95135a2 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\", " @@ -792,7 +707,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee cf31aca4294d486cb0e25c6436996d17 +#: 8f097ae5ff6a4be0b7428345362dc55e msgid "" "The benefit of explicitness and isolation are flexibility, portability, and " "scalability; tools and workflows described with CWL can transparently " @@ -801,77 +716,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 cc7adbdc66df4aeaad1429f7268c90c0 +#: 60c56fa6a67346d6966f0d841213e11b msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 -#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf -#: 71beb059c9e54a9ab5430f0dc44e07ea 84679c5b03a3469294de849d9abe0a82 -#: fd690fdd46344e0e8d9fc546f6d4013b +#: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 +#: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de 89ddaddb64f64b0c86c7e89da0edfaae +#: 3fcbf810c86f4cf7b8499de88147aa95 msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 e920a824207746ffae63242d33137ac7 +#: e242228b6b3d440cbca8418050220267 msgid "" "The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 51d619152aa44651889ff2006c8f5800 +#: 6e01963a01cb49e39692455256679bfc msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 88f3f5dd8aa6401793b89e8de3b8c7a7 +#: ed81ea2234b041c79449dcd20f886cb6 msgid "" "The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 f1f9ee90d07c4381a8bb0851bdac231e +#: e8e3996f6a894b4f9cc266b46cb8d756 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b e3b710dabec2482d8ec1072d64d4e1f8 +#: 085e4d1a7a9744d2884f3003c64ca174 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 -#: 418699fcb6c241dcbeeed81d82e9f84f +#: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 -#: 28b6521a55aa4ab190ca998a59c52609 +#: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that " "are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 -#: 0e4969399eda48b98d883a3fc1540633 +#: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 -#: 6d59f082157b494ebcfff2f649abc524 +#: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 msgid "" "The software and configurations listed in this section are prerequisites for " "following this user guide. The CWL standards are implemented by many " @@ -881,13 +790,11 @@ msgid "" "(though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 -#: 2b83beccbc1b43969b705156b9c29482 +#: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf -#: 594fe5e0aaf0499ebfa9218aaad4d08d +#: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 msgid "" "There are many implementations of the CWL standards. Some are complete CWL " "runners, while others could be plug-ins or extensions to workflow engines. " @@ -895,35 +802,29 @@ msgid "" "md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 -#: f69c7c75a36048f5af0ed1b56df9320d +#: ../../src/introduction/prerequisites.md:19 1df6c63de3914af68f758054fe6955f4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b -#: f28638ffb8394ccead4ac52f30adc627 +#: ../../src/introduction/prerequisites.md:21 ceaa3a6bebab45a0907ee0cad01429a2 msgid "" "We recommend using an up-to-date operating system. You can choose any of the " "following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 -#: 8993d7d5c8d24fc5a9c7005800c0a1f1 +#: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf -#: 2073109799e748d68304f5558c82b105 +#: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 -#: 9fb2c31bd36d495786397c7a7d6b3417 +#: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 -#: 43e1957537034c5886574118fc2533da +#: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem " "for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " @@ -933,13 +834,11 @@ msgid "" "recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 -#: e3a3d9b94b1e44c48f298dfcdcd27104 +#: ../../src/introduction/prerequisites.md:35 051d7cd7d3a94baa865d180afdd71688 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 -#: 8a385803ed3945ff81d38a3543a69d94 +#: ../../src/introduction/prerequisites.md:41 1a93aaf5bd5e4862b15e0636b4478640 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL community. " @@ -947,8 +846,7 @@ msgid "" "in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 -#: bf56727d93994d3995b0af0c68c2c583 +#: ../../src/introduction/prerequisites.md:46 edd0613118a2493c876652bdcb9e0fbf msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create and " @@ -956,31 +854,26 @@ msgid "" "`cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d -#: 9a959bd914d543b78f9625f03df95765 +#: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 -#: 198ce7d893a04fcb806ec1671838d588 +#: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` and " "`conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 -#: cc2be8feeab54a22a0b64a2a72991003 +#: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b -#: 749c672e8c234c1c9a5eb2cc9b77c4e3 +#: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 -#: 29c64936318a4a2ba882e1eae8f03f57 +#: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -991,29 +884,24 @@ msgid "" "command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 -#: 44106744147f45bab675eb66148531c7 +#: ../../src/introduction/prerequisites.md:79 4473e41281fb4e738e4eb26c2d178934 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 -#: 6d84c6890f564b4baf7b34f6a52cbfc4 +#: ../../src/introduction/prerequisites.md:84 548393974d4d4acc91738f9bc13a3a48 msgid "" "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 -#: 7eb67993e8ca48dc929e1a992f78cb39 +#: ../../src/introduction/prerequisites.md:86 2ab3963cf9504ec097eda2b14f3448c4 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 -#: 52886c54c3c54b83896c52ebd7d53fad +#: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 -#: 097945c33f7542e2bae2e9f7ba1cf84d +#: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be invoked " @@ -1024,75 +912,63 @@ msgid "" "environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 -#: 3853bfc6a85747019c615a50c7ca6b40 +#: ../../src/introduction/prerequisites.md:101 b2360ef646854422ad6c0f90fa49306f msgid "" "The CWL community publishes a Python package with the name `cwlref-runner` " "that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 -#: 662230f538504f44941c6f4801f6251c +#: ../../src/introduction/prerequisites.md:104 c9fadfa85a2641378e99a462e8e8d940 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 -#: 1c9eb9e2bb9e40a9985ada16c34eea2d +#: ../../src/introduction/prerequisites.md:111 abb8993ede4d4e479d88d2e848546f68 msgid "" "Now you can validate and run your workflow with the `cwl-runner` executable, " "which will invoke `cwltool`. You should have the same results and output as " "in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 -#: 7f53ba159979461393c0f278fe97fb30 +#: ../../src/introduction/prerequisites.md:115 ba0f7606e6174e53a8bf23c1ccd99250 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 -#: 7e8077c2dd584eda89ead60ecc5eabf3 +#: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 -#: 1787a3c749ee48218b87c8401f6255d7 +#: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For " "that, the first thing you need to do is copy `true.cwl` workflow into a new " "file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a -#: a52ca4ce9a184e938c3a5cac9cb882ca +#: ../../src/introduction/prerequisites.md:129 d989516c873f4446bba005f42796b8b9 msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 -#: 41d3287a9a774a73aefd49bd709764bf +#: ../../src/introduction/prerequisites.md:135 e9d8610478094a98b5b5a0f568a315de msgid "" "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 -#: 3b9d30094611400b85b55db163cb303e +#: ../../src/introduction/prerequisites.md:137 d6d8131f91b740189e56ab9d90bee55a msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 -#: b6ea77357b4f45528ed1379f8fe67cfd +#: ../../src/introduction/prerequisites.md:144 def7400a00e84070a4bd80c2367d3bde msgid "" "And finally, you can execute it directly in the command-line. On execution, " "the program specified in the shebang (`cwl-runner`) will be used to execute " "the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f -#: 8797ce327d7443fdb3d4617d3fc2cf7f +#: ../../src/introduction/prerequisites.md:148 564e7be94d254e52a6c44b234d6ddc63 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 -#: 896b6896b1e44d0cab5f35e7d0dd88e3 +#: ../../src/introduction/prerequisites.md:154 bb5fe42ddd814ad4ac1071c0b18f24c2 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute the " @@ -1102,55 +978,47 @@ msgid "" "`` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 -#: 4b839d23d72f4d3fbe4f1ce7e568b20b +#: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed -#: a42b9ab315b5402493e4ce0067d0a18e +#: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 -#: 2f63483960634a7782f95e9e2feaa5a6 +#: ../../src/introduction/prerequisites.md:167 28d33daee6e246c8a6d1382208e19c39 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting " "and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 -#: 3471105073204d7998aaf790b73f785d +#: ../../src/introduction/prerequisites.md:171 b071d7c87b7a4817b871085a652cd580 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 -#: 0b8b47511b5e4296b7438be0ad2604ed +#: ../../src/introduction/prerequisites.md:172 97658a1b16874ba8b0bb748242d0da64 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 -#: 3e3eec00f23f4f21873ddb005204a875 +#: ../../src/introduction/prerequisites.md:174 6198aa6769b74ef0a2a1ba539789f3ee msgid "" "The CWL community also maintains a list of editors and viewers: " msgstr "" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 -#: 2ceb25f2668442839e3e9f4512772a03 +#: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c -#: 20c753c5371b43ed834fa741b0ce7692 +#: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1158,8 +1026,7 @@ msgid "" "com/>." msgstr "" -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c -#: a19c4fc9fa404912a0389337536d9c25 +#: ../../src/introduction/prerequisites.md:185 2db34e925a81422986ccb868463a7a42 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1167,67 +1034,57 @@ msgid "" "and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 -#: a0f38c1e28ca4850b3986617625acbf2 +#: ../../src/introduction/prerequisites.md:191 d677fb155b0343ba8771398cca967fed msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for pulling " "images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 -#: 37e1162f30894a1ca7dada9870ffa3da +#: ../../src/introduction/prerequisites.md:198 22ed0b55de38408393af4a8309a995ea msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the next " "section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 -#: 1c25a51edf6f47c5979c721b19cf11b5 +#: ../../src/introduction/prerequisites.md:199 5ded73cae5db40ad840c3022e7cd447f msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 -#: ace930cf878d45a99f12b71bf0987a87 +#: ../../src/introduction/quick-start.md:1 23e5613df7c94e5f938c85b14f5441e4 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a -#: 46587a5e0d534af5867ae4f70a116bee +#: ../../src/introduction/quick-start.md:3 3b425afc63d841d4be57c92b25b4ed2d msgid "" "This section will show you a brief overview of what CWL is, and where you " "can learn more about it. No previous knowledge of CWL is required, but you " "must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee -#: a0774d4e779e46f7a983922425203066 +#: ../../src/introduction/quick-start.md:7 75a26c48d3e04e24abb96d81cb31c94e msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 -#: 1658ee6f3cac4d04afc732aa758b1f48 +#: ../../src/introduction/quick-start.md:12 88b4ecd45ea44dd4befe3ce89b30f6c2 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " "example below shows a simple CWL “Hello World” workflow annotated with " "comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb -#: d8e2bc671b894f3fa8a091261754c728 +#: ../../src/introduction/quick-start.md:16 e1789ef78bd64332a18d8601094a0f72 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 -#: 683a469bf4824c64a8ea32e048d5df73 +#: ../../src/introduction/quick-start.md:22 196ceef96c27434eb4b0b7222c2fe73c msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the " "same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 -#: b7c50413f7864a86815f3b581561cdb5 +#: ../../src/introduction/quick-start.md:27 e6a44130c6b44d5bb6451a147f28dd8c msgid "" "In CWL, there is a distinction between a command-line tool and a workflow. " "But for the sake of simplicity, we are using the term “workflow” here. You " @@ -1235,13 +1092,11 @@ msgid "" "section." msgstr "" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 -#: d2ed66bdfcab4f7dad95b00c95d4a3d6 +#: ../../src/introduction/quick-start.md:32 340b46acc7a34b7b978f5a734f529553 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 -#: 4dcbe776a70645e5a6c7513348fa6bee +#: ../../src/introduction/quick-start.md:34 139e48dcf0474fea932ca07a0001d208 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the CWL " "*Reference Runner* for the specification, and it is compliant with the " @@ -1249,13 +1104,11 @@ msgid "" "`cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 -#: bae5b03fb74541e6ad79277a576e0516 +#: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 -#: 8ff0d7a8d37b48488e4504ff8e3adcc5 +#: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea msgid "" "If installing the cwltool using the pip command doesn't work for you, the " "[prerequisites](prerequisites.md) section contains other ways to install " @@ -1263,38 +1116,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 -#: 6255b499b9b144128afaeed64fabe8e5 +#: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe -#: e861db9c43ed4b8ba262af8e435a350a +#: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " "workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 -#: c6318f06bcd74cda8c1f0caef9452b51 +#: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 -#: c862e745217244d28cd4c2f0842e203f +#: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 -#: eba007736b92434a9711f683e64bb153 +#: ../../src/introduction/quick-start.md:65 961a385b340141e980aa4f8791fa2f12 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 -#: aebc2caf5d1b47f1b7cc0aa53e5a684e +#: ../../src/introduction/quick-start.md:70 c48cd1be543d4ccbab964b28c2e08584 msgid "" "Another way of passing values to your workflow input parameters is via an " "*Inputs Object*. This is a file containing the input fields with their " @@ -1302,25 +1149,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 -#: 1242171f8b854562bb7848b06d2d065d +#: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c -#: 24e82ecf7926428386a89f18a34eb00c +#: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 -#: 00e75efe03554835bc33ebaed0652626 +#: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 -#: 4ba34ec455704844a9cfcbac3522ea0c +#: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but it " @@ -1328,54 +1171,46 @@ msgid "" "Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 -#: c0e9673440db454bb51af04432aeddbb +#: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 -#: 39a23a9d02ab4bccb36d6a714639509b +#: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f msgid "" "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 -#: 23a878e0166b40d78984a2263f63b760 +#: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 -#: 5d9c435820674bf4b1c5d3fef5df736d +#: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 msgid "" "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" "Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b -#: e724ee53db1940b9b09a909f4db531a4 +#: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 msgid "" "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." "org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff -#: 7820eb801a8145feb603145f153263b9 +#: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 msgid "" "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." "replace('VERSION', cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b -#: e8db3f10be294f13abe3a4418bbae4b6 +#: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 msgid "" "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" "Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d -#: 95211ea6924148a6a1fa5ae8facc2c7b +#: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. The information on this page has been migrated to the [FAQ](/faq." @@ -1383,19 +1218,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 b742a74d586e42e6b0480b7af3e49c9e +#: 3821c2d16b254672a494522e47386cb0 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 cd3da03d43044ec9843e476a54e704be +#: 412a05f3492349a7bd26ea0c30e9bd80 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf 0d48e2f07d784504a17cad0ae20262c2 +#: 1232f6c81da141cb8482294eee5955dc msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files in " @@ -1405,55 +1240,52 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c 4d372b89f0ce451db2a505b1754b8356 +#: 485bb71673144e3f90f05b420b7079ac msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 573e903ef3d34514ab7b20e79c446567 -#: cfb40fbe52174d3799a6bec175db60a5 +#: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 +#: 5d48d9a2e977431f9a3625abaa466f5f msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 95841b1c75c84f01bd5fcb7cf3afe78d +#: fcc1151a2e8b4a84b8595c7f913781a1 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb c8bca3654ebb4b29bf3f028b4c65fa35 +#: 4a291c7ac7c84257b7402567d8364a36 msgid "" "And now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a 1432105e38014a6d9d0cf80007141007 +#: 3b1ae26038fd498ca0ae23aa70a35d3f msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 bcad473b34ec43f7906253123a1661fa +#: 40388ebefb6947089c4a0f6d5d6e92e8 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" -"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." -"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " -"specification for details." +"designated output directory. Other parameters include `$(runtime.tmpdir)`, " +"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " +"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " +"the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 -#: e1c8949e663b4debaf87735f1d62a2fc +#: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 -#: dcc991b647d34ffc8ea3bf9c3a38258d +#: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d msgid "" "The following are a set of recommended good practices to keep in mind when " "writing a Common Workflow Language description for a tool or workflow. These " @@ -1461,15 +1293,13 @@ msgid "" "although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 -#: f26c222638e54187b8bb62fe30b66bc3 +#: ../../src/topics/best-practices.md:8 935500b0e6e249eba585644cddbd0253 msgid "" "No `type: string` parameters for names of input or reference files/" "directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 -#: 23720e4ab3d1407597f1d1c2a4d4d90c +#: ../../src/topics/best-practices.md:11 96f924d6e02f4005b35d463e49be2982 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that " @@ -1484,8 +1314,7 @@ msgid "" "anyone, e.g. [Apache 2.0][apache-license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f -#: b3638183c59744c897246af7dab5d10e +#: ../../src/topics/best-practices.md:20 25e0a5c93ccc49bc8b6206c7c2e3de5c msgid "" "If possible, the license should be specified with its corresponding [SPDX " "identifier][spdx]. Construct the metadata field for the license by providing " @@ -1495,50 +1324,43 @@ msgid "" "provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc -#: 2c0291133b964ad8b751f8a8ed2338fc +#: ../../src/topics/best-practices.md:26 34ad53bc5a40446daa0dac4571600d1e msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 -#: 325c8c4058f045aa8fbd705238122798 +#: ../../src/topics/best-practices.md:28 4c397ffd2e9148e39bdd614683a98a78 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 -#: 05333866485b43479352f7ee9326c7fd +#: ../../src/topics/best-practices.md:37 1ed7f7e73afb4bd2ad2e29b65d020ff1 msgid "" "For more examples of providing metadata within CWL descriptions, see [the " "Metadata and Authorship section of this User Guide](../topics/metadata-and-" "authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 -#: f8140ec6e9cc41ee88ec4bde61a44d47 +#: ../../src/topics/best-practices.md:40 13b058dfa3cd4bbea54ae7d5a56c4c50 msgid "" "Include [attribution information][license-example] for the author(s) of the " "CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" "[orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 -#: 1d68f50dafaf4cc1851e2d67b3e78603 +#: ../../src/topics/best-practices.md:44 69369b917c1a45199343266650b1b220 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 -#: b283942434c54456a3f29fbb0960b6c4 +#: ../../src/topics/best-practices.md:47 0245a61fd2ef4fb69cbb8d732086fb8f msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" "identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb -#: 0b4477c5b0184e59aa0c07161008a7bf +#: ../../src/topics/best-practices.md:50 e9a56e3634a042279cae1745b7820658 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1546,70 +1368,61 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 -#: 9741651d51f249ffba1820694ab78e92 +#: ../../src/topics/best-practices.md:55 8a180861a66c4aaa9e8fdefd929ed829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 -#: 5e76d4a9708244ff91f2587350d684a4 +#: ../../src/topics/best-practices.md:58 00f333a383b64578b32c687b42924a77 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" -"$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. " +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " +"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. " "[Full IANA media type list][iana-types] (also known as MIME types). For non-" "bioinformatics tools, use or build an appropriate ontology/controlled " "vocabulary in the same way. Please edit this page to let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a -#: 89e7028e55b54f968e87b9c1c3caeecf +#: ../../src/topics/best-practices.md:66 6b960d362bb540299f0560c14c5f2d8c msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c -#: 88e2338fb2614ef29dc497d8c01a2f2f +#: ../../src/topics/best-practices.md:69 9cf9342bf0864e87b495913d8e06d021 msgid "" "Each `CommandLineTool` description should focus on a single operation only, " "even if the (sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 -#: 0f3aad35924344659eb5a6719ab2b8f0 +#: ../../src/topics/best-practices.md:73 587b048324e447cb85844d8c64ae9a1e msgid "" "Custom types should be defined with one external YAML per type definition " "for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 -#: 877cbb1d537b46d3b6d05b2d8c025e70 +#: ../../src/topics/best-practices.md:76 d8df6bbd5d324f7c9f48edb33e113b75 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae -#: 5c0debbc1c1b428ebb32b589b99fe17d +#: ../../src/topics/best-practices.md:78 2235174088ad48a89d4fc21223e627b7 msgid "" "If useful, include a top-level `doc` as well. This should provide a longer, " "more detailed description than was provided in the top-level `label` (see " "above)." msgstr "" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 -#: 1ff97183191240edb98f0cc365cc028b +#: ../../src/topics/best-practices.md:82 a0f0953a1a9f40cebd4dbe028784ff96 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list of " "valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a -#: 22f7725deb07422fa0a7bc2e6f01e4d0 +#: ../../src/topics/best-practices.md:85 0ec380c683534892b6b8b8fcea84f765 msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. One " "common example: manipulating `File` names and paths? Consider whether one of " @@ -1617,36 +1430,31 @@ msgid "" "`nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 -#: 982313839ccc4f5a8527fe9a854c78eb +#: ../../src/topics/best-practices.md:90 65f23741db4e4a6abda8e5f7e036753a msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 -#: 267c9d10ab5e4b6c8a6104952deb1690 +#: ../../src/topics/best-practices.md:93 34c2caee8eb84e01a37033b67eb4aaba msgid "" "Complex workflows with individual components which can be abstracted should " "utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " "workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 -#: 2eff0eec58c94f4d8986a4cb91b14b8e +#: ../../src/topics/best-practices.md:97 d7c7484b2f1048aea9802400410f0858 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics " "software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 -#: f38db701740b442c89ce58e937bd35c5 +#: ../../src/topics/command-line-tool.md:1 a905abc2eead4dbaa035235936025499 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 -#: 034aac9e186645e384c28bb2a739cfff +#: ../../src/topics/command-line-tool.md:3 eb91b6dab34d4d5f9854ac580a6cbde2 msgid "" "A command-line tool is a type of Process object that can be run by itself or " "as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " @@ -1654,59 +1462,52 @@ msgid "" "command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab -#: 5f835cdfc0ae4f378d8dad6ae7ab1855 +#: ../../src/topics/command-line-tool.md:8 7caeb91564634091a932f1270c4f5ef9 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The following " "example contains a minimal example of a CWL command-line tool for the `echo` " "Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 -#: 02900cb8ae4c4da89d264b76a984d6cd +#: ../../src/topics/command-line-tool.md:19 c6ac4a60d102407991f40b892fb60560 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 -#: 753e48d6dfd54a88a12773b996f182d7 +#: ../../src/topics/command-line-tool.md:50 51d3ce421db345f5ab19e02fbbc51df2 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d -#: c7ed6d1654c54bf390e933ef0f847b99 +#: ../../src/topics/command-line-tool.md:57 8311d1430e624435b7b04bf2574a90c5 msgid "" "The example above uses a simplified form to define inputs and outputs. You " "will learn more about in the [Inputs](../topics/inputs.md) and in the " "[Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e -#: 0a0f855ce34449a0a37c036105c65839 +#: ../../src/topics/command-line-tool.md:68 d1c03e5f19d64ea89276d126de6e4bda msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 -#: c4300454f49548f49e4bd186192515a1 +#: ../../src/topics/command-line-tool.md:69 8494b43e98dd424db7d57aa1d731f7b4 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network access. " "If a command-line tool is written manually in CWL v1.1+, there is a need to " "specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e -#: f985d58070de4c0fb5f5a491fd4dc31c +#: ../../src/topics/command-line-tool.md:83 8c4573fb120149269a0fe3a1ba6c9ef8 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " "Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b 2f4e2c85677a4e56a35b6bef36d67334 +#: e1c709ac0fb249928d14aeced6551ae0 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d 13c6d5600a30406c81ffa25ce42eb0c8 +#: c26c9c640e0747c8b2c2977c860c9d82 msgid "" "Sometimes you need to create a file on the fly from input parameters, such " "as tools that expect to read their input configuration from a file rather " @@ -1714,17 +1515,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff 3bf773b8560e44a3a37c68b6fcdc6a23 +#: edbe918d7df14cafb440e171e46c6de3 msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 68b8578d2f6442929941ed2522b218ad +#: 6d457d9b4ae746d384e65d9a37ca3591 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df 755149ed46c348c2b723b49c3b3152a8 +#: 868394c1b8374ee6bbd43463e73d7edc msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the value " @@ -1732,7 +1533,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 54b7ff590d52454eb87d9f23fca44501 +#: 08a9e08cba674db09c9bfbef37e9579f msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later " "during command line tool invocation. That means that any genuine need for " @@ -1742,7 +1543,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa a7c74a4a74c9414e9f29fa20bab7e295 +#: 6f6f437753dd4eddae0b2ea62046fe39 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1750,14 +1551,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 0cbf233379024800bcebb963e0a3eb6f -#: ae3bc02e4f3b404c89f3c461a62c5bc4 dc32a2bacf2d4c8cb841be6eb8b839ad +#: 096b17907bc3452d9927ef2fb6f5c11f 78ed5d8fb9bd4e068023d2c717e20f62 +#: c3a2e9e6b4414597a17db6d55d98e9d1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d 34a56bc23af44353a003ee295fb2c609 +#: ac783e6415a44cb59d4b425bac5087b7 msgid "" "Before we run this, let us look at each step in a little more detail. The " "base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1765,7 +1565,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c c7855ec1f09d4945afcb0aec22567b31 +#: b9e6e15b541149c6a2d3922c11405267 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " "array, we need a `-` on the first line of each element of the array, in this " @@ -1777,7 +1577,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 5c60492e27014735bb9a86307ee654d6 +#: 87088899567a4402aeb34605d3c6b06b msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1787,23 +1587,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f -#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 80a9c04358e64ca28ef4879ad74ef733 -#: a2b470f06ad94871970b7d95339fd369 dc65b4b5e48e48a6ada03da0fac18a51 -#: ea2360c5286b43ccabac202dfa97fbe7 ee4ca94dadf64ab69a70b6cd4eaf451a +#: 304c1bfe5ecd4d26b5dfaf9ad2e2c7f8 3ef7f0e3099147d78fd2d30bfa73cc6b +#: 4fef79a30282456eb9b5dd34a5eec0b1 afe775762ed348e5982b99bcf1451606 +#: f0689cd0e5b34414b6693331186ee4a3 msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 -#: 285d23ef9bbc46c9890ae7957d487c12 +#: ../../src/topics/custom-types.md:1 9f1967411aa7497fa43a4851f0645d6e msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a -#: 3edd322daad940d8957f88a2637876b5 +#: ../../src/topics/custom-types.md:3 90bd62e4ef8b41e398a5c9b31f132774 msgid "" "Sometimes you may want to write your own custom types for use and reuse in " "CWL descriptions. Use of such custom types can reduce redundancy between " @@ -1812,25 +1608,21 @@ msgid "" "to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc -#: a1bd9b0dfa234e6caa6a684e981d89b5 +#: ../../src/topics/custom-types.md:9 3465527b8ff4407587f7c46fa9fa2a98 msgid "" "The example below is a CWL description of the [biom convert format][biom] " "tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 -#: 0aeacb6ac20f4ebca3600425ca32f5f4 +#: ../../src/topics/custom-types.md:12 c0cc869690804ada96a5c1813d17b895 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c -#: 1c813ebce2904f008b5b33656f673ebc +#: ../../src/topics/custom-types.md:18 01f369931c8142c08fe821a0ca31bf92 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 -#: cc36359e94c841d3aa5cbb26a094e1d5 +#: ../../src/topics/custom-types.md:24 0b3ff704cdea44e28aee3c704ca98e27 msgid "" "___Note:___ To follow the example below, you need to [download the example " "input file](https://github.com/common-workflow-language/user_guide/blob/main/" @@ -1838,15 +1630,13 @@ msgid "" "*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea -#: dc79668b05e8439591a0beb4b57acc66 +#: ../../src/topics/custom-types.md:30 cb456bcae0dd41ffbc514eeea283e130 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to be " "used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e -#: 08aba4f77aa442d4a34aa1535f78c49e +#: ../../src/topics/custom-types.md:46 c610173365d04c57900b22f4024b47b4 msgid "" "The reference to a custom type is a combination of the name of the file in " "which the object is defined (`biom-convert-table.yaml`) and the name of the " @@ -1857,27 +1647,23 @@ msgid "" "hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e -#: 63431a972f994bccacf55d5fac0d614e +#: ../../src/topics/custom-types.md:53 c2b2e18d55c94721812431583cfc4725 msgid "" "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 -#: 55e7695aca4f4319b1cf7551105a8782 +#: ../../src/topics/custom-types.md:55 3e61c3920a7a45db8917c348bd44384d msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 -#: 0c5ab34ebbf54ff6940b8ce3f080d744 +#: ../../src/topics/custom-types.md:61 cd87d210b03c4da2a7608b40a6bbcca0 msgid "" "In order for the custom type to be used in the CWL description, it must be " "imported. Imports are described in `requirements:SchemaDefRequirement`, as " "below in the example `custom-types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c -#: f97e18d2d3b946468c4fac227920e011 +#: ../../src/topics/custom-types.md:76 7af9ba3219e44ed49b8da781db5d6fb5 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number of " @@ -1887,31 +1673,26 @@ msgid "" "this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 -#: 62644031403548898ff36addbc0b1f6f +#: ../../src/topics/environment-variables.md:1 eae1994f3a4d481b863b5125c7f4a383 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 -#: 595630b0687c4467aa65bfed289281f4 +#: ../../src/topics/environment-variables.md:3 8bd8c06d416740b69d126eb9f5f24ad3 msgid "" "Tools run in a restricted environment and do not inherit most environment " "variables from the parent process. You can set environment variables for " "the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 -#: 34e005c135864a89a00e817d79118e2e +#: ../../src/topics/environment-variables.md:7 11c6bffc620b4c789b29ab4034a8bfbd msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 -#: b624f9f99c294e6996f212c8b62f20b0 +#: ../../src/topics/expression-tool.md:1 89888b1b994546ce8a93f9630b4bb07e msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 -#: 14df63ab847e4efca820f712548cd076 +#: ../../src/topics/expression-tool.md:3 191d3010b9244b39bc3bc50246ac7ad7 msgid "" "An expression tool is a type of Process that can be run by itself or as a " "Workflow step. It executes a pure JavaScript expression. It is meant to be " @@ -1919,38 +1700,32 @@ msgid "" "on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 -#: 91d4224b41c6473f936c03bd0ab9d370 +#: ../../src/topics/expression-tool.md:8 3437ed6e184748e4af1ef62f32c8cef1 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe -#: 519989399dab493ea41941ed85cb9670 +#: ../../src/topics/expression-tool.md:17 c3ae1ef318bb4e0fada76c353dd5f6f1 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 -#: 28dd1cf24309404eaf717d417272e094 +#: ../../src/topics/expression-tool.md:48 a7f5e04d242c48a7b3deffb5ff6528be msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a -#: 3f536ad8c86d442c8bbe61777dbb1a54 +#: ../../src/topics/expression-tool.md:67 32b6841faed044409bc618cba54a22f0 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains a " "JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 -#: b9e9894c6d024e60929d020dbaa553f0 +#: ../../src/topics/expressions.md:1 6821ba7a84a44d309d245c429948ad09 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 -#: 482debe1a40f490b90d4ece1b3f9d732 +#: ../../src/topics/expressions.md:3 8167269bc3a64c72bd6c909362350a15 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1958,8 +1733,7 @@ msgid "" "CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 -#: 708346038be745d097685970cc462f4a +#: ../../src/topics/expressions.md:9 c0f75603a6024063a6911f17c70908cc msgid "" "JavaScript expressions should only be used when absolutely necessary. When " "manipulating file names, extensions, paths etc, consider whether one of the " @@ -1968,79 +1742,67 @@ msgid "" "practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 -#: 99347b6b2c404a4b9bbcc96e0b4bd925 +#: ../../src/topics/expressions.md:16 7faec63b389a4c07b6929b7a78f0cc70 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 -#: e6629f0914324c76a08fe179575b73d5 +#: ../../src/topics/expressions.md:22 d7dca89942f949d58cb18cb94bb7de72 msgid "" "As this tool does not require any `inputs` we can run it with an (almost) " "empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 -#: 2287002a87184fb9b95d775a368f0e46 +#: ../../src/topics/expressions.md:25 1abc1a21c0764415b138099e0e21432b msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 -#: c23d4543d9f949a9a7015fdcbb40dcd0 +#: ../../src/topics/expressions.md:31 b8b5a50a82e44e49a37c6396f1ff9464 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object is " "represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d -#: c04a9dcc84b84f37bcf32c3790672038 +#: ../../src/topics/expressions.md:35 b38d66c12ab74dfc9395e69d9c04bbf5 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc -#: 9f27c79365db455d9d31053576ebe05e +#: ../../src/topics/expressions.md:37 8417aa7a9d034361a41def6b71e93413 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 -#: a2b3ad1e2c884e24948a915c3305aee1 +#: ../../src/topics/expressions.md:47 c1f672b377da4605b9c5098ebb6e1147 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 -#: dd7665bbc5e9449588c9539e3c1910de +#: ../../src/topics/expressions.md:54 af52f5197e8545d2be22cc0f7f03648c msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " "describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 -#: 0972c757f7c74ea9beabf6b9ef9dbf4c +#: ../../src/topics/expressions.md:62 5e12ce15018942bf9010ce6519c17b00 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 -#: 175de3b9854546568f60a20cc19887de +#: ../../src/topics/expressions.md:64 e2e9c5f7b681427a9589476649e5a9d8 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c -#: 0c286e5ba1714a059a95b566fe49be31 +#: ../../src/topics/expressions.md:66 8a74763ead0147bbaf3892e552fad546 msgid "" "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 3029c1dfe5424c2b812597b03ea76178 -#: a5503b6c524e4848aa308b0f4c26d774 +#: ../../src/topics/parameter-references.md:64 0aab7de8d69f49438d4eeed17316df68 +#: 75f90cb870d14d0dbb4c4ee80d32a65e msgid "`arguments`" msgstr "" @@ -2048,39 +1810,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e -#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 -#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 0e03befa46c74dc2b09420e1eb2a6fbd -#: 50f81e7ab73a4713bbc60f6f5609b906 718dc3def33c462786174fb42097981f -#: 9c2acd930553458eb105f96213b5d7b0 d4bf86a995d546c0a9159b3f29a84125 -#: e98424244f554c7399e9e7ad560849a6 +#: ../../src/topics/parameter-references.md:86 0b9d8268c177489b86b8eaa638dfa063 +#: 204cd6d8375a4462a8247863a96df906 2b7e56ceb4ad49a8b29a58b10bad7c0a +#: 81f15c64379941d8ac2a681b3879761c f11ae7d801db45989b598864dc6291c9 +#: fc4534b475334f7281d1740c9a78f640 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff 2be930b5da674874a0b634eca3ad9346 -#: ce445ad0f00f403985eed1328103a500 +#: ../../src/topics/parameter-references.md:66 70e9085b21f640d6893309a3375c0511 +#: f529003dd7a64bc7be0ccef8dbfa84b3 msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 2fe48d6404864ea39ef0634169f67be1 -#: 43453d90db244c558a815ca872dc716c +#: ../../src/topics/parameter-references.md:67 3fceb522ba6245129b826c342eaf31b4 +#: a5f71add5b8345a4bfa02853ef8a6d35 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 78eaa318ba81407e9ca9c2c1702ead11 -#: f5da7058f7f146d584314a5bf4de5498 +#: ../../src/topics/parameter-references.md:68 018300196ea24550988a0156894b5e85 +#: 2c799286e8204ed9a83c3fc006988139 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e -#: 7189f4415d204fb388c4a7e927e15b71 +#: ../../src/topics/expressions.md:72 25d91d6624bd42e7948e29c684e8e441 msgid "" "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" @@ -2091,15 +1846,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc -#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd -#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 -#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 17a83cc91963434e89822a3e46df8401 -#: 194d3e48d38c476fa8f731e3bc2d8c7f 3a3000a6446b4ef4ac66a28acb13b136 -#: 5cc35210e95e4f2ba6a1a6f118926fdd 68b3d1481a4e4375b1b0c4fca8285374 -#: 94f2bc195bc0487da014bc3f4d2dc8fa b92b4eff2429437d9da911ca68cef954 -#: fc0a1353e87e479d8c8b6c973d547465 +#: ../../src/topics/parameter-references.md:90 0944d6525c3c460aa4b5a0e72552ca4d +#: 1187b0d330cb470fbea82a8b8c95aa28 265602307ccd42458ba47ac1b689242c +#: 2febce1b1ad74b18af3a9b3fa137c780 3215ee41f96541cbbda60a1167386c2f +#: 80efeab6ec0e447bbe158cbaa57f83d8 8d2bbd91b4ab4faa923fc1a14ec49dd5 +#: b4a6e640275b4fc7a18e3083e86b72a1 msgid "`format`" msgstr "" @@ -2108,62 +1859,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 -#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d -#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f -#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 5478cbeadc64412bbb32619fae9b9958 -#: 6950cbe52d334fe58bf4fa20e5f1f8ca 6b5bda581d0047819c6d92edd8ac9045 -#: 8248329fbe504b3a96bcd890908b070f 978c0fea8ed1481a9f06b6abb31ebd21 -#: a24ba514d66d49cea281fd4c9c7a2b8d b6e2c8e7abf74d64b2915063dda8479b -#: bc184adfad0e4642bc864d367b8779b7 +#: ../../src/topics/parameter-references.md:91 480b2e4207574b27b8d33dfe5e9ab64e +#: 4b4149a3b97a4de5b2d7fd84bd547ffe 7af1a82df41e40d0a430babafe1bc5e2 +#: be01787b66e34074af32bb45dcce8657 be099ab533504a7596fd56ec1ce7ca5d +#: c8b96271665444608f601a460dd28fb3 cb6dfa7bc68b41929a5247d929c2f94a +#: f7f452e92f6d4a14ba3912c62699019a msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac -#: 5bba2d465e0a4c5d9575406d1294a225 +#: ../../src/topics/expressions.md:75 4811c1b9867b44caa70dec4b91970484 msgid "" "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 -#: da385d3cde614749887e195ea6d95291 +#: ../../src/topics/expressions.md:77 0b1f2a8986e0419a90e484d3a945a037 msgid "" "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 -#: 487c95417f8e48be8391163578ca9519 +#: ../../src/topics/expressions.md:80 dbc02876870d49d2b9e39db4133a0f62 msgid "" "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 48437402c00147d4b4ca8bd6b38a5823 -#: bdcb3920048f4e578a4005fc2e30233b +#: ../../src/topics/parameter-references.md:78 97339a3fa43849f7b292f4643b5fe35c +#: da8b81b1e1884406a188fb04825ef90e msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 121556d49d584cc491a15ef8404ce462 -#: 183ba52666744f7ca5772939db2efd6c +#: ../../src/topics/parameter-references.md:79 077e7b0d2dde443699050af8c63ab912 +#: c8cbe3dfd0984221ae72012ea26edc6f msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 08ad064936d8406f8c3852526f4f863d -#: 30c927925c6b483b80b583ca7c735437 +#: ../../src/topics/parameter-references.md:80 3f07f4a8594640c2b2da4da521872b59 +#: 573f7e4b72ec4c47ab2e54e2c4877d9c msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 -#: 32a26dd9c5f84e88995f093cda953ac9 +#: ../../src/topics/expressions.md:84 f03011b3479b47c690604c508d95c263 msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" @@ -2171,108 +1911,93 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff 05ee6df2f9b247629d148fd59c293660 -#: e7b7d782b6ac49b3aa0c8d8ce7ff04d1 +#: ../../src/topics/parameter-references.md:84 1ec3f913909b4e04bb602767d23bd85d +#: 2f7130500b8c450fa4af226b18e38407 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 -#: b0cccc07e5bb4effb60424623351499e +#: ../../src/topics/expressions.md:88 a5849a856a374cda807ecf48034af915 msgid "" "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 4e5281c8663c4b6e8851be10f50143f1 -#: b5c22c66397e4268b4b3d53b9a253a3a +#: ../../src/topics/parameter-references.md:87 bd8bbd60aaff4e7aacec91bcbad500f4 +#: f0c99004211e4adf8c0b524d5bbcc12b msgid "" "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." "html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 98a28fec818e42af9e177e17fa12aa7a -#: c37d0b1fd75e44a28b3b6409f912e865 +#: ../../src/topics/parameter-references.md:88 96c544cf213245cfb3d1f5196223c6cc +#: c6a04d4f3ef24104b0a86f9093935c13 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 -#: dcc42c6c49964a4ca7bcf2124e26ebfd +#: ../../src/topics/expressions.md:92 946e0437a48b4d5da2a29d489250cbaa msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](https://www." "commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f -#: d2ba352ac5fe427ea7ceb0bde01458ba +#: ../../src/topics/expressions.md:95 1f287ebf87ae4e93bd1ac65cc1d01bf4 msgid "" "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 235cfd6e9baf48698102447fcb83e0e1 -#: 8aad01df8d8d4ab7905a5da7ce7f6bbf +#: ../../src/topics/parameter-references.md:93 0d0f4f0e12174d588c131afef70efc5f +#: a74e0e3499d644b4a9d999d3555f03de msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 058ba8c9c2da4ebf8b2291600dafd611 -#: cea47d3e10f641a2b64f08ee100ea6bf +#: ../../src/topics/parameter-references.md:94 b2e31c38f7cb4ecabd6b9b89ef051c0e +#: ddc9d9ae72a64a76a2a8e2bba22584ee msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 3b039de5ad144207ae337aa88b3b1a1f -#: e0ecfe44b34e45dea513459b6b3e44a6 +#: ../../src/topics/parameter-references.md:95 12f86817dfc14f2bb39509886d56017f +#: 8a94f2c3b1674162a268f67935a3025b msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 1cfc6cb0be4e4ddd90f546adb796b805 -#: b62f6eaa7c394792929dda83a187c632 +#: ../../src/topics/parameter-references.md:96 a800acfefb3f433fae2cdda9ac4a795a +#: bcb58fc2447a4472b86913871b8c12ee msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 8b13b0e4071444179b26401929de8a10 -#: 8ffb471129c04fc6bb52b782fbd09f9b +#: ../../src/topics/parameter-references.md:97 5be337d412ba4d48877e991d535e810c +#: e6cf2f8498db4f549193be20d87e16f9 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 331f58b998cd4d309940ebfcc60a44f8 -#: 5041700e6ccc48989e395a6dcb1be3c4 +#: ../../src/topics/parameter-references.md:98 3bc61c8197664f12a98d1ac38b421b38 +#: 9973a87f747445ad89ce959420cac5fd msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 14402b41c64548f8a9691c3b7ccaf3ac -#: cb4837a2b25343d2880a07143f85f40e +#: ../../src/topics/parameter-references.md:99 0f5dc4f5a4c64f818e2e22f20472ae84 +#: 2ec9d1f191f44686b1cb8622336d6b92 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 -#: 1d1c2894600544b686a8ec3c36cdf767 eaa30e987ec543ef8d6f7171de5525f0 +#: 5382ff97ad2f419dbe1bed266997aa84 74406f77013443f28d4d6306c54b0df1 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 -#: 065c97a553904db6ba61c20cf9d9939c +#: ../../src/topics/expressions.md:104 f594a20dc038457e815dc17bae6e031d msgid "" "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" @@ -2280,39 +2005,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 -#: 36be05289972455ea4a60aa1f0b9cbdf 49e1ab5bc5734debb83060759d5c3236 +#: 5814f96ee4ec4822aecad33c8eda0473 c46c44268b2a4b96b1df13e53e82e54c msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce -#: f8e37cd35aea4bbb92d28e8d7e803ebb +#: ../../src/topics/expressions.md:106 b9824103ef8745bab30b65887c82f62f msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b -#: de816d1dc9f24c0cbef86fd6a09eff6b e265df9d1cfe439bb798ab6cd32485af +#: 28b23f84c64549e7a0fe444ccc3e1b05 fdd5d742a6764e5db2281ed844bf3475 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 -#: 0363e32e12604eb896f4bdf6bbefd550 8b5289393b7f477699d007ded45a4df1 +#: b6123c911c804f3c8cb596d2aa495b2b d81a7d8b7db444409b286e5f1d863968 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 -#: 2c704cae43d64ecbbed33d18eb3f66f3 89acc8f8387d4643a844ac3efb186000 +#: eb6255a0f8d748588d87e7ad38e507bd fffc5a80bd68495396d32b7a1821eb4e msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 -#: 0597c6c214924e75ba2f212cd6b0c9f2 +#: ../../src/topics/expressions.md:110 b00a8a2a572742e0929470550433e929 msgid "" "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" @@ -2320,27 +2039,23 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 -#: 1eb1c2432dd943f6a27a1f8b92e3981b 5b9ba9380f10425b809c6157a1f0b052 +#: 9b34c95e483e47f3828e79bf929a23b4 c968eebaf0114b23b789e9ce68e7588d msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 -#: b4cc7cc55cf04449b291a27514fc99ae +#: ../../src/topics/expressions.md:116 7c8fb996d1af4cfdb0d49d8ed2696745 msgid "" "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 -#: cdb48eff43e7459fbf3ed21eb7791d66 +#: ../../src/topics/expressions.md:118 75a29e9ff2cf4b5bb6afa87a741a111b msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib` " "attribute that allows users to load external JavaScript files, or to provide " "inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d -#: 67a4dc675c0e444585d579954b99614e +#: ../../src/topics/expressions.md:122 5233d8baa8b74391bf8fee5ae2324234 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2348,8 +2063,7 @@ msgid "" "the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b -#: ea3238db48494ab7b044bab9f96590af +#: ../../src/topics/expressions.md:128 343e8b78a1f94b8cbafac05212e5a333 msgid "" "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." "org/v1.0/CommandLineTool.html#Expressions) that the only version of " @@ -2358,63 +2072,53 @@ msgid "" "in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c -#: baf2f6ac8d514705a1f7bf7ea8c71d2e +#: ../../src/topics/expressions.md:135 0657ee8f03d8462ca6ca6fc538386b0d msgid "" "For example, we can use `InlineJavascriptRequirement` and write a JavaScript " "function inline in `expressionLib`. That function can then be used in other " "parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e -#: ef45f4e14fb943cd9fbf179f5d3680e5 +#: ../../src/topics/expressions.md:139 e3c593cf50da426f8d9df215c7db0bc9 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 -#: 030261615c38485d83ed986c9c98ce15 +#: ../../src/topics/expressions.md:146 b971e53c3ed847f1b7c7a6d50e344baf msgid "" "Running this CWL workflow will invoke the JavaScript function and result in " "the `echo` command printing the input message with capital initial letters:" msgstr "" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 -#: 1728e2370cbb49ab97bee4c2f74fff2d +#: ../../src/topics/expressions.md:149 d2315d46369f4e9d9c871d7f88f7006e msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 -#: 4514fc0c99ac4688a37bf30bffe139e8 +#: ../../src/topics/expressions.md:155 04fdaa45a7ed47d5830181611bda924e msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db -#: 33804649720143e5a70e890af9ad9119 +#: ../../src/topics/expressions.md:158 8d7686f62f314d98aae8c262befd5283 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 -#: c114496be4c243d6834776e17bf15010 +#: ../../src/topics/expressions.md:164 e68ee17607be4a06a66f9fc67624aff5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac -#: c784e86f14f54e4982db206741fbd96e +#: ../../src/topics/expressions.md:171 76b85d3729274fc08adfadcbf1172650 msgid "" -"The `custom-functions.js` file is included in the CWL document with the `" -"$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 -#: f9de69aad9b44afabded71221c84adc2 +#: ../../src/topics/expressions.md:175 29f334957fa940c289f385160cca6d63 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 -#: b853c964611e45c2b37a8ac3c34a4133 +#: ../../src/topics/expressions.md:181 6d255ae6b92a48fa9b7b98443cc2f5bb msgid "" "Finally, note that you can have both inline and external JavaScript code in " "your CWL document. In this final example we have added another entry to the " @@ -2423,18 +2127,15 @@ msgid "" "functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b -#: a10d143210b94f83857f62e972d69134 +#: ../../src/topics/expressions.md:186 89734e7855654b2e8bfddeea96241539 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f -#: b07734b172664040aff04f83bd4395a5 +#: ../../src/topics/expressions.md:193 1915f8e68f624027827d28f8e17d2dec msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 -#: 1f9a5377a1f04ee3b8a9ae22390e0cae +#: ../../src/topics/expressions.md:200 750f94edb4f84e45a276f6ab28fad95e msgid "" "The `$include` statement can be used to include a file from the local disk " "or from a remote location. It works with both relative and absolute paths. " @@ -2442,13 +2143,11 @@ msgid "" "html#Include) from the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 -#: 359bb6448aa140f8b940baf769c13db6 +#: ../../src/topics/file-formats.md:1 2e9e8cfaf48a43a88c31a855dac4f748 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a -#: c4aba730bee14931b051d6aead7c2dae +#: ../../src/topics/file-formats.md:3 c574b54d998243f28d2caa91434968a7 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This helps " @@ -2456,8 +2155,7 @@ msgid "" "simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 -#: c4dfcff573424bccb97580fdd1ef27a1 +#: ../../src/topics/file-formats.md:8 b0ec34507eea473c91d6ada09a1c5c09 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM in " "our example), reference a local ontology for your institution, or do not add " @@ -2466,39 +2164,33 @@ msgid "" "file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a -#: 1457fa489c894f1bae8a3949ef200527 +#: ../../src/topics/file-formats.md:14 a688e39859734a518c0fcc19f532a432 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` section " "of the document in greater detail, so don't worry about these for now." msgstr "" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f -#: cc4fa87d57b344ed8961c31bc4397e71 +#: ../../src/topics/file-formats.md:17 e068422ad9b84ca1b27008127928cc0f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 -#: 091815ab1d824787a1460ce11ffb834d +#: ../../src/topics/file-formats.md:20 8c3ef5e145b14299bf3671add0da56ac msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 -#: 414b68dac4654163b3dc13e140ffdbf8 96fad38b4aea461493bf0827476163bd +#: 0d92f1c0f1ce448fb698e9b390b45c15 fc4773204ebc4e3789bb076dff0d0393 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e -#: 4f71de1140974e73ab033fe7dd9dc165 +#: ../../src/topics/file-formats.md:32 900abc5aa6a940f48f9c93e79cd1c47f msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b -#: b84e3294c8f648aab634e59b6f58441e +#: ../../src/topics/file-formats.md:34 0390555b96c84aadbd9325c152972087 msgid "" "Below is an example of a parameter file for the example above. We encourage " "checking in working examples of parameter files for your tool. This allows " @@ -2506,13 +2198,11 @@ msgid "" "parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc -#: 6d9ae44900d64532906532432881d29d +#: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d -#: 5b99384b3a854832bcca2fb02bdfc1b6 +#: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c msgid "" "___Note:___ To follow the example below, you need to download the example " "input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff -#: 3141fc6828024c3e8201e88ca10e19ee +#: ../../src/topics/index.md:1 0b8b9b7f533543a49f876421ce6057d9 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 -#: 5f8c8ea68d7f46fead000315226ec164 +#: ../../src/topics/inputs.md:1 1b6cfac3a92347d4b98bb54de1e26870 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea -#: 86c18e5105b1400d86d413e28ad72f48 +#: ../../src/topics/inputs.md:3 53dd5f476f064cbf9b9826d1e80eb830 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e -#: fa15037f9b0b4a2c9a1f4cff9b8fde43 +#: ../../src/topics/inputs.md:5 420b33d143fc44d1b237bc678f0af663 msgid "" "The `inputs` of a tool is a list of input parameters that control how to run " "the tool. Each parameter has an `id` for the name of parameter, and `type` " "describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a -#: fba6d2b7843e466abee33183103cf47d +#: ../../src/topics/inputs.md:9 55136332e3bb48f892cf6a74c67a4ac6 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*, " "and *null*; complex types are *array* and *record*; in addition there are " "special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 -#: 09f5a55611d14e39b2266245b79ed763 +#: ../../src/topics/inputs.md:13 cb2527899cc04b6d8060c4d57883beb5 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed -#: bdfb39c2656040858616afe731111d1a +#: ../../src/topics/inputs.md:16 c79668b856b14243b4fad0f46dc5d6d7 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d -#: c306335ff07e4c03955fe87cad16efd1 +#: ../../src/topics/inputs.md:18 ed6f3e5c7b3f403a9a94359983107645 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e -#: 50bd3db6bfb348eea13ba4714ecb2a20 +#: ../../src/topics/inputs.md:24 034075eb09db4897a96d3332408427db msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 -#: 5d32cfb6f6ed4dd8b11ed316830edba8 +#: ../../src/topics/inputs.md:26 08181d391cc543a5a81d3257654df213 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 -#: b90fb1b2d38b42c1bad2d9667aaa22fd +#: ../../src/topics/inputs.md:33 15215522e38242c4b17ec3aa089269d4 msgid "" "You can use `cwltool` to create a template input object. That saves you from " "having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b -#: 6029a96abf9c4d7295eb86d435a1f58d +#: ../../src/topics/inputs.md:40 64bd3382ec234ec8a50217b794b96916 msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " "> inp-job.yml`, and then modify the default values with your desired input " "values." msgstr "" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 -#: 902e9df74f78431ca9cf1421a26e097a +#: ../../src/topics/inputs.md:44 3611c1ca498a4197a4a6612c60f5f565 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b -#: 9760d15bad144e70a86dc0a8da72363a +#: ../../src/topics/inputs.md:47 da924e8142d34e86bcb5de1cd1da71ca msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da -#: 75bf3fae131049308441bc496f543f6e +#: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line, using the command `cwltool inp.cwl inp-job.yml`. The following " @@ -2616,8 +2291,7 @@ msgid "" "command line:" msgstr "" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c -#: 38d8a9c157404bb496bc49f1e427bf99 +#: ../../src/topics/inputs.md:64 dcc3f2a47a6449efb857af63ed4b65d0 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2625,8 +2299,7 @@ msgid "" "specified" msgstr "" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 -#: 502994ee84234f048e545633bb04cd3c +#: ../../src/topics/inputs.md:70 cf54a30ae24f4013bb19f379a7ca67be msgid "" "The field `inputBinding` is optional and indicates whether and how the input " "parameter should appear on the tool's command line. If `inputBinding` is " @@ -2634,16 +2307,14 @@ msgid "" "each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c -#: 551b06b8a3064bcd8d0f1693a4c0ee94 +#: ../../src/topics/inputs.md:83 ff75644bae9c46af8379d78360d4c696 msgid "" -"Boolean types are treated as a flag. If the input parameter \"example_flag" -"\" is \"true\", then `prefix` will be added to the command line. If false, " -"no flag is added." +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 -#: 1838e7438be5449c91c6406a7e40d8cb +#: ../../src/topics/inputs.md:95 e90abe59a84e48d4b8d6caa737e087aa msgid "" "String types appear on the command line as literal values. The `prefix` is " "optional, if provided, it appears as a separate argument on the command line " @@ -2651,8 +2322,7 @@ msgid "" "string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e -#: 098bb02c941a4bf2a8d4dd9ab3bf052e +#: ../../src/topics/inputs.md:109 9275236d87b646cab1058dd750e11a50 msgid "" "Integer (and floating point) types appear on the command line with decimal " "text representation. When the option `separate` is false (the default value " @@ -2660,8 +2330,7 @@ msgid "" "example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 -#: b43194d2b3ef4fc6a8c4b58741317b29 +#: ../../src/topics/inputs.md:124 6a39929af73f4ba9b6455ed9fd287e08 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the parameter " @@ -2670,15 +2339,13 @@ msgid "" "provided in the input, nothing would appear on the command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 -#: e17c55c9ed034dd68f4d24272a61d2f1 +#: ../../src/topics/inputs.md:131 44ce716561cc4dff8fef1ca59f816c7c msgid "" "Input files are read-only. If you wish to update an input file, you must " "[first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 -#: c97a6945e4bc49888d280bbc43c3c069 +#: ../../src/topics/inputs.md:134 9f1da592350f40ee88920465e2004148 msgid "" "The value of `position` is used to determine where parameter should appear " "on the command line. Positions are relative to one another, not absolute. " @@ -2689,20 +2356,17 @@ msgid "" "position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 -#: 503666cda07b4d7397c65561714d8034 +#: ../../src/topics/inputs.md:142 5116d91f247f44518eb21840415f6eaa msgid "" "The `baseCommand` field will always appear in the final command line before " "the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 -#: e5463be0a00d42e386aa6fd3dfacaeaf +#: ../../src/topics/inputs.md:146 08b26d1688e3470288e73d587f052d88 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d -#: 14b98bd0ef4a4065a24e66443458d607 +#: ../../src/topics/inputs.md:148 f91994a4279a41bda3de41fe79008c62 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to provide " @@ -2711,28 +2375,23 @@ msgid "" "after the type name to indicate that input parameter is array of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 -#: 98fa5dab117e41d4a42da8d78c533c64 +#: ../../src/topics/inputs.md:154 4b93a4f980634e88a8f34a38703fc906 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 -#: 116c212444da4488b32abdbd725db98a +#: ../../src/topics/inputs.md:160 de3e760ebb0e4ae099deddb978046a2c msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 -#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d -#: 065e556e01b34c35b6be4b54b7cc0203 4745f370dcbd4ee8bbf4b3a20ac5b9fe -#: d11761f2d576464f8a2c63bdec02d410 +#: ../../src/topics/outputs.md:105 06ec811e8f0e43b8b929198533ac8082 +#: 797c06f0605d4e4ba306c2803a7834f9 d76d42c490a24b6daed944f45fe7a351 msgid "" "Now invoke `cwltool` providing the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 -#: b3bf1d7e95704682b1bae17472eaa4bc +#: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 msgid "" "The `inputBinding` can appear either on the outer array parameter definition " "or the inner array element definition, and these produce different behavior " @@ -2741,8 +2400,7 @@ msgid "" "concatenated into a single argument separated by the item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d -#: 04bc655130234786b06b2d5b9e693635 +#: ../../src/topics/inputs.md:185 3d8711f0135e4ab1b59fce94c83b97c0 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` in " "`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " @@ -2752,13 +2410,11 @@ msgid "" "arrays of arrays, arrays of records, and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 -#: e2c18a43b2794448b45c489dd2fa951e +#: ../../src/topics/inputs.md:191 6f146779d6a84888948751b8b1fd0515 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d -#: 38968ed627514ef38e43b3d1e4a5e25f +#: ../../src/topics/inputs.md:193 e5970a83876e4b5e9a02f2ab0030eb83 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be provided " @@ -2766,55 +2422,46 @@ msgid "" "parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 -#: 06aab84eceeb41d087b7e295ffa21586 +#: ../../src/topics/inputs.md:198 0db71b22173846d7b8d4aeb66d2ed8ed msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 -#: a0317edb8b964cd2a36c59eaa6df302a +#: ../../src/topics/inputs.md:204 f90fd48656a7424aac304987adf1b068 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f -#: 5a3d1b82c79c4ccdb7d06381f4d0acda +#: ../../src/topics/inputs.md:215 3c8bd9134a1c4bda9461362df3257d6b msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b -#: e1fc6c3a324a46ee84b0eb59f8396552 +#: ../../src/topics/inputs.md:217 63bd06780bb949e5b1a1d10389c8c23f msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add -#: f22e7d9e23b541ef88f3254095147519 +#: ../../src/topics/inputs.md:233 0d448baa57f14e7783d3167611e8c659 msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the first " "matching item (`itemC`) is added to the command line and remaining item " "(`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea -#: d473d2fa11f64e8fa86554b5777c98e4 +#: ../../src/topics/inputs.md:236 202239a6e90044e39b676d641aa6d58a msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c -#: 290461c321d14d23b39003b93008a7cb +#: ../../src/topics/inputs.md:252 512ecb3349b0450cb741de4ed2d2e850 msgid "" "In the third example, only `itemD` is provided, so it appears on the command " "line." msgstr "" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 -#: add43f7531bb4c6988053ae799c366f0 +#: ../../src/topics/inputs.md:255 185ff0bb49e841c592b29112eb171bdc msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d -#: b12b6f5e34c14dbc9b40458d92e6797f +#: ../../src/topics/inputs.md:257 6cd5df09e4594d78a526f199ac577881 msgid "" "If you use exclusive input parameters combined with expressions, you need to " "be aware that the `inputs` JavaScript object will contain one of the " @@ -2822,21 +2469,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb -#: 4d8f38679952486095a77692387db2d3 +#: ../../src/topics/inputs.md:262 9db9f784a5cd4ca5b90691d1e2e827ea msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from an " "enum." msgstr "" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 -#: 47ec49759e274e59834192b794ec2d9b +#: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 -#: 0657044c742348fe9e63f662692570a1 +#: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you provide a " @@ -2844,16 +2488,14 @@ msgid "" "should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 -#: 30c21cafda144f848bfe79d8e232296e +#: ../../src/topics/inputs.md:280 76611ebb19764bdc8a1f6eacfb76138f msgid "" "However, if you do not provide any input value, then `file_format` will be " "evaluated to a `null` value, which does not match the expected type for the " "output field (a `string`), resulting in failure when running your workflow." msgstr "" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 -#: 1cc8ea6abb684470b7790808acea2be1 +#: ../../src/topics/inputs.md:289 bf9750d215be4294b1cf1e0490a0796a msgid "" "To correct it, you must remember to use an or operator in your JavaScript " "expression when using exclusive parameters, or any parameter that allows " @@ -2863,12 +2505,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 c3b84742343449f9b3866285d98b53bb +#: 612f9efa0ed04559a174c37958def6f7 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 0a1b08fe707c41089ad3d4895960ba17 +#: 57eb990c11f044dfb60c012a92a30eb1 msgid "" "Implementation extensions not required for correct execution (for example, " "fields related to GUI presentation) and metadata about the tool or workflow " @@ -2883,7 +2525,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b 5bc4ef6584c74b948ffd5c0bddf8e569 +#: a6e6155cb8ff40fb9d8b1fff3e94fb02 msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to cite " @@ -2891,17 +2533,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 47ee25d60a4a4faa80476797954ec7a9 +#: 063c28fc9e654dfd91c66da164ac1d3d msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 195d4a8d5aad41159beffafd198d4640 +#: 8fcd2ae1ce8d4c7f951281ced81ab32d msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 b0c5946fbf79415aa74c8e72fa88cf85 +#: 639533652456427480fa311da7beb4f0 msgid "" "For those that are highly motivated, it is also possible to annotate your " "tool with a much larger amount of metadata. This example includes EDAM " @@ -2911,17 +2553,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e a98236fc1be745a69271855e1b5eecdb +#: 266808daf2004bbd9830045fbc67a541 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f -#: 5f0da8d7e06a47fda38053dbadcbec18 +#: ../../src/topics/operations.md:1 fd9b715bfa3243b19a919ad19843232d msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 -#: 23d41792b0524742878a6ab8f3ff0fe1 +#: ../../src/topics/operations.md:3 fb568063fa7a4cbe83c271772d3d62bc msgid "" "An Operation is a type of CWL process, just like a workflow, a command-line " "tool, or an expression tool. It is a step of a workflow that specifies " @@ -2929,66 +2569,56 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d -#: c0f723242f11464392dfc32f67a3b67b +#: ../../src/topics/operations.md:7 981486166754435cbcd8152e93679405 msgid "" "You can create operations to visualize a workflow during development, before " "you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf -#: c9f3a48a3a064cb3b1759effe724301d +#: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 -#: fbad0b0144984ae78b84307ea68d0a03 +#: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like a " "command line tool or an expression. You can also plot it with the CWL Viewer " "or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 -#: 59e9ff3276454ff19eb351ff33737f12 +#: ../../src/topics/operations.md:24 02c372245dc9453ea0841026335e405b msgid "" "The output of the command above can be rendered with a Graphviz renderer. " "The following image is rendered with the Sphinx Graphviz directive (this " "user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 -#: ba74f2ab7f6d4c178f3c4c43c461afbd +#: ../../src/topics/operations.md:55 d331327285d1434e8c17187737345919 msgid "" "If you try running it with `cwltool`, the command will fail since `cwltool` " "does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb -#: 93c8b61a12134991ae9bb78223e2017e +#: ../../src/topics/operations.md:58 72705f8940bb4194bc5554fcc29eed49 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f -#: cbbdba36dc3841f2b1d820f369a8c680 +#: ../../src/topics/operations.md:66 76b7c63107e94323859904415d07d31c msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A " "CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de -#: 4649c8d743f448ab94ee589a1b3a342a +#: ../../src/topics/outputs.md:1 ebf56d267612461799bf801136e61b69 msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d -#: 1a9d6e2e33244d01b820cf11fe2beaff +#: ../../src/topics/outputs.md:3 f9cff6b272a24ef6ada90e263c1b1784 msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 -#: 233c8865faac4d6c8ec7704e9a997719 +#: ../../src/topics/outputs.md:5 e482821911004cdd8c3ff1539c69368a msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name of " @@ -2996,8 +2626,7 @@ msgid "" "parameter." msgstr "" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 -#: 5aab1c0db3d5449cbb4a0f0dad615d87 +#: ../../src/topics/outputs.md:10 e11fcfe1e84b476ea879810b76ff2cb8 msgid "" "When a tool runs under CWL, the starting working directory is the designated " "output directory. The underlying tool or script must record its results in " @@ -3006,20 +2635,17 @@ msgid "" "from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 -#: 46b4eeb3ce8946dca0f8a94c399b4c96 +#: ../../src/topics/outputs.md:16 65c73a37f06a4782bf43f4acf4f1c77e msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 -#: 8d322609948a4d6e87d7962b3d29df2f +#: ../../src/topics/outputs.md:19 e172dde545164fefac826d910ddd399e msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c -#: 9fdcb55e965444ee8b5d74a2a9870d27 +#: ../../src/topics/outputs.md:21 225f4d04c28149898f06bd771f741358 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -3027,85 +2653,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f -#: e4c490f599a0469a821aa8e74f4ef0ef +#: ../../src/topics/outputs.md:26 14e9e446768a454ea786b3256b49632e msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a -#: b8ed6ebe6928455cb094ea430e21e5d4 +#: ../../src/topics/outputs.md:32 4bd659cee1904868a7c33345f94f1300 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 -#: 3e65c52d218946fc83b8c3e6adcb21fe +#: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb -#: 03751b45cdf647b689a3a69156989db5 +#: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 msgid "" "And now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d -#: 1b6f59623f5d4cd984426da21b8438bf +#: ../../src/topics/outputs.md:51 44cdca5b777441baa246c87940df7264 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 -#: 095902cca30944d19a0d5f17f582e3b0 +#: ../../src/topics/outputs.md:62 edb34af3b22d418d9a6178c0ecbb8b80 msgid "" "The `glob` field consists of the name of a file in the output directory. If " "you don't know name of the file in advance, you can use a wildcard pattern " "like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 -#: 6d95fbfa321144a9932f26ab5f9ddc74 +#: ../../src/topics/outputs.md:65 10e68fad866f4187981f0b365b957b03 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 -#: 8be7ef160e8b421a89124a639dc7fd84 +#: ../../src/topics/outputs.md:67 77e1261484964ba9ac67d9fc9139a1d6 msgid "" "To capture a tool's standard output stream, add the `stdout` field with the " "name of the file where the output stream should go. Then add `type: stdout` " "on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 -#: fcf4490c351d4cd6a208345308168ef7 +#: ../../src/topics/outputs.md:71 c66bd08354d54ccb9e3e1da89634a816 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 -#: 00f1bb92a38b4f3a8c0065ac75530689 +#: ../../src/topics/outputs.md:89 7d4056355da1451dbed6733fba8c3c38 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d -#: 1477d0fc5c4c4f82bcc1c8e6ba8eed4d +#: ../../src/topics/outputs.md:91 8fed80f9633a4e87a67c651dc3160ce6 msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 -#: dee904cb678d4eb49dc829d6590b267a +#: ../../src/topics/outputs.md:93 6cba36e037d54f93add05fb16d2359bd msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae -#: a21c1fd3194a49ae992a743023653dc5 +#: ../../src/topics/outputs.md:99 08862892ecf849a1ba2f25ecc9e98227 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 -#: e72c526da47a455da4b10e33938d1600 +#: ../../src/topics/outputs.md:112 c5dcc68bb28041b3b96ac1af716b0db8 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -3113,13 +2725,11 @@ msgid "" "mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 -#: 6447f4b8bb5f4f93bd8ec2c7b1fb09cb +#: ../../src/topics/parameter-references.md:1 53b95fd10d61462daf153d45e5517dad msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 -#: 1faea30495a440a68dbd1647dacc404c +#: ../../src/topics/parameter-references.md:3 0702e71de81e493dac08a91d667569e3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file we " @@ -3132,47 +2742,40 @@ msgid "" "specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 -#: 0c0a3f58a93f492dbfca14523809aacc +#: ../../src/topics/parameter-references.md:13 a1703da32ad64fd2b8bdd423605b50bd msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 -#: 460842f202db493dbb901be73a02797f +#: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 -#: 2591c2cf9e5f402281031ea8dd41a251 +#: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 msgid "" "Create your input files and invoke `cwltool` with the tool description and " "the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 -#: b093abbff3614b2ba0141f07376a5220 +#: ../../src/topics/parameter-references.md:36 1bcdd99111bd4bc5b75a8297bb61d9bb msgid "" "Certain fields permit parameter references which are enclosed in `$(...)`. " "These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 -#: fda3718113354215bd2ac212553fb2d4 +#: ../../src/topics/parameter-references.md:47 32eae36c593e43a9a6b4e103a0c2028a msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" -"$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 -#: 271e78089c274154a0233289d705e628 +#: ../../src/topics/parameter-references.md:51 1d785e8a450140a982142aa0fa906257 msgid "" "The value of the \"inputs\" variable is the input object provided when the " "CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 -#: 29ab4fa0876b4c11a0c7482cca56ed80 +#: ../../src/topics/parameter-references.md:54 e862bb8bc3e84e24a2aa5ec34298cfd5 msgid "" "Note that because `File` parameters are objects, to get the path to an input " "file you must reference the path field on a file object; to reference the " @@ -3180,112 +2783,101 @@ msgid "" "path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 -#: 78e1857c5bd54af1b7ca4728879e6219 +#: ../../src/topics/parameter-references.md:59 46ffaab11be040cea96a294d9a814738 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad -#: dae7873015254aa7874379164c90a8d0 +#: ../../src/topics/parameter-references.md:61 890d619c415741179c83ffcd56833fbe msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 -#: 7a45deb4682b49fd86d62fae41831db8 +#: ../../src/topics/parameter-references.md:63 373e1847d9f745d7a749928642c8e0e3 msgid "" "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 -#: 442f77a69b314cba8e8857470263c706 +#: ../../src/topics/parameter-references.md:69 90d3624e062c41c7a6d1a9824515d0df msgid "" "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 -#: d4455241f14549b791e59fc1f942c8cb +#: ../../src/topics/parameter-references.md:72 76d09490bd464b708c28991dbff0104e msgid "" "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f -#: ff4b1c05c5804ec7846043ae8814ad21 +#: ../../src/topics/parameter-references.md:74 f33c76e590dd4feaac1e3cf568069d33 msgid "" "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 -#: 119e026b595f49c090d62aa7b7c77de4 +#: ../../src/topics/parameter-references.md:77 74ed4a06c1984c58826ddceb1a45a4ea msgid "" "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 -#: 5449d9c5687544a3bfbf8b2b25640a83 +#: ../../src/topics/parameter-references.md:81 eba3362d34354daa89dc516722c6fbd0 msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" "v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 -#: b3191a7bd03d4ff18802ae0f5d419676 +#: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd msgid "" "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 -#: ea9cfbbd4cbd4f26ba4b0cb50d58635b +#: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." "org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c -#: 7d39ed2a3a724dc1a75e6b2cdf87d91d +#: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 msgid "" "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 a1306ee650344278ae39d6086b1ed7d9 +#: 2fad0c2bc2834350826b22c454d33cf0 msgid "" "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 21d76d22f3044460b925fee68ac74454 +#: 9e303aa89a9b4447b0dbdc5ac0a0eb9e msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 6b8a5c59217c4928874710ead1456622 +#: 7a4eb47c25a54d11a00eb73e9333ad1c msgid "" "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae a9f6d09055c24029a5f85c3a663c4202 +#: 8a957bc8e577476bb59647661b3c0990 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 d3948618f9274ad0a333722567efeea5 +#: 2b31f1dec3f5498e9e363a4f1f50dc8d msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb 44623c81141345a0b0080e719e1418ab +#: 5a5f84ecc2f449bf9f037dc9da0ac670 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -3295,14 +2887,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 6e80d82ed57b441b8292961ec3163213 +#: ee89f1526c1f4452b4e36ba67bb59747 msgid "" "In this example, the software requirement being described is InterProScan " "version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 fc61f369e720463f8a5cd6c751d1d5e6 +#: c76cec44f5424f6087df28aa33c521a2 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -3311,7 +2903,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 f20aadbfc13243498ad199376c314e72 +#: 072d7b3ce3284ed994ff0736b43bbb86 msgid "" "As well as a version number, a unique resource identifier (URI) for the tool " "is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " @@ -3326,13 +2918,11 @@ msgid "" "main tool citation and the URL to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 -#: e66956313b8f4f02bb96cfb256e2a7d4 +#: ../../src/topics/staging-input-files.md:1 395d611104604a28b78e11b112a95027 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 -#: f18c5a8fcbe84135a6e06cbf8008cd63 +#: ../../src/topics/staging-input-files.md:3 811b4db0b1794fa89dc870f6cb59a3cd msgid "" "Normally, input files are located in a read-only directory separate from the " "output directory. This causes problems if the underlying tool expects to " @@ -3342,31 +2932,26 @@ msgid "" "base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 -#: 87fe14c9a0594602aa56a7706e089458 +#: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 -#: 6e10063f55b747e1b07d6109ab7b046b +#: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 -#: e8831832b32449f4a8a3dde3c1b479cd +#: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 msgid "" "In this section you will find ways to troubleshoot when you have problems " "executing CWL. We focus on `cwltool` here but some of these techniques may " "apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da -#: 9c86467137864626a2079cb6cecb71c0 +#: ../../src/topics/troubleshooting.md:6 6db8a02139644598894220d538c590b9 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 -#: 24b66a3e2e464ec6a85b5dfbaad1cbf4 +#: ../../src/topics/troubleshooting.md:8 f0da0f6283d44bcc95224eb9fe2d1764 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor output " @@ -3375,8 +2960,7 @@ msgid "" "directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b -#: 6d28f1cd40c045f384313c4d74073ed2 +#: ../../src/topics/troubleshooting.md:14 e2fc28b44ffe4254892a7c7973dc80c4 msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " @@ -3385,20 +2969,17 @@ msgid "" "of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b -#: 5235ff0c35c54396aceb799a65f6158e +#: ../../src/topics/troubleshooting.md:20 505c7cf9ee9c4af1aeed29002eed1b33 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f -#: fc49344510594559b4f888bc45093b51 +#: ../../src/topics/troubleshooting.md:27 4c31fd11a28943538690d04baa2b5dd0 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " "(`cwltool` will create the directory for you if it does not exist already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac -#: 6e62be8d7d1344e8917904278b508518 +#: ../../src/topics/troubleshooting.md:35 a8532ac700014db4bd8ef690a27fb844 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -3406,8 +2987,7 @@ msgid "" "can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 -#: c91b3a2818b143f58bd37da63479c560 +#: ../../src/topics/troubleshooting.md:44 94a6148512b24b90b87fd1312a926d75 msgid "" "Each workflow step has received a unique ID (the long value that looks like " "a hash). The `${HASH}.status` files display the status of each step executed " @@ -3415,8 +2995,7 @@ msgid "" "output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 -#: 86f283bc522c4be2adfac16256f01b0e +#: ../../src/topics/troubleshooting.md:48 ec4165b7c25c449db6a8804161805e80 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " "the `step_b`). After fixing the typo, when you execute `cwltool` with the " @@ -3426,8 +3005,7 @@ msgid "" "now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 -#: 5362aa1d28344968953ab9cb389ccd8e +#: ../../src/topics/troubleshooting.md:59 5c0b71a6376848d4aa491854ea2d185d msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had " "been cached, and there was no change in its execution or output. " @@ -3437,18 +3015,15 @@ msgid "" "re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 -#: 4bb1aafde4f745a083d3a276497523dc +#: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 -#: b00987baf6974ff9b7e3b8cdfd7abd9a +#: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 -#: 9ac51c5a2a0a45859e14d9e388edd5f0 +#: ../../src/topics/using-containers.md:5 2420b16855cf4b25af5bcb87413f6dd9 msgid "" "[Docker][docker] containers simplify software installation by providing a " "complete known-good runtime for software and its dependencies. However, " @@ -3461,40 +3036,34 @@ msgid "" "containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 -#: 5494ccdb1a354b2386c82bd9a6f0b6a9 +#: ../../src/topics/using-containers.md:15 f5266ee2c2b34170bc89cb501b869893 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the container." msgstr "" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a -#: 4cfa8fc2bb224883946d5f63b372de82 +#: ../../src/topics/using-containers.md:18 728166bf41504e1d89b755400742a1b4 msgid "" "This example runs a simple Node.js script inside a Docker container which " "will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 -#: e16c1922527a46e28bb5d933614cdaf7 +#: ../../src/topics/using-containers.md:21 104351ac29d247cb8e017228e2c9b3d8 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 -#: 7498a71704be462abef71c42e6b83d1b +#: ../../src/topics/using-containers.md:27 e11a38bfb30b404c99d223647960cb16 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed -#: ac0689bff9db46ea8bff8cd35cde86f3 +#: ../../src/topics/using-containers.md:33 7ed0bd21e998417cb02fdcb8e44734b6 msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that is " "really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 -#: c4b7da5575674ca3ae734424022ef090 +#: ../../src/topics/using-containers.md:44 9dcddf6812ba4bc2a7d6c5fcdb978a68 msgid "" "`baseCommand: node` tells CWL that we will be running this command using the " "Node Js runtime that is meant for Javascript files. We then need to specify " @@ -3507,27 +3076,23 @@ msgid "" "called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 -#: d24fcecc17d0461cbd8689067f770c0d +#: ../../src/topics/using-containers.md:52 bc1a09475f154562a4db445bf81ac92f msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " "the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 -#: 833d4d3b3f0e4c7cb8b1d35cb9a78a7e +#: ../../src/topics/using-containers.md:55 2e117019ace84604a8ed5a31214c2587 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 -#: 50fc0573276e4dd4a47208ed81109991 +#: ../../src/topics/using-containers.md:69 d0d5b2a1a008411e92859a72101088c1 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 -#: f72e10e746604421904057ddf7078d3e +#: ../../src/topics/using-containers.md:72 591d1cd0282b4095a267b44da7d59804 msgid "" "In this example, the path to the script `hello.js` is `/home/me/cwl/" "user_guide/hello.js` outside the container but `/var/lib/cwl/" @@ -3535,51 +3100,43 @@ msgid "" "invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 -#: ee126833f6014e378c7841c4048dae85 +#: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 -#: 0325bd610aa747b0b657afa0c978a1eb +#: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 -#: 7c901105cf6949909d87be5681331368 +#: ../../src/topics/workflows.md:13 7530029ec04746f2a888dcbc10aa5ce4 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 -#: 74138d0c2ded4311bf688df4a28387b5 +#: ../../src/topics/workflows.md:41 c1f1d644b37b4f018b87e15249d8758d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier examples." msgstr "" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 -#: 1ec4773e7319414b997d746d1965ff56 +#: ../../src/topics/workflows.md:51 2d07232b7d9c415b8ad971e8cbcd9577 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb -#: 5f860dd70e3b435188c61a538e5de0ef +#: ../../src/topics/workflows.md:81 fa1f770ffeba4b74bcb200cd3949e070 msgid "" "A command-line tool or expression tool can also be written directly in the " "same CWL document as the workflow. For example, we can rewrite the `echo-" "uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa -#: a9c56df6dca441dfabda7fa54fbe56c6 +#: ../../src/topics/workflows.md:91 570020792e824c2ba732bcc2c0134aa1 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a -#: 586d561ddf724319b3da9ae857828648 +#: ../../src/topics/workflows.md:150 8a50c511004941d0917a8f0d471467f0 msgid "" "Having separate files helps with modularity and code organization. But it " "can be helpful writing everything in a single file for development. There " @@ -3587,39 +3144,33 @@ msgid "" "pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe -#: f3e80b1903534065a30323611c267e9b +#: ../../src/topics/workflows.md:160 4d2bf0341836405d9729c47d8020faea msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this " "user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 -#: 6ed53c6f9fb94d4ab3d10532c605c46b +#: ../../src/topics/workflows.md:165 dd6fc85f74984517b284853a0d46c122 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c -#: 3fcfdf43b0a049388634625c45e0b1bb +#: ../../src/topics/workflows.md:167 f857d80cd5d84622a560c895ab260a92 msgid "" "This workflow extracts a java source file from a tar file and then compiles " "it." msgstr "" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 -#: 49415efafae64f94b66cb46ca2bbd40a +#: ../../src/topics/workflows.md:170 02e7e81cdf7e4226973f910cd57b8ccf msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 -#: 4806a2ef982944e8b073fafd416d3d74 d45701eeaa6e42feb4ef79d2fc4af756 +#: 3a88d92f41aa4daaad4f4cc6829184b3 646367f222ea41e5987561941d17c4f9 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 -#: 155cd684ff304258ae374b2e13090e5f +#: ../../src/topics/workflows.md:180 aaba75eb272245db82d072fed97b311c msgid "" "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" "github.com/common-workflow-language/user_guide/blob/" @@ -3629,39 +3180,33 @@ msgid "" "_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 -#: d8bdb44011274f94b606277799a6fa6f +#: ../../src/topics/workflows.md:183 f8a6e1af5f0349a5a384be0629c37ac8 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a " "run:" msgstr "" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda -#: 9e1d9bc2f83743ea9964ec418d225200 +#: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 -#: a1240eab3ef746cf82a2c5451042b888 +#: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 -#: a73cdc43a8e44973808027c29903afa3 +#: ../../src/topics/workflows.md:205 84293afa7a6c40f2af0b980c89581fc7 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde -#: 4277837a9fd443378d5ca3d9252993c9 +#: ../../src/topics/workflows.md:212 e66daf8af53849109936c36ca7d2b2c9 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a workflow." msgstr "" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 -#: 09b714af60ee4ecc8ab1b95eac8284dd +#: ../../src/topics/workflows.md:221 8fbfbb587b264dcf98a3cea16dd36ef3 msgid "" "The `inputs` section describes the inputs of the workflow. This is a list " "of input parameters where each parameter consists of an identifier and a " @@ -3669,8 +3214,7 @@ msgid "" "workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 -#: 3e99a3be9265463daf74b00a21d89cff +#: ../../src/topics/workflows.md:233 5cdbc4771ea841b4960362b930de2af6 msgid "" "The `outputs` section describes the outputs of the workflow. This is a list " "of output parameters where each parameter consists of an identifier and a " @@ -3678,8 +3222,7 @@ msgid "" "the `compile` step to the workflow output parameter `compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 -#: 1c4a959d43b74686ab801a26ef412b3d +#: ../../src/topics/workflows.md:248 2e8a41fe43984dc6b4cf430e1ff66b28 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second step " @@ -3690,8 +3233,7 @@ msgid "" "parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 -#: 55daf180336d4045ac0cc4c14af98cfc +#: ../../src/topics/workflows.md:256 78c20aa5a5724da6a4c908849c571334 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input " @@ -3699,8 +3241,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 -#: 5ae40eb04d5440d5ba882a74aa5b9708 +#: ../../src/topics/workflows.md:261 1606a2f059eb4b0c9e90f2f0cbbe779b msgid "" "The ``in`` section of the workflow step connects these two input parameters " "to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " @@ -3709,15 +3250,13 @@ msgid "" "parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea -#: f93e9b776a4544018877b7a13399609b +#: ../../src/topics/workflows.md:267 b456b11e2760479bbf81a773a3e1f8ee msgid "" "The `out` section of the workflow step lists the output parameters that are " "expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed -#: 0e587435e3884334bc51a4abf4b4d785 +#: ../../src/topics/workflows.md:278 0fa01fcec32049c989ad1d68841c74de msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3727,13 +3266,11 @@ msgid "" "section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 -#: 81b98764289245c79f18fcff478f4a9b +#: ../../src/topics/workflows.md:285 2bc9829f95584a269eb577c610b2a80c msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e -#: 9baddec4015f40ad82ea2dee30305654 +#: ../../src/topics/workflows.md:287 0e5e6445bfcb42a4bd03612316dd7225 msgid "" "Workflows are ways to combine multiple tools to perform a larger operations. " "We can also think of a workflow as being a tool itself; a CWL workflow can " @@ -3741,20 +3278,17 @@ msgid "" "the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 -#: 986c3dd9460b42b3b20e2d01ba1fbe51 +#: ../../src/topics/workflows.md:297 0b83c1028b0e43ba972609e4302bc8a2 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 -#: 4558f174fea445fd97b80d963fc74f43 +#: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 -#: 532823a13154401090e9fee3e018fda9 +#: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d msgid "" "This two-step workflow starts with the `create-tar` step which is connected " "to the `compile` step in orange; `compile` is another workflow, diagrammed " @@ -3762,23 +3296,21 @@ msgid "" "supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a -#: 7b6f46b70bac4f848a956ea160243621 +#: ../../src/topics/workflows.md:314 2e9797fcd4f04f56b5d2b2f1a3e306d5 msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows." +"cwl\">\"Visualization \"Visualization" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 -#: 3861b4a31f71471b97bf9dc18cc80594 +#: ../../src/topics/workflows.md:322 28f4139911b44eeeb7afd31e9f7cae7b msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " "CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3786,8 +3318,7 @@ msgid "" "to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 -#: a10c37f65ac14ef2a5971872bc9b8f9a +#: ../../src/topics/workflows.md:336 4a6cb397a20241beab24d956920a8379 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and `*.java` " @@ -3796,8 +3327,7 @@ msgid "" "workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be -#: 34175f932716406f836840732618caee +#: ../../src/topics/workflows.md:341 dccb5472a5dc42b7946dd9245a71ecf0 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar " @@ -3806,8 +3336,7 @@ msgid "" "specific input/output names, as those also appear in its usage as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 -#: 0d132dc39cdf4818bc8e20132073f669 +#: ../../src/topics/workflows.md:347 de1e18b69f654cabb75e52b47058030a msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3815,16 +3344,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 -#: 9f8c45f077974cf79612ee83df3d152b +#: ../../src/topics/workflows.md:366 b947e62f4b3b4c10b95737f1839bcc5a msgid "" "In this case our step can assume `Hello.java` rather than be parameterized, " "so we can use hardcoded values `hello.tar` and `Hello.java` in a " "`baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 -#: 435f80d0599b4d93ae1339e8c7bc020a +#: ../../src/topics/workflows.md:383 2ed0258a3a104ed5ba3b6b95ad998839 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This is " @@ -3833,8 +3360,7 @@ msgid "" "filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 -#: d39b024a1a8d4eae8d7fd3c929a782e9 +#: ../../src/topics/workflows.md:389 6584c0995288450b8a01c35fa231afb6 msgid "" "In this example we had to prepare a tar file outside, but only because our " "inner workflow was designed to take that as an input. A better refactoring " @@ -3842,8 +3368,7 @@ msgid "" "which would simplify its usage as a tool step in other workflows." msgstr "" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 -#: 3cbbe074843d4306b762d2fbc6fe9850 +#: ../../src/topics/workflows.md:394 19237513fd134c33801a7af08f74e70c msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL " @@ -3851,13 +3376,11 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 -#: 7118b6e09b9f44129c7d98d90570f2c2 +#: ../../src/topics/workflows.md:398 b66e0d0a36994b3182a3784bda8ffc19 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 -#: 70f3e73ee3714f22ad6ee43dd5ece703 +#: ../../src/topics/workflows.md:400 3bfb9851302248568bb4535ddc87a27f msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish to " @@ -3868,8 +3391,7 @@ msgid "" "different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 -#: 279495257ead4a4fa725c7d68c504162 +#: ../../src/topics/workflows.md:411 78a5a600f8cc49ce8055c77a596ad833 msgid "" "The most common reason a new user might want to use scatter is to perform " "the same analysis on different samples. Let's start with a simple workflow " @@ -3877,27 +3399,23 @@ msgid "" "strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd -#: 86d1d742bb5c4a9898aa573ce648f0ec +#: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 -#: f4987847f46e4a2db54127ec7ebcadf7 +#: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 msgid "" "Aside from the `requirements` section including `ScatterFeatureRequirement`, " "what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c -#: 80e7c22dfe4d40749f2e9c3bf02bf8bc +#: ../../src/topics/workflows.md:429 7ab022708a9642ab8aa2e79ea7810381 msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f -#: e930bb5d430a41d9b5bf49e473dd2ed1 +#: ../../src/topics/workflows.md:441 fe144641fc8040b283f15b2b99ecb5a2 msgid "" "Here we've added a new field to the step `echo` called `scatter`. This field " "tells the runner that we'd like to scatter over this input for this " @@ -3905,8 +3423,7 @@ msgid "" "the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d -#: 4076e9eb67ed4bd5942f089e394bad26 +#: ../../src/topics/workflows.md:445 f13d1b071a7f4a75a4cdee40ecef14fa msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if you " @@ -3914,70 +3431,59 @@ msgid "" "to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 -#: 1b44092e87b840de8f1d022676d0990d +#: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be -#: a8afac626f5d4240a57267085b9bef26 +#: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 -#: 0896efc674bc402495c6e73c6c352523 +#: ../../src/topics/workflows.md:458 f5b8681b3c3b4890a86d7b9fb812d958 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " "calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f -#: 91a53d918d4b47bdbe0b0a6d4adfc0dc +#: ../../src/topics/workflows.md:466 74e70fec6d2447bbbd2a5bc8af1fa58c msgid "" "You can see that the workflow calls echo multiple times on each element of " "our `message_array`. Ok, so how about if we want to scatter over two steps " "in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 -#: 8325682d51d8421b9ea507f424f71e73 +#: ../../src/topics/workflows.md:469 76fed9e7ad1d4792b7bb364bb684eeb2 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding the " "following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de -#: 503d068602d8477a820b91d835fa3f28 +#: ../../src/topics/workflows.md:472 bef387d9be1f4ca19a97023cfdd1c910 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 -#: 4e768b91eb274a5cb157f1e3fe2f85cd +#: ../../src/topics/workflows.md:480 eea1be83da574f39914566d835701b4a msgid "" "And add a second step that uses `wc` to count the characters in each file. " "See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a -#: 18ec5231b7bf4c9ea59361b325fcdd01 +#: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b -#: 87fd118dc2774cf08db0a3ba56520da5 +#: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under each " "step:" msgstr "" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d -#: 8168ffcb23124b3f839a9862a7ec0958 +#: ../../src/topics/workflows.md:491 e6e1a79638d74547b00c64e3c8b05710 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 -#: 37c222ea14904fd4a8fa93a1e0103239 +#: ../../src/topics/workflows.md:497 03fb16e74bf14c49b43e35ef6cb45030 msgid "" "Here we have placed the scatter field under each step. This is fine for this " "example since it runs quickly, but if you're running many samples for a more " @@ -3994,8 +3500,7 @@ msgid "" "welt!`. You can see how this might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df -#: d392813fc6d14851a294a391426d41f6 +#: ../../src/topics/workflows.md:509 eca3380c60094df2b91b44b5f7718fae msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can " @@ -4003,45 +3508,38 @@ msgid "" "step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b -#: 652155460eaa42b6856c16cffdb845c0 +#: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb -#: 6313cb377dc249e0b2262a3fe732fe32 +#: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 msgid "" "Now the scatter acts on a single step, but that step consists of two steps " "so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 -#: 11f73cf24fb044e3a3afb3adb6137708 +#: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 -#: def9e62bf73f49eebce09677954e2a92 +#: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 -#: 200dfe47d09d4b0b9e4acf29b7e038da +#: ../../src/topics/workflows.md:527 8f7ee09c9d6b491195e2d80315dae398 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 -#: 858bda7fb6524e9dbfb35596ce6a6d07 +#: ../../src/topics/workflows.md:566 966acff0d3d24104ae9673df8a790fb1 msgid "" "The first thing you'll notice is that this workflow is only compatible for " "version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 -#: 28897819504247a3a6cf9a9d9476b63b +#: ../../src/topics/workflows.md:573 d60e1df759654f1b873276cf0296f234 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when` is " @@ -4049,8 +3547,7 @@ msgid "" "from the workflow contains a value `< 1` this step will be executed." msgstr "" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 -#: 4f8fd11e29b048e1851299002c3a48c4 +#: ../../src/topics/workflows.md:587 69aa8d3c9d9a4fe4a62875827648d95f msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " "will pass the first conditional step and will therefore be executed and is " @@ -4058,75 +3555,62 @@ msgid "" "skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec -#: ed33196347d949eda752a081c7af4657 +#: ../../src/topics/workflows.md:607 fee34c880e964e08b040adf2d3831803 msgid "" "When a value of 3 is given the first conditional step will not be executed " "but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 -#: 738c67568dbb4f2bbb5756fc5e727c01 +#: ../../src/topics/workflows.md:627 cb9e82cf4b484ca7be19612b14fbdf33 msgid "" "If no conditions are met for example when using `--val 2` the workflow will " "raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e -#: 19b016a1fec14056a9812c1c195c7c90 +#: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c -#: a513367d60a74f559339c05d8ef10eb7 +#: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers and " "humans. This guide introduces the features of YAML that are relevant when " "writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 -#: 5e30680941164047a47f98417e916188 +#: ../../src/topics/yaml-guide.md:13 2cc21093311548cd837aa7b3f0939093 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea -#: ca02f2bf1d754d5190f296674245b936 +#: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee -#: 466615194bb541fdbe2e6515b50531b3 +#: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a -#: 33e664d59a30407891336db290a8a5b2 +#: ../../src/topics/yaml-guide.md:19 179290eee12343dd9aa4d49207cf7c68 msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c -#: 3e52ab079dcf4fc6a3f052a517f4d31b +#: ../../src/topics/yaml-guide.md:20 7880db40e98e4aaabdc96def3d9f515d msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc -#: abcad6b7d37a4342a90c2d5952ea1232 +#: ../../src/topics/yaml-guide.md:21 75f3b499494b445f9f9a532d178cbc10 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 -#: 500a489e4fae4d1abaa8883f632d1a24 +#: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 -#: 546c1ef51a63487c91c98059dd46b0cb +#: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 -#: 72b4262833054edd9efe6078381de654 +#: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the `:` " @@ -4136,8 +3620,7 @@ msgid "" "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b -#: 7b7e8242660744b791ba3868e4ed7e37 +#: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 msgid "" "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " "and `home` - with their four respective values. Values can be character " @@ -4145,8 +3628,7 @@ msgid "" "Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 -#: 492d994a541c4c948fb5da9041153bcf +#: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c msgid "" "Values may be wrapped in quotation marks, but be aware that this may change " "the way that they are interpreted i.e. `\"1234\"` will be treated as a " @@ -4157,33 +3639,28 @@ msgid "" "numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 -#: e2209269db394f3988f18b147a57677c +#: ../../src/topics/yaml-guide.md:61 d18c1f5ef55d4bb6b8334438fcbc96b8 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 -#: e15c39c65aca47f690264d8008463bec +#: ../../src/topics/yaml-guide.md:63 dc6869049fc143b4af91d172a419a125 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program interpreting " "the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d -#: afa546fcb7fb447d939d4a167f206f79 +#: ../../src/topics/yaml-guide.md:76 c3c7f5ecfedb4884ad5e91bb79ba2a7c msgid "" "If there is anything on the line before the comment, be sure to add at least " "one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf -#: 7dd375e0fd964413af4957396d2a0474 +#: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 -#: af8ef039a64a4c0783d7229dbdac65ef +#: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, these " @@ -4194,8 +3671,7 @@ msgid "" "are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 -#: 3ce968cb39a443059f6a828b3c8c2f33 +#: ../../src/topics/yaml-guide.md:104 ce790af50da540eb9108ad89eae037cf msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -4207,13 +3683,11 @@ msgid "" "graphical representation of the `inputs` object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 -#: 3c2f48a8e616400b9a8ffb4b6f7efc9b +#: ../../src/topics/yaml-guide.md:127 c3c9ef616b5d472a894ad6330267bcd2 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 -#: c432b1656e0e49ef87aa3d6e42acad84 +#: ../../src/topics/yaml-guide.md:129 b8a7360f6e0640aa9a2c4907c1ba3fe8 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) section " @@ -4223,30 +3697,25 @@ msgid "" "where each value is defined on its own line and preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 -#: cac5e52767f74ce98693e2a19ee1eb0d +#: ../../src/topics/yaml-guide.md:146 363da878600a4d229efe0ba79835d73c msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d -#: 101666907f8b4fb994e25ceffcf04a13 +#: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d -#: 5461960a469042a487b89e440f856aea +#: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " "can also be defined in YAML using the native JSON syntax. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc -#: e31349c164c84a9da46e2fb1861793df +#: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 -#: 49a0b3dfdc9e4d58b6bc966db979ace8 +#: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd msgid "" "Native JSON can be useful in indicating where a field is intentionally left " "empty (such as `[]` for an empty array), as well as where it makes more " @@ -4256,130 +3725,50 @@ msgid "" "file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d -#: e08ec8c473e847f98e8a18b9ca0f2670 +#: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 -#: 6ee7bfb4a9e04dd19b5180bca5b02705 +#: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " "while we wrote this guide, though it also covers features that are not valid " "in CWL." msgstr "" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 -#: 42614ab7ba1546f89abeb8f48991271c +#: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 -#: b8df5b8393ed4d869c066640fe83ec7b +#: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to the " "list." msgstr "" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c -#: 5b9aee5af41f438b9f4208294bf97f4a +#: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 -#: a71d3022dcfc44979cca4655ea51ad42 +#: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b msgid "" "[Introduction to Workflows with Common Workflow Language: For Contributors.]" "(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f -#: 42b5a982e86f46dfbfcd7bfcc99d72a5 +#: ../../src/tutorials.md:11 3505468d39c34a20bc55f431a3c697f7 msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f -#: 12dc402d053044b78d69927dd391fe9d +#: ../../src/tutorials.md:13 e5731a11b89e492d8d751100a46c5226 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f -#: 687c20e2e4bc4f869c7ee9390e61476a +#: ../../src/tutorials.md:15 cdfeabb88f6245d9a687197d242ed3f9 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 -#: a975fbb3ea7d467881ce0245de538295 +#: ../../src/tutorials.md:17 997679b781a84add9b6d8b1900deec35 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" - -#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the `Creative Commons " -"Attribution license `_. The following is a human-readable " -"summary of (and not a substitute for) the `full legal text of the CC BY 4.0 " -"license `_." -msgstr "" -"Todo el material instructivo del proyecto Common Workflow Language y los " -"cambios en la estructura también están disponibles bajo la `licencia " -"Creative Commons Attribution `_. Lo que sigue es un resumen " -"legible por humanos (y no un sustituto) del `texto legal completo de la " -"licencia CC BY 4.0 `_." - -#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 -msgid "to **Share**—copy and redistribute the material in any medium or format" -msgstr "" -"**Compartir**—copiar y redistribuir el material en cualquier medio o formato" - -#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 -msgid "to **Adapt**—remix, transform, and build upon the material" -msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" - -#: ../../LICENSE.rst:23 be38276e7b374f57b9997391bf898a62 -msgid "" -"**Attribution**—You must give appropriate credit (mentioning that your work " -"is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a `link to the license `_, and indicate if changes " -"were made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." -msgstr "" -"**Atribución**---Usted debe dar crédito de manera adecuada(mencionando que " -"su trabajo se deriva de un trabajo que tiene «Copyright © The Common " -"Workflow Language Project» y, cuando sea práctico, con un enlace a " -"https://www.commonwl.org/ ), brindar un `enlace a la licencia `" -"_, e indicar si se han realizado cambios. Puede hacerlo en cualquier forma " -"razonable, pero no de forma tal que sugiera que usted o su uso tienen el " -"apoyo de la licenciante." - -#: ../../LICENSE.rst:31 f00d5c3846034c2ea116c2f74786d9fc -msgid "" -"**No additional restrictions**—You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" -msgstr "" -"**No hay restricciones adicionales**---No puede aplicar términos legales ni " -"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " -"permitido por la licencia. Con el entendimiento de que:" - -#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"`OSI`_-approved `Apache 2.0 license `_." -msgstr "" -"Excepto cuando se indique lo contrario, los programas de ejemplo y otro " -"software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la `licencia Apache 2.0 `_ aprobada por la " -"`OSI`_." - -#: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index fd0da8d1..b49c961f 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -9,29 +9,27 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-27 16:02+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" +"Language: pt\n" "Language-Team: Portuguese \n" -"Language: pt\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.16-dev\n" +"Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 ../../LICENSE.rst:2 -#: 75de2be8809847b8bf1ccd42aa694a24 +#: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 ../../LICENSE.rst:5 -#: 2edd71801f6245ef821887a74f21b94c +#: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 msgid "Instructional Material" msgstr "" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +#: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c msgid "" "All Common Workflow Language project instructional material and changes to " "the structure are also made available under the [Creative Commons " @@ -45,29 +43,26 @@ msgstr "" "humanos de (e não um substituto para) o [texto legal completo da licença CC " "BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 ../../LICENSE.rst:12 -#: 90cc755d172e4c82b882b4ee620fe652 +#: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 msgid "You are free:" msgstr "Você tem o direito de:" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +#: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 msgid "" "to **Share**---copy and redistribute the material in any medium or format" msgstr "" "**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " "formato" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 d66dcbf95ccc41aaa53be523487ec913 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 ../../LICENSE.rst:18 -#: 430ff4de74924bc3a3b2c7e809ea4456 +#: ../../LICENSE.md:17 ca1c299a1b834b868bcdd4ca9f244696 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e ../../LICENSE.rst:20 -#: 2173e2af49be41ee97a74c4e879faf25 +#: ../../LICENSE.md:19 6133f79f93be4991a6f5290f72d1a63d msgid "" "The licensor cannot revoke these freedoms as long as you follow the license " "terms:" @@ -75,7 +70,7 @@ msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " "termos da licença:" -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +#: ../../LICENSE.md:24 2d6ce81add1043629b676187f890288c msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " "work is derived from work that is Copyright © the Common Workflow Language " @@ -92,7 +87,7 @@ msgstr "" "mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " "uso." -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +#: ../../LICENSE.md:32 f3f22597b6f845208a0cce3b3b2c8f5d msgid "" "**No additional restrictions**---You may not apply legal terms or " "technological measures that legally restrict others from doing anything the " @@ -102,8 +97,7 @@ msgstr "" "medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " "algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 ../../LICENSE.rst:35 -#: f6aae4a5cd0547118c8a3240ca2b4be6 +#: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef msgid "" "You do not have to comply with the license for elements of the material in " "the public domain or where your use is permitted by an applicable exception " @@ -113,8 +107,7 @@ msgstr "" "material que estejam no domínio público ou cuja utilização seja permitida " "por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 ../../LICENSE.rst:38 -#: a40c173be35b4c1b92e83f42bfe2382c +#: ../../LICENSE.md:39 c836a570faaf449d9716da5f75556627 msgid "" "No warranties are given. The license may not give you all of the permissions " "necessary for your intended use. For example, other rights such as " @@ -125,12 +118,11 @@ msgstr "" "direitos, tais como direitos de imagem, de privacidade ou direitos morais, " "podem limitar o uso do material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea ../../LICENSE.rst:44 -#: 3d7ca3f2cede4d5f998bf014bd970748 +#: ../../LICENSE.md:44 896f9966e5014e8a88b060be3063fe09 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +#: ../../LICENSE.md:46 007f8613dc234c3fa8d5d92b18af0eb1 msgid "" "Except where otherwise noted, the example programs and other software " "provided by Common Workflow Language project are made available under the " @@ -140,7 +132,7 @@ msgstr "" "fornecido pelo projecto Common Workflow Language são disponibilizados sob a " "[licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +#: ../../LICENSE.md:51 227bc635a06f49dbb771fd9b62157d00 msgid "" "Unless required by applicable law or agreed to in writing, software " "distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " @@ -150,9 +142,8 @@ msgid "" msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 5ad4be9b62d54c95a913795b514676fd -#: bdd540403a5746ff99edf2dcad0e3122 dfc7702e073140c985cf47272a20214d +#: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd +#: d6055d3f15604ce6940770c7b561d4c5 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece of " @@ -161,36 +152,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f -#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 +#: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 -#: 3060770b3bef41d7bcfcdfb413d7689c +#: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 -#: 48bb9f628b344ba1a3b67ae1cb264e3c +#: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 -#: 7e3684e9672643738846756e1ebafd18 +#: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 -#: 187ceabb7fd9480bb8cf0f2da47f65ef +#: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 -#: b548b76bcc85420a9b30792386105139 +#: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 msgid "" "This example demonstrates how to change the name of an input file as part of " "a tool description. This could be useful when you are taking files produced " @@ -198,139 +183,117 @@ msgid "" "names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f -#: 9ce692b78ead47e4b0f8cdae8837d35b +#: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 -#: 6df1201c159343da9e7515379980d6a0 +#: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 msgid "" "This example demonstrates how to change the name of an output file from the " "default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 -#: f9ab1d0dc1c842b6abb5385268c1d3bd +#: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 -#: 9f6a84ab6a9343b6ad7db826f8964362 +#: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb -#: fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 msgid "" "The first method involves adding the folder containing your scripts to the " "`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 -#: 3a871012fcfd4f3ebeca0cb86ec93435 +#: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 -#: d954edfff2584288ac8c600733070d2e +#: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc msgid "" "After that, make the script executable with the command `chmod +x scriptname." "sh`" msgstr "" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 -#: af6b1e37d6be4450a761854480ec9aab +#: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be -#: 31f4a2d43062493ca64c648f80afc8e9 +#: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa msgid "" "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 -#: 41c54e71b6cd4f63b2a619a515240d34 +#: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 -#: 8edc3541ad134ab5a1d23c724f1f0a4e +#: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 msgid "" "The second method involves including an input of `type: File` in the script " "itself:" msgstr "" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 -#: ac0ea81eba8842a18801ab03cbf80a57 +#: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 -#: 52be1a5640234feabe958ff7ade33653 +#: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c -#: c6db734d5aef4f4f99676bdebf9c83c9 +#: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their input " "binding makes use of `self`. Below is an example workaround for this, " "pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 -#: a9f7b47c0dd741739795da39bf114879 +#: ../../src/faq.md:165 60f009e3714c405695da069204b196ea msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 -#: e3fdd9228b924905a4a1f4b2b7ad7159 +#: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 msgid "" "Below is an example showing how to specify different strings to be added to " "a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c -#: 3f7cda1437cc48f18745a827ebb74582 +#: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d -#: 5aeaba2cae64442e816bbd458aee833a +#: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a msgid "" "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" "Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 -#: 5af827a402834978addd82c70be6b5ab +#: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 -#: 6d69e42bd8e443c4b19d80807c7efd6b +#: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 msgid "" "The input must be an array consisting of exactly one entry for each input " "link. If \"merge_nested\" is specified with a single link, the value from " "the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 -#: 404640397b6e40c2a2cd5cf85ab3b1c0 +#: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 -#: 1682c2486e224770b62269709a8663cf +#: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -339,61 +302,51 @@ msgid "" "destination step." msgstr "" -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd -#: 9078fc009bc145808813c9cc2b734b58 +#: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 -#: d4b5a54a400c409cb7984428f6a03ec8 +#: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 -#: 9e8dbee6e8f84d08b1a54fffa06394ef +#: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 msgid "" msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c -#: 1d846bfb5f054d09a4afad1da8e4b642 +#: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 -#: 2d0e95fec8084787b734388d60188574 +#: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 msgid "" "For command line flags that require a specific input as the argument an enum " "type can be declared in CWL. **Specifying null here is known as long form " "style. It does the same thing as the question mark on the other inputs.**" msgstr "" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd -#: eccc4a364330470fa474dcaaa3433390 +#: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 msgid "" msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 -#: e945f6a337af4e4686bed482a4fe6c39 +#: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c -#: 8a3efaa0ad1548428bcfd6e01d135cdc +#: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 -#: cdab644adc5643708870fb08c06cbfca +#: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 -#: 089a5a0b076b44aeaab4d69ee3c79f97 +#: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c msgid "" "To properly set fields in a record input type, you need to pass a dictionary " "to the input to properly set the parameters. This is done by using inline " @@ -402,93 +355,76 @@ msgid "" "be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 -#: 561172559c6f41a68819608fd9e58bb0 +#: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 -#: c5ee4946d2e840abaa3dc796a62652c7 +#: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 -#: 4f2069a2113c414db18eca95550e9e09 +#: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 -#: 31f3390e6771414ba7bf57c044c4b0c4 +#: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c -#: 3b77ce4930ae46d5be9f6965e8c54727 +#: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 -#: 06f36bbe4d3840229b7374f27b86ae80 +#: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a -#: 3cb2f70d00274a4dafd972ccd8c519c2 +#: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a msgid "" "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde -#: 093a1529262043ef84a99675054938e0 +#: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 -#: 45b6d9acbfaa47e5984184f7da554d0a +#: ../../src/faq.md:373 857024702f624885be706c405b7a088e msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 -#: 5705c9bacca5405ca6f14315a5575db8 +#: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 -#: 82bfc285b59a439ca97d3278997f0fce +#: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 -#: 181d5130101d45ccb22aebae3d154c2f +#: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 -#: e864390b5ddb423aaa10e9d33d257dc1 +#: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 -#: fe637c32fb15427a9045679b5da42ec5 +#: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d -#: 1f8004b9df8547029d82e57f9abdc979 +#: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 msgid "" "If it is not possible to change the input identifier, then you can use an " "alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 -#: 70990dc5a0034099921ceb89c89e2dcc +#: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e -#: f679e26f18d9455f945fd13361a9c906 +#: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 msgid "" "The CWL standards are built around (optional) Docker format containers. The " "reference runner and several other CWL implementations support running those " @@ -496,13 +432,11 @@ msgid "" "Singularity format container is not part of the CWL standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 -#: fcd0273dbdd84e728cfd8fbe239f2a01 +#: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 -#: 173ddbd1e7c64927a8dcb12a2a2140f8 +#: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d msgid "" "You can use the --js-console option of cwltool, or " "you can try creating a JavaScript or TypeScript project for your code, and " @@ -513,26 +447,22 @@ msgid "" "dd>" msgstr "" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e -#: 662fe273e2fb4042b688512955e450a1 +#: ../../src/index.md:1 1506b4e7ee014a01bfdb067489501a9e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab -#: a15b52205f0145feaac298510e4d678a +#: ../../src/index.md:3 0ce058b5210d46a0b78eb78dbca07a9f msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 -#: 512aa0c7166b429e8116f71eef007f79 +#: ../../src/index.md:7 3404c064950d453d8af446e8b6554cb6 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 -#: b1b19e17a18540939cb3bb7f8a700cab +#: ../../src/index.md:9 1e239cad669648e48694eaf91284766a msgid "" "If you find that something is missing from this guide, or if you would like " "to provide other feedback, file an Issue on the [project repository for this " @@ -540,13 +470,11 @@ msgid "" "clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f -#: d58b36ac43ac44139897be752fbb1f87 +#: ../../src/index.md:16 9dba2e06f1be4a50b1fabaaf216d02b4 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 -#: 6726cf3585a646a8b4cbeb543cf84a38 +#: ../../src/index.md:18 ba4074bbb69e4096a808001afaf2e0dc msgid "" "If you are a beginner user get started with the [Introduction](/introduction/" "index.md) section. For advanced users the subsections of the [Topics](/" @@ -554,8 +482,7 @@ msgid "" "CWL." msgstr "" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 -#: 2e504aa7c46a426fa959e7254e9a84a5 +#: ../../src/index.md:23 ad34a37bf4ec488bb825a34456f4fe8d msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -563,18 +490,15 @@ msgid "" "and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c -#: e7be0df0838b432d9c7f296d777f120b +#: ../../src/index.md:28 2bd8eb5957ed40f4a72a6b7408044c78 msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 -#: 173e0816db20432c8d9dba1de5393dee +#: ../../src/introduction/basic-concepts.md:1 8bb0df5531474301a185f1ba375320df msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 -#: 30eacc583f6841719e2142d283811d97 +#: ../../src/introduction/basic-concepts.md:3 653373e1f11e4f81ad561378854a71fc msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are expected " @@ -585,21 +509,18 @@ msgid "" "this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 -#: 791b8f38a14147bbaa174c7eb595f17e +#: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf -#: 1a3989dcbb9844b39d84bf6df6b352ed +#: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered in " "this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 -#: db1bbc6e980f404f9f3fcd08e92ee9a3 +#: ../../src/introduction/basic-concepts.md:25 74e92eb0a4e64098b5aaf08d043e0641 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -609,20 +530,17 @@ msgid "" "and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d -#: acc7887c65974114996f700a38a7eccc +#: ../../src/introduction/basic-concepts.md:33 baa40b445f3c409b9a3e10a85fa38bfd msgid "" "The model used for the specification version is called Semantic Versioning. " "See the end of this section to [learn more](#learn-more) about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d -#: d2476d9bcff44f21b8d84a3a0d87a246 +#: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 -#: f86415e4d78e48c4a8a76ced81221b98 +#: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a msgid "" "An implementation of the CWL specification is any software written following " "what is defined in a version of the specification document. However, " @@ -630,26 +548,24 @@ msgid "" "implementations are licensed under both Open Source and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 -#: c5524d73708c4c779980528864506fd4 +#: ../../src/introduction/basic-concepts.md:44 b1c864d6775048cab01eb3de641f6475 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud " "and high performance computing environments where tasks are scheduled in " "parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf -#: ac46a9f8850a434bac5bc2b41ee6294e +#: ../../src/introduction/basic-concepts.md:51 a05d24121e534d65947eb26e4dada5b7 msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 9bba7c4f783942e4a299603430601363 +#: ace0388fd04845e79d31ec99a48a8a3f msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 e2140e0f0e7747ef8383887c20a7945a +#: 70ecd37237e14ae19539f2bf692882ed msgid "" "A process is a computing unit that takes inputs and produces outputs. The " "behavior of a process can be affected by the inputs, requirements, and " @@ -658,39 +574,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f 15bf490724cd46dcbcfab44633c5a9a2 +#: 38121b4b00324bebb6499184b3dcb5c1 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b 51d52d051e654a8395239f88df7c9d8c +#: e0c278f52e824673ac708885d985b7d2 msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 eb496cc818524fa7bae5a22ddd00a19c +#: 6b4d0f0651cc46f5abf195b281967913 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f c4a22d12e7f149ff901d27de32b9361d +#: 88bdc9e046e4487cb0eee3f1d4819e57 msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 7618de899a7043989d77baacf62eb7b2 +#: 12eed3ef7d444585b150bbdab0665bc8 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a 6f1544a220664b79b04bf008058b5a91 +#: dfc85226313d46f9868dc4de53546a69 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 fbd14ac9a2f541478a320ed4cbc69e13 +#: f636b10c47734e589291de95443d8115 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be used " "to simplify workflows and command-line tools, moving common parts of a " @@ -699,7 +615,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef da4dba50d25d4533b3dbb92f54d32a30 +#: bb51025d04444dd5b16000d5d6a3f41a msgid "" "Operation is an abstract process that also takes inputs, produces outputs, " "and can be used in a workflow. But it is a special operation not so commonly " @@ -708,7 +624,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 ce11c9f8d65c4268984d0384d95144cc +#: 93dbaa0aa2c6493ab22a937c6861fac4 msgid "" "The workflow is a process that contains steps. Steps can be other workflows " "(nested workflows), command-line tools, or expression tools. The inputs of a " @@ -717,7 +633,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 3a201aa497e84f70855bb2251e7e3281 +#: fcde5ef65ebf45a3b4b67eec993a1729 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through *requirements*. " @@ -725,23 +641,23 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 b78f7fa2be1c4bb090f6da895457ad1e +#: c8ff34ff5d3b4a508e8c291196d08067 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 f7e95d264ffa4e2db0864faccd9e5a0e +#: fe25f15fc11c49ab827b884d081c3df0 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 3f1e5b01e49a4dc1b1c99936a4589afc +#: 2b93b6219142431ca748a404a56ced5d msgid "" "`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee 03c3048f38ae4938a484cf02001877b3 +#: 0094b13b26014ba3be61769b422802f5 msgid "" "Some CWL runners may provide requirements that are not in the specification. " "For example, GPU requirements are supported in `cwltool` through the " @@ -751,7 +667,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e f9715b5ec65c405c849bb030c1927060 +#: 576a0778d3dd44f68cb241346f441660 msgid "" "Hints are similar to requirements, but while requirements list features that " "are required, hints list optional features. Requirements are explained in " @@ -759,12 +675,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 442662f50e9e4620970ce32b1b127969 +#: 7d98949fe97744158fad81f41d780de9 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 2b34c786af3840e88f29d214e19dc837 +#: fc142b791aa1434aa75b0782248de988 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -777,7 +693,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a dd6aadff8cf54ce78ea6b317afbaddb0 +#: c3fc91ae3bae4e3db60e8271e95135a2 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\", " @@ -786,7 +702,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: 8f097ae5ff6a4be0b7428345362dc55e msgid "" "The benefit of explicitness and isolation are flexibility, portability, and " "scalability; tools and workflows described with CWL can transparently " @@ -795,77 +711,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 d10cf45b3c7f49dc98bc0e5d1246f224 +#: 60c56fa6a67346d6966f0d841213e11b msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 -#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf -#: 332b6e8b831e4bc5aed3745938230a57 ce7fc63b808d4499b9bf9828c2dafe35 -#: ebf339ed376a4d3b89b15b4d5afe593b +#: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 +#: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de 8badec9987ba40609cf1f626172b2b2d +#: 3fcbf810c86f4cf7b8499de88147aa95 msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 c75a8b4bf0e24781bf6713cf6f013cd1 +#: e242228b6b3d440cbca8418050220267 msgid "" "The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 6e01963a01cb49e39692455256679bfc msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 07cca9a33d8f4b77ac6ad35ca8b95655 +#: ed81ea2234b041c79449dcd20f886cb6 msgid "" "The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 31db11c8ddf2423192a8b2063b3e91c2 +#: e8e3996f6a894b4f9cc266b46cb8d756 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b d81dd96143ea444aa78ff45cfa0584b3 +#: 085e4d1a7a9744d2884f3003c64ca174 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 -#: c54984605872472190ae7771809a20db +#: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 -#: 01a237b8ec2f46c9acd31d142591ce75 +#: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that " "are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 -#: 3fb9888b666945eab1e3ff109646c574 +#: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 -#: 5fb0486762354f93853fff209f835c08 +#: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 msgid "" "The software and configurations listed in this section are prerequisites for " "following this user guide. The CWL standards are implemented by many " @@ -875,13 +785,11 @@ msgid "" "(though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 -#: 5f1e7a608e0b455196d191c845a5c98e +#: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf -#: 7ba4b5c51be24f5392949d06ee42e018 +#: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 msgid "" "There are many implementations of the CWL standards. Some are complete CWL " "runners, while others could be plug-ins or extensions to workflow engines. " @@ -889,35 +797,29 @@ msgid "" "md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 -#: e2d3e6dd13b14d819a504c35da6fe8e7 +#: ../../src/introduction/prerequisites.md:19 1df6c63de3914af68f758054fe6955f4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b -#: 91251d1f0efb4d4cb083b4517ff3107a +#: ../../src/introduction/prerequisites.md:21 ceaa3a6bebab45a0907ee0cad01429a2 msgid "" "We recommend using an up-to-date operating system. You can choose any of the " "following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 -#: 6ad263e267514c5fb05794d3d76d418d +#: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf -#: 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 -#: 5195706d9c6c4573aff135fd539759a2 +#: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 -#: 9c4506915e4c40599527bc1d2b18645b +#: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem " "for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " @@ -927,13 +829,11 @@ msgid "" "recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 -#: 37d9eb784ec1425786158f98e3f63890 +#: ../../src/introduction/prerequisites.md:35 051d7cd7d3a94baa865d180afdd71688 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 -#: 572f493a985141a1b92dafbdba92790d +#: ../../src/introduction/prerequisites.md:41 1a93aaf5bd5e4862b15e0636b4478640 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL community. " @@ -941,8 +841,7 @@ msgid "" "in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 -#: 9606d3c4849f4b17b2e55a298210f055 +#: ../../src/introduction/prerequisites.md:46 edd0613118a2493c876652bdcb9e0fbf msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create and " @@ -950,31 +849,26 @@ msgid "" "`cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d -#: 754fc59967d94ffa935284676d55ffed +#: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 -#: 2905c6362d4146e8b35bc74744841972 +#: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` and " "`conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 -#: 091278ece252483a9838fb771de3e04e +#: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b -#: 0928a5c668c3414a945bc9eda147892c +#: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 -#: 56f3c481762848298214a88e559fc0f9 +#: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -985,29 +879,24 @@ msgid "" "command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 -#: 710c266ab4a5477b84d6ea987420fa20 +#: ../../src/introduction/prerequisites.md:79 4473e41281fb4e738e4eb26c2d178934 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 -#: cc353db5da2546bb88a77ce1a202ff9d +#: ../../src/introduction/prerequisites.md:84 548393974d4d4acc91738f9bc13a3a48 msgid "" "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 -#: b62df08ec96f4cdb887600079856dd76 +#: ../../src/introduction/prerequisites.md:86 2ab3963cf9504ec097eda2b14f3448c4 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 -#: 97e02557293440d1a58ba659dad21113 +#: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 -#: 0935c3ff01634c75b5c91546dc36c7b9 +#: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be invoked " @@ -1018,75 +907,63 @@ msgid "" "environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 -#: cfb37fd605164a8d9cc75bf892ce97c0 +#: ../../src/introduction/prerequisites.md:101 b2360ef646854422ad6c0f90fa49306f msgid "" "The CWL community publishes a Python package with the name `cwlref-runner` " "that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 -#: 5f06a7a6aae343d989a5b30979c600f6 +#: ../../src/introduction/prerequisites.md:104 c9fadfa85a2641378e99a462e8e8d940 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 -#: 5f956260f3874b6dbeaf3ad7ecc09c9a +#: ../../src/introduction/prerequisites.md:111 abb8993ede4d4e479d88d2e848546f68 msgid "" "Now you can validate and run your workflow with the `cwl-runner` executable, " "which will invoke `cwltool`. You should have the same results and output as " "in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 -#: d35e4effec554a638d6c3047ef3fd05f +#: ../../src/introduction/prerequisites.md:115 ba0f7606e6174e53a8bf23c1ccd99250 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 -#: 15a1f944a0d642729d3736ed1c907074 +#: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 -#: fa34c808bb494ddfa3f3926bc42e650c +#: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For " "that, the first thing you need to do is copy `true.cwl` workflow into a new " "file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a -#: 0c15f62eb7534e809f625f3fa213e92d +#: ../../src/introduction/prerequisites.md:129 d989516c873f4446bba005f42796b8b9 msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 -#: d67719a6f0ce4ba1bb6152a10507b729 +#: ../../src/introduction/prerequisites.md:135 e9d8610478094a98b5b5a0f568a315de msgid "" "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 -#: 1c96e75281844bfab0578bab2e816854 +#: ../../src/introduction/prerequisites.md:137 d6d8131f91b740189e56ab9d90bee55a msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 -#: bece1fc3c3f842b0b30d8f1b7fbfc200 +#: ../../src/introduction/prerequisites.md:144 def7400a00e84070a4bd80c2367d3bde msgid "" "And finally, you can execute it directly in the command-line. On execution, " "the program specified in the shebang (`cwl-runner`) will be used to execute " "the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f -#: a7caa36b0f83448b91ef2e76e30abc51 +#: ../../src/introduction/prerequisites.md:148 564e7be94d254e52a6c44b234d6ddc63 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 -#: 39321e93e9994fcca20b425aa45c2894 +#: ../../src/introduction/prerequisites.md:154 bb5fe42ddd814ad4ac1071c0b18f24c2 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute the " @@ -1096,55 +973,47 @@ msgid "" "`` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 -#: 601cf500d76c4e0287af4429a46b36d2 +#: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed -#: b286d5359e184ef58054c72df4014629 +#: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 -#: e14423edd829401faed0950772123240 +#: ../../src/introduction/prerequisites.md:167 28d33daee6e246c8a6d1382208e19c39 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting " "and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 -#: 889c44360bd54a0e85e7f0e61aa6593c +#: ../../src/introduction/prerequisites.md:171 b071d7c87b7a4817b871085a652cd580 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 -#: 7b9bff73624947ac90a99c7880e2e911 +#: ../../src/introduction/prerequisites.md:172 97658a1b16874ba8b0bb748242d0da64 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 -#: c5ff687c86ef4ccaae25d8bcfbd5f873 +#: ../../src/introduction/prerequisites.md:174 6198aa6769b74ef0a2a1ba539789f3ee msgid "" "The CWL community also maintains a list of editors and viewers: " msgstr "" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 -#: 0a610a9632064deb824afd0719429d3a +#: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c -#: ec0c47438a5242cb99dffa7a4997e95a +#: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1152,8 +1021,7 @@ msgid "" "com/>." msgstr "" -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c -#: aae94ac2114641f186eac0f4117223eb +#: ../../src/introduction/prerequisites.md:185 2db34e925a81422986ccb868463a7a42 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1161,67 +1029,57 @@ msgid "" "and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 -#: 209e072724ed4d27b37e9bff6d55d811 +#: ../../src/introduction/prerequisites.md:191 d677fb155b0343ba8771398cca967fed msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for pulling " "images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 -#: 3bf47876e3694e6cadb05123326459cb +#: ../../src/introduction/prerequisites.md:198 22ed0b55de38408393af4a8309a995ea msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the next " "section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 -#: 459a65b8e67c4a9aaa03138c1abe94ad +#: ../../src/introduction/prerequisites.md:199 5ded73cae5db40ad840c3022e7cd447f msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 -#: 898eb29ac7714c69840b795633953a05 +#: ../../src/introduction/quick-start.md:1 23e5613df7c94e5f938c85b14f5441e4 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a -#: 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: ../../src/introduction/quick-start.md:3 3b425afc63d841d4be57c92b25b4ed2d msgid "" "This section will show you a brief overview of what CWL is, and where you " "can learn more about it. No previous knowledge of CWL is required, but you " "must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee -#: 32dd2e28cf0f40b6930750f0162355eb +#: ../../src/introduction/quick-start.md:7 75a26c48d3e04e24abb96d81cb31c94e msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 -#: 471c47d311074ecfac071b6d52d9cfb6 +#: ../../src/introduction/quick-start.md:12 88b4ecd45ea44dd4befe3ce89b30f6c2 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " "example below shows a simple CWL “Hello World” workflow annotated with " "comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb -#: 5078140028ea4d04973cb9cd20f0607e +#: ../../src/introduction/quick-start.md:16 e1789ef78bd64332a18d8601094a0f72 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 -#: ab127d4ba0a44526ab129587a8160923 +#: ../../src/introduction/quick-start.md:22 196ceef96c27434eb4b0b7222c2fe73c msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the " "same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 -#: d5cc6b4295a74f3586f022b0227759b3 +#: ../../src/introduction/quick-start.md:27 e6a44130c6b44d5bb6451a147f28dd8c msgid "" "In CWL, there is a distinction between a command-line tool and a workflow. " "But for the sake of simplicity, we are using the term “workflow” here. You " @@ -1229,13 +1087,11 @@ msgid "" "section." msgstr "" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 -#: 585a4fe583ce44e180a062742b3b0849 +#: ../../src/introduction/quick-start.md:32 340b46acc7a34b7b978f5a734f529553 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 -#: 0d81b0c9ea58420789d1d71cca32ce88 +#: ../../src/introduction/quick-start.md:34 139e48dcf0474fea932ca07a0001d208 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the CWL " "*Reference Runner* for the specification, and it is compliant with the " @@ -1243,13 +1099,11 @@ msgid "" "`cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 -#: ea4ab0782d8049d8b1b89cea4ae60048 +#: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 -#: f6f3b7453a254f828bd4c9e9fef92bed +#: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea msgid "" "If installing the cwltool using the pip command doesn't work for you, the " "[prerequisites](prerequisites.md) section contains other ways to install " @@ -1257,38 +1111,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 -#: 3bf9050175d4444ebbbabe219412574f +#: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe -#: e03f72a14dcf4bf38ce8232598ca761d +#: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " "workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 -#: 3dcfb2facd324dccb3084c02487625dc +#: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 -#: b8531da183964b02bca19f818ec076d4 +#: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 -#: 7ba1ddebeb2843179fe99fc410b193c6 +#: ../../src/introduction/quick-start.md:65 961a385b340141e980aa4f8791fa2f12 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 -#: a6dc303e9d284b60bf1102212505ca27 +#: ../../src/introduction/quick-start.md:70 c48cd1be543d4ccbab964b28c2e08584 msgid "" "Another way of passing values to your workflow input parameters is via an " "*Inputs Object*. This is a file containing the input fields with their " @@ -1296,25 +1144,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 -#: 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c -#: 6d1d6f42ada2418ba0a1de1371825b9f +#: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 -#: 1cd924fe8ace4a82ad8701f37b5e7d84 +#: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 -#: aa297c52cd964291a47bb91c0135156b +#: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but it " @@ -1322,54 +1166,46 @@ msgid "" "Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 -#: 28b02c90397745bfbacc03c3b1034939 +#: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 -#: ef2a4f39f01049b891868b84d968c0dd +#: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f msgid "" "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 -#: 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 -#: 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 msgid "" "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" "Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b -#: 46f6f8d050ce4f8c897056167d9707a7 +#: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 msgid "" "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." "org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff -#: 5ee00ee409b746dc951ca1d4c360e624 +#: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 msgid "" "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." "replace('VERSION', cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b -#: d4af972281174b8999eab55ee0ab1a0e +#: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 msgid "" "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" "Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d -#: 80401cfffae042ab9ec4b3754af04b25 +#: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. The information on this page has been migrated to the [FAQ](/faq." @@ -1377,19 +1213,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 32f86f911ebe4a4c94975f81742333f3 +#: 3821c2d16b254672a494522e47386cb0 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: 412a05f3492349a7bd26ea0c30e9bd80 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf c53ceee943ad4acea779e072b9137889 +#: 1232f6c81da141cb8482294eee5955dc msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files in " @@ -1399,55 +1235,52 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c 7dfe9dffbf5744299bf232599644c7f6 +#: 485bb71673144e3f90f05b420b7079ac msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 +#: 5d48d9a2e977431f9a3625abaa466f5f msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 1f3c23a4769043ca985b8ddfed19391d +#: fcc1151a2e8b4a84b8595c7f913781a1 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb f81b43c7cb194a1cad8672129223c833 +#: 4a291c7ac7c84257b7402567d8364a36 msgid "" "And now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a a20073a8f5374eb1bc8531ff33e622b6 +#: 3b1ae26038fd498ca0ae23aa70a35d3f msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 d08869beca3a4774baf1097b63e79474 +#: 40388ebefb6947089c4a0f6d5d6e92e8 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" -"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." -"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " -"specification for details." +"designated output directory. Other parameters include `$(runtime.tmpdir)`, " +"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " +"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " +"the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 -#: 109b773789024b2b9c063a6169c6169f +#: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 -#: 959fa04f88e54d42b9b774cc95d85ee0 +#: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d msgid "" "The following are a set of recommended good practices to keep in mind when " "writing a Common Workflow Language description for a tool or workflow. These " @@ -1455,15 +1288,13 @@ msgid "" "although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 -#: 64674980c3f24c45bbfbf3f957dda55e +#: ../../src/topics/best-practices.md:8 935500b0e6e249eba585644cddbd0253 msgid "" "No `type: string` parameters for names of input or reference files/" "directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 -#: 90f2e4265919446a902e17627f4420e2 +#: ../../src/topics/best-practices.md:11 96f924d6e02f4005b35d463e49be2982 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that " @@ -1478,8 +1309,7 @@ msgid "" "anyone, e.g. [Apache 2.0][apache-license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f -#: 6b5f91a749fd44b5acfd6071c9913342 +#: ../../src/topics/best-practices.md:20 25e0a5c93ccc49bc8b6206c7c2e3de5c msgid "" "If possible, the license should be specified with its corresponding [SPDX " "identifier][spdx]. Construct the metadata field for the license by providing " @@ -1489,50 +1319,43 @@ msgid "" "provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc -#: 5fe2962837b14f0e9989063be4a506c3 +#: ../../src/topics/best-practices.md:26 34ad53bc5a40446daa0dac4571600d1e msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 -#: 4e1bdea962ed4618884cb9d1d59d7509 +#: ../../src/topics/best-practices.md:28 4c397ffd2e9148e39bdd614683a98a78 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 -#: 37eff4ca02e843259f6ffa38e4a87a04 +#: ../../src/topics/best-practices.md:37 1ed7f7e73afb4bd2ad2e29b65d020ff1 msgid "" "For more examples of providing metadata within CWL descriptions, see [the " "Metadata and Authorship section of this User Guide](../topics/metadata-and-" "authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 -#: ae47231c203d40a98c10045038ea9b65 +#: ../../src/topics/best-practices.md:40 13b058dfa3cd4bbea54ae7d5a56c4c50 msgid "" "Include [attribution information][license-example] for the author(s) of the " "CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" "[orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 -#: 018a6d5dbf1044559b365c7b9017eb3f +#: ../../src/topics/best-practices.md:44 69369b917c1a45199343266650b1b220 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 -#: e073d8f990c44b09a73d642cfe49bebd +#: ../../src/topics/best-practices.md:47 0245a61fd2ef4fb69cbb8d732086fb8f msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" "identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb -#: e04fae88d9b64493ac69eaee24585098 +#: ../../src/topics/best-practices.md:50 e9a56e3634a042279cae1745b7820658 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1540,70 +1363,61 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 -#: b26b9c9b1c4346a297a31c9721f0172a +#: ../../src/topics/best-practices.md:55 8a180861a66c4aaa9e8fdefd929ed829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 -#: b50500c3c3f54b16a535a16175a44653 +#: ../../src/topics/best-practices.md:58 00f333a383b64578b32c687b42924a77 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" -"$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. " +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " +"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. " "[Full IANA media type list][iana-types] (also known as MIME types). For non-" "bioinformatics tools, use or build an appropriate ontology/controlled " "vocabulary in the same way. Please edit this page to let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a -#: 623f3a804199449bb85e23e00c8bb507 +#: ../../src/topics/best-practices.md:66 6b960d362bb540299f0560c14c5f2d8c msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c -#: effea0b1356447c0899ca0746667ea31 +#: ../../src/topics/best-practices.md:69 9cf9342bf0864e87b495913d8e06d021 msgid "" "Each `CommandLineTool` description should focus on a single operation only, " "even if the (sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 -#: 00e8ef87864c4ca2b2c1c0548b02b38d +#: ../../src/topics/best-practices.md:73 587b048324e447cb85844d8c64ae9a1e msgid "" "Custom types should be defined with one external YAML per type definition " "for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 -#: 6e6f48d70b894a6c959ca30fe6bad772 +#: ../../src/topics/best-practices.md:76 d8df6bbd5d324f7c9f48edb33e113b75 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae -#: 02fe08760a4a4ab49e96f4e51316a81d +#: ../../src/topics/best-practices.md:78 2235174088ad48a89d4fc21223e627b7 msgid "" "If useful, include a top-level `doc` as well. This should provide a longer, " "more detailed description than was provided in the top-level `label` (see " "above)." msgstr "" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 -#: 172ed7915a654964ba63f860b2d65330 +#: ../../src/topics/best-practices.md:82 a0f0953a1a9f40cebd4dbe028784ff96 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list of " "valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a -#: 4d0a2871a7484e21b3c39c4dbaaa63fc +#: ../../src/topics/best-practices.md:85 0ec380c683534892b6b8b8fcea84f765 msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. One " "common example: manipulating `File` names and paths? Consider whether one of " @@ -1611,36 +1425,31 @@ msgid "" "`nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 -#: 1eea9f1e284447718141f5417b6bb433 +#: ../../src/topics/best-practices.md:90 65f23741db4e4a6abda8e5f7e036753a msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 -#: 509411d353fe4314b087b81b09ea960b +#: ../../src/topics/best-practices.md:93 34c2caee8eb84e01a37033b67eb4aaba msgid "" "Complex workflows with individual components which can be abstracted should " "utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " "workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 -#: a54bc80bf08243bba67d98dd682ee134 +#: ../../src/topics/best-practices.md:97 d7c7484b2f1048aea9802400410f0858 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics " "software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 -#: 69ecdaea24ef42eebef9d86e5d716b11 +#: ../../src/topics/command-line-tool.md:1 a905abc2eead4dbaa035235936025499 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 -#: 3cc5847468d1478bb5589dee68147189 +#: ../../src/topics/command-line-tool.md:3 eb91b6dab34d4d5f9854ac580a6cbde2 msgid "" "A command-line tool is a type of Process object that can be run by itself or " "as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " @@ -1648,59 +1457,52 @@ msgid "" "command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab -#: 98c6bc409420485095ae65d6b0b9a3a0 +#: ../../src/topics/command-line-tool.md:8 7caeb91564634091a932f1270c4f5ef9 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The following " "example contains a minimal example of a CWL command-line tool for the `echo` " "Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 -#: ebe23e5378514f888a9ec32a2adb1e98 +#: ../../src/topics/command-line-tool.md:19 c6ac4a60d102407991f40b892fb60560 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 -#: 387cfe85604f424f8d31c4a4c9c15edb +#: ../../src/topics/command-line-tool.md:50 51d3ce421db345f5ab19e02fbbc51df2 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d -#: 7b1d65754e854693bb60289c97d3fb5d +#: ../../src/topics/command-line-tool.md:57 8311d1430e624435b7b04bf2574a90c5 msgid "" "The example above uses a simplified form to define inputs and outputs. You " "will learn more about in the [Inputs](../topics/inputs.md) and in the " "[Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e -#: f440cef729c8410281432307a4da8d55 +#: ../../src/topics/command-line-tool.md:68 d1c03e5f19d64ea89276d126de6e4bda msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 -#: 4fbb8ceb1b59480583ac611142167049 +#: ../../src/topics/command-line-tool.md:69 8494b43e98dd424db7d57aa1d731f7b4 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network access. " "If a command-line tool is written manually in CWL v1.1+, there is a need to " "specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e -#: b87869204838415bbf694214e3680593 +#: ../../src/topics/command-line-tool.md:83 8c4573fb120149269a0fe3a1ba6c9ef8 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " "Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b 12cf5f2264504c44a2173e858bb2c283 +#: e1c709ac0fb249928d14aeced6551ae0 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d 7694f9cabfe04308bbddd2c88ae6d9b9 +#: c26c9c640e0747c8b2c2977c860c9d82 msgid "" "Sometimes you need to create a file on the fly from input parameters, such " "as tools that expect to read their input configuration from a file rather " @@ -1708,17 +1510,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff b557dc4f8ef549b98f59412a918643de +#: edbe918d7df14cafb440e171e46c6de3 msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 3011eb003c084285b30cfa56a8da45b6 +#: 6d457d9b4ae746d384e65d9a37ca3591 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: 868394c1b8374ee6bbd43463e73d7edc msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the value " @@ -1726,7 +1528,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 ce78b2d147054da895beba66d0ecdab4 +#: 08a9e08cba674db09c9bfbef37e9579f msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later " "during command line tool invocation. That means that any genuine need for " @@ -1736,7 +1538,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa a973846ec5a946eeaff02c5b00997da9 +#: 6f6f437753dd4eddae0b2ea62046fe39 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1744,14 +1546,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 294fd83a97a64249bac38f7482159372 -#: 9e8eb1542db640ff9e300649ce50dc9d ccec7f73b9d948e79a6cdf32bc124092 +#: 096b17907bc3452d9927ef2fb6f5c11f 78ed5d8fb9bd4e068023d2c717e20f62 +#: c3a2e9e6b4414597a17db6d55d98e9d1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d 22948f19cb78485f8f86244686a35c09 +#: ac783e6415a44cb59d4b425bac5087b7 msgid "" "Before we run this, let us look at each step in a little more detail. The " "base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1759,7 +1560,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c 001d9579bfce438e865377fb9c2df776 +#: b9e6e15b541149c6a2d3922c11405267 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " "array, we need a `-` on the first line of each element of the array, in this " @@ -1771,7 +1572,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 e62618db8995428bb3f260e03ac8f459 +#: 87088899567a4402aeb34605d3c6b06b msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1781,23 +1582,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f -#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 457756c4e9544f068af897113358cc89 -#: 6d5ae75431424ea788c3440606f22940 98e0548845fa447fb05a29c9fc2f17b5 -#: de5e8aad4e3046bf9bfc2ad8ccba17d0 e9801b2142cd45368a73ef9b121c1d08 +#: 304c1bfe5ecd4d26b5dfaf9ad2e2c7f8 3ef7f0e3099147d78fd2d30bfa73cc6b +#: 4fef79a30282456eb9b5dd34a5eec0b1 afe775762ed348e5982b99bcf1451606 +#: f0689cd0e5b34414b6693331186ee4a3 msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 -#: ee2bca9bdbb74b60a706c3118d6a17ba +#: ../../src/topics/custom-types.md:1 9f1967411aa7497fa43a4851f0645d6e msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a -#: e63ae9694f40438d872d141ae824a42d +#: ../../src/topics/custom-types.md:3 90bd62e4ef8b41e398a5c9b31f132774 msgid "" "Sometimes you may want to write your own custom types for use and reuse in " "CWL descriptions. Use of such custom types can reduce redundancy between " @@ -1806,25 +1603,21 @@ msgid "" "to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc -#: 750fdd4c270e46a09f79e867358f7414 +#: ../../src/topics/custom-types.md:9 3465527b8ff4407587f7c46fa9fa2a98 msgid "" "The example below is a CWL description of the [biom convert format][biom] " "tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 -#: b3f688cc82444ef7a7a0aa63dac39cac +#: ../../src/topics/custom-types.md:12 c0cc869690804ada96a5c1813d17b895 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c -#: 3638be18b4f64cf08053d512e590dda3 +#: ../../src/topics/custom-types.md:18 01f369931c8142c08fe821a0ca31bf92 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 -#: 7d5b9c21739c48f18c13614ca6967f6b +#: ../../src/topics/custom-types.md:24 0b3ff704cdea44e28aee3c704ca98e27 msgid "" "___Note:___ To follow the example below, you need to [download the example " "input file](https://github.com/common-workflow-language/user_guide/blob/main/" @@ -1832,15 +1625,13 @@ msgid "" "*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea -#: 8fea29993f944d8d8d3181afa29bd0a6 +#: ../../src/topics/custom-types.md:30 cb456bcae0dd41ffbc514eeea283e130 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to be " "used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e -#: 02d0b648d70f49d7892f690be06df585 +#: ../../src/topics/custom-types.md:46 c610173365d04c57900b22f4024b47b4 msgid "" "The reference to a custom type is a combination of the name of the file in " "which the object is defined (`biom-convert-table.yaml`) and the name of the " @@ -1851,27 +1642,23 @@ msgid "" "hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e -#: 0743bef42b9a42328849c8c2f9da9eed +#: ../../src/topics/custom-types.md:53 c2b2e18d55c94721812431583cfc4725 msgid "" "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 -#: 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: ../../src/topics/custom-types.md:55 3e61c3920a7a45db8917c348bd44384d msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 -#: be848f30769543eb9c0be55263e3f758 +#: ../../src/topics/custom-types.md:61 cd87d210b03c4da2a7608b40a6bbcca0 msgid "" "In order for the custom type to be used in the CWL description, it must be " "imported. Imports are described in `requirements:SchemaDefRequirement`, as " "below in the example `custom-types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c -#: cbff44a64ba4432cb59a82f82c2f0103 +#: ../../src/topics/custom-types.md:76 7af9ba3219e44ed49b8da781db5d6fb5 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number of " @@ -1881,31 +1668,26 @@ msgid "" "this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 -#: 617f1c0084cf42d9be4c7a8fa5a48432 +#: ../../src/topics/environment-variables.md:1 eae1994f3a4d481b863b5125c7f4a383 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 -#: cee79afa3c6f43c29ef05e06b7843d35 +#: ../../src/topics/environment-variables.md:3 8bd8c06d416740b69d126eb9f5f24ad3 msgid "" "Tools run in a restricted environment and do not inherit most environment " "variables from the parent process. You can set environment variables for " "the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 -#: 225903b11efa417989df42de86ad2451 +#: ../../src/topics/environment-variables.md:7 11c6bffc620b4c789b29ab4034a8bfbd msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 -#: 1a5f058290064c1cad05e63eb127fcbb +#: ../../src/topics/expression-tool.md:1 89888b1b994546ce8a93f9630b4bb07e msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 -#: 74ad8d69cf294ae880dbbe28e25b3545 +#: ../../src/topics/expression-tool.md:3 191d3010b9244b39bc3bc50246ac7ad7 msgid "" "An expression tool is a type of Process that can be run by itself or as a " "Workflow step. It executes a pure JavaScript expression. It is meant to be " @@ -1913,38 +1695,32 @@ msgid "" "on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 -#: 5293e8ee9b3b4f59947cfc164ef111c4 +#: ../../src/topics/expression-tool.md:8 3437ed6e184748e4af1ef62f32c8cef1 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe -#: ffa1955c759942c68e7589429e5ea86b +#: ../../src/topics/expression-tool.md:17 c3ae1ef318bb4e0fada76c353dd5f6f1 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 -#: 038bc0ba5f6a405a8255a7be76979baf +#: ../../src/topics/expression-tool.md:48 a7f5e04d242c48a7b3deffb5ff6528be msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a -#: fae1c63de02e48c0969a98e4c49b2e06 +#: ../../src/topics/expression-tool.md:67 32b6841faed044409bc618cba54a22f0 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains a " "JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 -#: 7093a94695524851a5463193f0701b78 +#: ../../src/topics/expressions.md:1 6821ba7a84a44d309d245c429948ad09 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 -#: dc8274ecb15948c29a31db89b12a58bd +#: ../../src/topics/expressions.md:3 8167269bc3a64c72bd6c909362350a15 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1952,8 +1728,7 @@ msgid "" "CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 -#: cec8eef8a5aa49778ecedd4195ab9f2c +#: ../../src/topics/expressions.md:9 c0f75603a6024063a6911f17c70908cc msgid "" "JavaScript expressions should only be used when absolutely necessary. When " "manipulating file names, extensions, paths etc, consider whether one of the " @@ -1962,79 +1737,67 @@ msgid "" "practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 -#: df100967597043c78112bf43b520cfab +#: ../../src/topics/expressions.md:16 7faec63b389a4c07b6929b7a78f0cc70 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 -#: 59ccf4daba39406581a6bc2d9bb1b7d2 +#: ../../src/topics/expressions.md:22 d7dca89942f949d58cb18cb94bb7de72 msgid "" "As this tool does not require any `inputs` we can run it with an (almost) " "empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 -#: 570cc75699dd4e0a987fc9aca9a01ee4 +#: ../../src/topics/expressions.md:25 1abc1a21c0764415b138099e0e21432b msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 -#: 9e123723048546d495ed5110d7177708 +#: ../../src/topics/expressions.md:31 b8b5a50a82e44e49a37c6396f1ff9464 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object is " "represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d -#: 26543894f6e04270b89ab702451bcc89 +#: ../../src/topics/expressions.md:35 b38d66c12ab74dfc9395e69d9c04bbf5 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc -#: f403c1d4e43a4aa0aef8488d2b5a6262 +#: ../../src/topics/expressions.md:37 8417aa7a9d034361a41def6b71e93413 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 -#: 249dffb569a944c897ce5862e5f28fad +#: ../../src/topics/expressions.md:47 c1f672b377da4605b9c5098ebb6e1147 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 -#: 1641c96aca2f4923885fe8a509eb3a49 +#: ../../src/topics/expressions.md:54 af52f5197e8545d2be22cc0f7f03648c msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " "describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 -#: bc63405a0d964df2bd9493996abc48fe +#: ../../src/topics/expressions.md:62 5e12ce15018942bf9010ce6519c17b00 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 -#: 5c191d1420db4e26aca31c1b1e34cb75 +#: ../../src/topics/expressions.md:64 e2e9c5f7b681427a9589476649e5a9d8 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c -#: d6a5c65e824a4bbc94578df9597d4716 +#: ../../src/topics/expressions.md:66 8a74763ead0147bbaf3892e552fad546 msgid "" "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: ../../src/topics/parameter-references.md:64 0aab7de8d69f49438d4eeed17316df68 +#: 75f90cb870d14d0dbb4c4ee80d32a65e msgid "`arguments`" msgstr "" @@ -2042,39 +1805,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e -#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 -#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 05c34a5a2e404a14b9d284a9d0c73bd3 -#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 -#: e7f1993580f0425098a719e83a64cc7f +#: ../../src/topics/parameter-references.md:86 0b9d8268c177489b86b8eaa638dfa063 +#: 204cd6d8375a4462a8247863a96df906 2b7e56ceb4ad49a8b29a58b10bad7c0a +#: 81f15c64379941d8ac2a681b3879761c f11ae7d801db45989b598864dc6291c9 +#: fc4534b475334f7281d1740c9a78f640 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: ../../src/topics/parameter-references.md:66 70e9085b21f640d6893309a3375c0511 +#: f529003dd7a64bc7be0ccef8dbfa84b3 msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 3f29e4a3087847e9af6f19166a8def9a -#: 92697d3179ec48898eaea9aba3c24dcd +#: ../../src/topics/parameter-references.md:67 3fceb522ba6245129b826c342eaf31b4 +#: a5f71add5b8345a4bfa02853ef8a6d35 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 c0eaef93bc3743279549bcfb8b014ca3 -#: d6722e3093884ad7b62696fbb2f48fdc +#: ../../src/topics/parameter-references.md:68 018300196ea24550988a0156894b5e85 +#: 2c799286e8204ed9a83c3fc006988139 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e -#: 37c493fdc2f0410a9748f8faf09ce5b5 +#: ../../src/topics/expressions.md:72 25d91d6624bd42e7948e29c684e8e441 msgid "" "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" @@ -2085,15 +1841,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc -#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd -#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 -#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 -#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef -#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c +#: ../../src/topics/parameter-references.md:90 0944d6525c3c460aa4b5a0e72552ca4d +#: 1187b0d330cb470fbea82a8b8c95aa28 265602307ccd42458ba47ac1b689242c +#: 2febce1b1ad74b18af3a9b3fa137c780 3215ee41f96541cbbda60a1167386c2f +#: 80efeab6ec0e447bbe158cbaa57f83d8 8d2bbd91b4ab4faa923fc1a14ec49dd5 +#: b4a6e640275b4fc7a18e3083e86b72a1 msgid "`format`" msgstr "" @@ -2102,62 +1854,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 -#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d -#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f -#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 662b36e3505f4ac3bb5070bb6e055217 -#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c -#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b -#: f71216a4b35e4157aece5ffa2602d8bf +#: ../../src/topics/parameter-references.md:91 480b2e4207574b27b8d33dfe5e9ab64e +#: 4b4149a3b97a4de5b2d7fd84bd547ffe 7af1a82df41e40d0a430babafe1bc5e2 +#: be01787b66e34074af32bb45dcce8657 be099ab533504a7596fd56ec1ce7ca5d +#: c8b96271665444608f601a460dd28fb3 cb6dfa7bc68b41929a5247d929c2f94a +#: f7f452e92f6d4a14ba3912c62699019a msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac -#: a3c775a0f04b4541a9b712bfe2e4e69a +#: ../../src/topics/expressions.md:75 4811c1b9867b44caa70dec4b91970484 msgid "" "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 -#: ef16c4a9a7ea415fa399297b63b9710c +#: ../../src/topics/expressions.md:77 0b1f2a8986e0419a90e484d3a945a037 msgid "" "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 -#: 2592e429c74c4ff5b8ba68a36f060c1a +#: ../../src/topics/expressions.md:80 dbc02876870d49d2b9e39db4133a0f62 msgid "" "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: ../../src/topics/parameter-references.md:78 97339a3fa43849f7b292f4643b5fe35c +#: da8b81b1e1884406a188fb04825ef90e msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: ../../src/topics/parameter-references.md:79 077e7b0d2dde443699050af8c63ab912 +#: c8cbe3dfd0984221ae72012ea26edc6f msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: ../../src/topics/parameter-references.md:80 3f07f4a8594640c2b2da4da521872b59 +#: 573f7e4b72ec4c47ab2e54e2c4877d9c msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 -#: f09e7371708b4c0685eef2a314791ccd +#: ../../src/topics/expressions.md:84 f03011b3479b47c690604c508d95c263 msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" @@ -2165,108 +1906,93 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: ../../src/topics/parameter-references.md:84 1ec3f913909b4e04bb602767d23bd85d +#: 2f7130500b8c450fa4af226b18e38407 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 -#: 6c37a1ff939748bf83a86c07c3d017fe +#: ../../src/topics/expressions.md:88 a5849a856a374cda807ecf48034af915 msgid "" "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: ../../src/topics/parameter-references.md:87 bd8bbd60aaff4e7aacec91bcbad500f4 +#: f0c99004211e4adf8c0b524d5bbcc12b msgid "" "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." "html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: ../../src/topics/parameter-references.md:88 96c544cf213245cfb3d1f5196223c6cc +#: c6a04d4f3ef24104b0a86f9093935c13 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 -#: 58a1773b1cf546d7890010fdebd47388 +#: ../../src/topics/expressions.md:92 946e0437a48b4d5da2a29d489250cbaa msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](https://www." "commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f -#: 230f3227ed1144f7abe0f8c231bebbd5 +#: ../../src/topics/expressions.md:95 1f287ebf87ae4e93bd1ac65cc1d01bf4 msgid "" "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 5c77dc9f8afe4dd88933943030e836f2 -#: c9534670f5f04769aa3749c3778eb705 +#: ../../src/topics/parameter-references.md:93 0d0f4f0e12174d588c131afef70efc5f +#: a74e0e3499d644b4a9d999d3555f03de msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: ../../src/topics/parameter-references.md:94 b2e31c38f7cb4ecabd6b9b89ef051c0e +#: ddc9d9ae72a64a76a2a8e2bba22584ee msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: ../../src/topics/parameter-references.md:95 12f86817dfc14f2bb39509886d56017f +#: 8a94f2c3b1674162a268f67935a3025b msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 266dfb5fe6a842078baf66073cac9623 -#: fe3b9fb45e01490498c5a35c012b3de8 +#: ../../src/topics/parameter-references.md:96 a800acfefb3f433fae2cdda9ac4a795a +#: bcb58fc2447a4472b86913871b8c12ee msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: ../../src/topics/parameter-references.md:97 5be337d412ba4d48877e991d535e810c +#: e6cf2f8498db4f549193be20d87e16f9 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: ../../src/topics/parameter-references.md:98 3bc61c8197664f12a98d1ac38b421b38 +#: 9973a87f747445ad89ce959420cac5fd msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 09120baec1464afb8aed4edd773bf509 -#: fec70bb106ad4d95a2d55ebdcf711afc +#: ../../src/topics/parameter-references.md:99 0f5dc4f5a4c64f818e2e22f20472ae84 +#: 2ec9d1f191f44686b1cb8622336d6b92 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 -#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 +#: 5382ff97ad2f419dbe1bed266997aa84 74406f77013443f28d4d6306c54b0df1 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 -#: 1dc4148caef748428a7d13caff37b1b1 +#: ../../src/topics/expressions.md:104 f594a20dc038457e815dc17bae6e031d msgid "" "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" @@ -2274,39 +2000,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 -#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 +#: 5814f96ee4ec4822aecad33c8eda0473 c46c44268b2a4b96b1df13e53e82e54c msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce -#: 947b1ca132a54ed39745cd12ebcd65e1 +#: ../../src/topics/expressions.md:106 b9824103ef8745bab30b65887c82f62f msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b -#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 +#: 28b23f84c64549e7a0fe444ccc3e1b05 fdd5d742a6764e5db2281ed844bf3475 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 -#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 +#: b6123c911c804f3c8cb596d2aa495b2b d81a7d8b7db444409b286e5f1d863968 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 -#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 +#: eb6255a0f8d748588d87e7ad38e507bd fffc5a80bd68495396d32b7a1821eb4e msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 -#: 5fa512d352d945e7a3e0d59b0987cd1b +#: ../../src/topics/expressions.md:110 b00a8a2a572742e0929470550433e929 msgid "" "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" @@ -2314,27 +2034,23 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 -#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c +#: 9b34c95e483e47f3828e79bf929a23b4 c968eebaf0114b23b789e9ce68e7588d msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 -#: 81e91df082834d2cab7ef1f62d8ba57a +#: ../../src/topics/expressions.md:116 7c8fb996d1af4cfdb0d49d8ed2696745 msgid "" "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 -#: e6bfd1dc2e324992b6c3332c11ae3445 +#: ../../src/topics/expressions.md:118 75a29e9ff2cf4b5bb6afa87a741a111b msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib` " "attribute that allows users to load external JavaScript files, or to provide " "inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d -#: acf10261df2944ec890d754fd56c6b28 +#: ../../src/topics/expressions.md:122 5233d8baa8b74391bf8fee5ae2324234 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2342,8 +2058,7 @@ msgid "" "the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b -#: bda6b8f398554b0c946c2c7d96308a42 +#: ../../src/topics/expressions.md:128 343e8b78a1f94b8cbafac05212e5a333 msgid "" "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." "org/v1.0/CommandLineTool.html#Expressions) that the only version of " @@ -2352,63 +2067,53 @@ msgid "" "in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c -#: 454c02c3918647039c90ae387005dea6 +#: ../../src/topics/expressions.md:135 0657ee8f03d8462ca6ca6fc538386b0d msgid "" "For example, we can use `InlineJavascriptRequirement` and write a JavaScript " "function inline in `expressionLib`. That function can then be used in other " "parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e -#: e1fad28bf9cb4c4c85eb74dd520ba107 +#: ../../src/topics/expressions.md:139 e3c593cf50da426f8d9df215c7db0bc9 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 -#: 9835d0b399b84a0084fe5a4d9e7e6405 +#: ../../src/topics/expressions.md:146 b971e53c3ed847f1b7c7a6d50e344baf msgid "" "Running this CWL workflow will invoke the JavaScript function and result in " "the `echo` command printing the input message with capital initial letters:" msgstr "" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 -#: 410ba7a5ac6349a98460c6337ee5c4fb +#: ../../src/topics/expressions.md:149 d2315d46369f4e9d9c871d7f88f7006e msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 -#: d2daf50d7f3d4de18331c8fd2c8a5786 +#: ../../src/topics/expressions.md:155 04fdaa45a7ed47d5830181611bda924e msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db -#: 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ../../src/topics/expressions.md:158 8d7686f62f314d98aae8c262befd5283 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 -#: f0ff919ffc12439d89d7b40f51ade84c +#: ../../src/topics/expressions.md:164 e68ee17607be4a06a66f9fc67624aff5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac -#: 307a17a893fc4dafaec2a63a95704644 +#: ../../src/topics/expressions.md:171 76b85d3729274fc08adfadcbf1172650 msgid "" -"The `custom-functions.js` file is included in the CWL document with the `" -"$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 -#: 7f393e86b114470f8dda47b2deec63aa +#: ../../src/topics/expressions.md:175 29f334957fa940c289f385160cca6d63 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 -#: c3f459b87b96435583637b3f1573e658 +#: ../../src/topics/expressions.md:181 6d255ae6b92a48fa9b7b98443cc2f5bb msgid "" "Finally, note that you can have both inline and external JavaScript code in " "your CWL document. In this final example we have added another entry to the " @@ -2417,18 +2122,15 @@ msgid "" "functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b -#: 9f676022eb2744839ca2109920250cb6 +#: ../../src/topics/expressions.md:186 89734e7855654b2e8bfddeea96241539 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f -#: ede7285f77864fb0aee6cfecc2c97fa0 +#: ../../src/topics/expressions.md:193 1915f8e68f624027827d28f8e17d2dec msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 -#: c55fb184bc614ee2b6e5e64611e5df9b +#: ../../src/topics/expressions.md:200 750f94edb4f84e45a276f6ab28fad95e msgid "" "The `$include` statement can be used to include a file from the local disk " "or from a remote location. It works with both relative and absolute paths. " @@ -2436,13 +2138,11 @@ msgid "" "html#Include) from the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 -#: 66b522f46ce242149386e79f63b32cf8 +#: ../../src/topics/file-formats.md:1 2e9e8cfaf48a43a88c31a855dac4f748 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a -#: 64a20285785d48ca86227a0cf6353ad4 +#: ../../src/topics/file-formats.md:3 c574b54d998243f28d2caa91434968a7 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This helps " @@ -2450,8 +2150,7 @@ msgid "" "simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 -#: 5f71bbe2c74e4260b79d4d9230d35397 +#: ../../src/topics/file-formats.md:8 b0ec34507eea473c91d6ada09a1c5c09 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM in " "our example), reference a local ontology for your institution, or do not add " @@ -2460,39 +2159,33 @@ msgid "" "file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a -#: 63bfff437e3348428f7e33ece7ec55e7 +#: ../../src/topics/file-formats.md:14 a688e39859734a518c0fcc19f532a432 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` section " "of the document in greater detail, so don't worry about these for now." msgstr "" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f -#: 6ce83d9c06e4436881aa47d94ef41e0b +#: ../../src/topics/file-formats.md:17 e068422ad9b84ca1b27008127928cc0f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 -#: 55006c594abf4e70a38e979568fadcf4 +#: ../../src/topics/file-formats.md:20 8c3ef5e145b14299bf3671add0da56ac msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 -#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 +#: 0d92f1c0f1ce448fb698e9b390b45c15 fc4773204ebc4e3789bb076dff0d0393 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e -#: 1a1905ff2d624eca952c8a53b3bee678 +#: ../../src/topics/file-formats.md:32 900abc5aa6a940f48f9c93e79cd1c47f msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b -#: 368ff92476b14f5c8331260eafc5acb5 +#: ../../src/topics/file-formats.md:34 0390555b96c84aadbd9325c152972087 msgid "" "Below is an example of a parameter file for the example above. We encourage " "checking in working examples of parameter files for your tool. This allows " @@ -2500,13 +2193,11 @@ msgid "" "parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc -#: 5d530afa23f349a79f54d51d40724747 +#: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d -#: 16f965f86712483aa7f95dfa3f944a17 +#: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c msgid "" "___Note:___ To follow the example below, you need to download the example " "input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff -#: dc629e2c90ed458b96107a6994676434 +#: ../../src/topics/index.md:1 0b8b9b7f533543a49f876421ce6057d9 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 -#: cf2f077cf8044079a7005e6e508dcd8c +#: ../../src/topics/inputs.md:1 1b6cfac3a92347d4b98bb54de1e26870 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea -#: 129e1d2a71894d28b009f4846754a75d +#: ../../src/topics/inputs.md:3 53dd5f476f064cbf9b9826d1e80eb830 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e -#: d6791bbe575042b9a7282c69407dd907 +#: ../../src/topics/inputs.md:5 420b33d143fc44d1b237bc678f0af663 msgid "" "The `inputs` of a tool is a list of input parameters that control how to run " "the tool. Each parameter has an `id` for the name of parameter, and `type` " "describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a -#: e8da87f8bb664334adf831995601f462 +#: ../../src/topics/inputs.md:9 55136332e3bb48f892cf6a74c67a4ac6 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*, " "and *null*; complex types are *array* and *record*; in addition there are " "special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 -#: de6c322618304207b6d1364d1ec2dc13 +#: ../../src/topics/inputs.md:13 cb2527899cc04b6d8060c4d57883beb5 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed -#: 43bdcf6dc1b14030bff27fa53289c02c +#: ../../src/topics/inputs.md:16 c79668b856b14243b4fad0f46dc5d6d7 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d -#: 056510b42ea64717996ab49c307bda86 +#: ../../src/topics/inputs.md:18 ed6f3e5c7b3f403a9a94359983107645 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e -#: 6852f5dbd9094c99bb68f2a88f76c9bc +#: ../../src/topics/inputs.md:24 034075eb09db4897a96d3332408427db msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 -#: f33b6800367248b7927d97ad7b4be5b5 +#: ../../src/topics/inputs.md:26 08181d391cc543a5a81d3257654df213 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 -#: 8ad812d7e88f4cbba83228ffb1711576 +#: ../../src/topics/inputs.md:33 15215522e38242c4b17ec3aa089269d4 msgid "" "You can use `cwltool` to create a template input object. That saves you from " "having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b -#: cc680bbf091a46f8b4b3dbe6324c040a +#: ../../src/topics/inputs.md:40 64bd3382ec234ec8a50217b794b96916 msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " "> inp-job.yml`, and then modify the default values with your desired input " "values." msgstr "" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 -#: 446ac81f078d46289a18f494748f482c +#: ../../src/topics/inputs.md:44 3611c1ca498a4197a4a6612c60f5f565 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b -#: 3d6d958d111943f3a2139b4dbb7810db +#: ../../src/topics/inputs.md:47 da924e8142d34e86bcb5de1cd1da71ca msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da -#: ba0ec9157709430c822f4e91459288e2 +#: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line, using the command `cwltool inp.cwl inp-job.yml`. The following " @@ -2610,8 +2286,7 @@ msgid "" "command line:" msgstr "" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c -#: 2565f8fd4a15429e887aeb71eacdff1e +#: ../../src/topics/inputs.md:64 dcc3f2a47a6449efb857af63ed4b65d0 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2619,8 +2294,7 @@ msgid "" "specified" msgstr "" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 -#: 659ed5c64fb546399b741553a347b8e8 +#: ../../src/topics/inputs.md:70 cf54a30ae24f4013bb19f379a7ca67be msgid "" "The field `inputBinding` is optional and indicates whether and how the input " "parameter should appear on the tool's command line. If `inputBinding` is " @@ -2628,16 +2302,14 @@ msgid "" "each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c -#: 3d87e69d41374fbab23b26d36c1aee03 +#: ../../src/topics/inputs.md:83 ff75644bae9c46af8379d78360d4c696 msgid "" -"Boolean types are treated as a flag. If the input parameter \"example_flag" -"\" is \"true\", then `prefix` will be added to the command line. If false, " -"no flag is added." +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 -#: 07bc81683e2c4ac68b379462bae95207 +#: ../../src/topics/inputs.md:95 e90abe59a84e48d4b8d6caa737e087aa msgid "" "String types appear on the command line as literal values. The `prefix` is " "optional, if provided, it appears as a separate argument on the command line " @@ -2645,8 +2317,7 @@ msgid "" "string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e -#: 3e304da2150f448d9e39715ac5f5deaa +#: ../../src/topics/inputs.md:109 9275236d87b646cab1058dd750e11a50 msgid "" "Integer (and floating point) types appear on the command line with decimal " "text representation. When the option `separate` is false (the default value " @@ -2654,8 +2325,7 @@ msgid "" "example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 -#: fd8a98686e3c4c609f79ae427f1558d3 +#: ../../src/topics/inputs.md:124 6a39929af73f4ba9b6455ed9fd287e08 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the parameter " @@ -2664,15 +2334,13 @@ msgid "" "provided in the input, nothing would appear on the command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 -#: f1a2e1bbb1104a4fab5a7f04cac845c7 +#: ../../src/topics/inputs.md:131 44ce716561cc4dff8fef1ca59f816c7c msgid "" "Input files are read-only. If you wish to update an input file, you must " "[first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 -#: 6a7f0ccd227e4f90a8c8ca96744bda68 +#: ../../src/topics/inputs.md:134 9f1da592350f40ee88920465e2004148 msgid "" "The value of `position` is used to determine where parameter should appear " "on the command line. Positions are relative to one another, not absolute. " @@ -2683,20 +2351,17 @@ msgid "" "position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 -#: 1f79d115d8a145189638c68c3095396c +#: ../../src/topics/inputs.md:142 5116d91f247f44518eb21840415f6eaa msgid "" "The `baseCommand` field will always appear in the final command line before " "the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 -#: 6e1b3e2d90184e34925891099d2b5cc1 +#: ../../src/topics/inputs.md:146 08b26d1688e3470288e73d587f052d88 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d -#: 4f6df7f13e42448eb4a53f03bc477b56 +#: ../../src/topics/inputs.md:148 f91994a4279a41bda3de41fe79008c62 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to provide " @@ -2705,28 +2370,23 @@ msgid "" "after the type name to indicate that input parameter is array of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 -#: dbc0b52627514ad0908969d0b4ddfdf4 +#: ../../src/topics/inputs.md:154 4b93a4f980634e88a8f34a38703fc906 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 -#: f173dd96ad124470a53573c86a8df203 +#: ../../src/topics/inputs.md:160 de3e760ebb0e4ae099deddb978046a2c msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 -#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d -#: af25945b530048b685891b1de4e35e72 cb07caa4ff0149b3ae832be53f8d76f6 -#: e0098a77080d4349b05ceb7735a5fdf5 +#: ../../src/topics/outputs.md:105 06ec811e8f0e43b8b929198533ac8082 +#: 797c06f0605d4e4ba306c2803a7834f9 d76d42c490a24b6daed944f45fe7a351 msgid "" "Now invoke `cwltool` providing the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 -#: 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 msgid "" "The `inputBinding` can appear either on the outer array parameter definition " "or the inner array element definition, and these produce different behavior " @@ -2735,8 +2395,7 @@ msgid "" "concatenated into a single argument separated by the item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d -#: 4459819ba75647d185986a3386939494 +#: ../../src/topics/inputs.md:185 3d8711f0135e4ab1b59fce94c83b97c0 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` in " "`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " @@ -2746,13 +2405,11 @@ msgid "" "arrays of arrays, arrays of records, and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 -#: 8f163bd34ded4785b6e28c8e2147e0dd +#: ../../src/topics/inputs.md:191 6f146779d6a84888948751b8b1fd0515 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d -#: 1799e11a7b9c4929a3d1379d7ea45d03 +#: ../../src/topics/inputs.md:193 e5970a83876e4b5e9a02f2ab0030eb83 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be provided " @@ -2760,55 +2417,46 @@ msgid "" "parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 -#: 9510c0b431a44b5e84e0b583de7c5446 +#: ../../src/topics/inputs.md:198 0db71b22173846d7b8d4aeb66d2ed8ed msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 -#: efb4eb6f5e994b50a52fa2c707dad1ce +#: ../../src/topics/inputs.md:204 f90fd48656a7424aac304987adf1b068 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f -#: 34599c6f10ce4104be2359a1b37f91cb +#: ../../src/topics/inputs.md:215 3c8bd9134a1c4bda9461362df3257d6b msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b -#: 0663ea7918994d3f9c45c652a3ed12db +#: ../../src/topics/inputs.md:217 63bd06780bb949e5b1a1d10389c8c23f msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add -#: a98dda6ca4b14edba467de638bba28fc +#: ../../src/topics/inputs.md:233 0d448baa57f14e7783d3167611e8c659 msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the first " "matching item (`itemC`) is added to the command line and remaining item " "(`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea -#: 10d0e9f8df8c47788703073b17529bc8 +#: ../../src/topics/inputs.md:236 202239a6e90044e39b676d641aa6d58a msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c -#: 9a0e1a130fba4d24a9168ca3e455cd23 +#: ../../src/topics/inputs.md:252 512ecb3349b0450cb741de4ed2d2e850 msgid "" "In the third example, only `itemD` is provided, so it appears on the command " "line." msgstr "" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 -#: 992a8c801ceb4233acf56b6bff315188 +#: ../../src/topics/inputs.md:255 185ff0bb49e841c592b29112eb171bdc msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d -#: 9027d23fa7074b789c3b86ca5ea17fa4 +#: ../../src/topics/inputs.md:257 6cd5df09e4594d78a526f199ac577881 msgid "" "If you use exclusive input parameters combined with expressions, you need to " "be aware that the `inputs` JavaScript object will contain one of the " @@ -2816,21 +2464,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb -#: 68b47710a8ea4b978428b42c627944e9 +#: ../../src/topics/inputs.md:262 9db9f784a5cd4ca5b90691d1e2e827ea msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from an " "enum." msgstr "" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 -#: d33e4cac65d14111a89c838c4d1759b9 +#: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 -#: 24cea1cf7d774b6ab56959f289cab39d +#: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you provide a " @@ -2838,16 +2483,14 @@ msgid "" "should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 -#: b866867d6f8e4d3999b62a85e6884ebc +#: ../../src/topics/inputs.md:280 76611ebb19764bdc8a1f6eacfb76138f msgid "" "However, if you do not provide any input value, then `file_format` will be " "evaluated to a `null` value, which does not match the expected type for the " "output field (a `string`), resulting in failure when running your workflow." msgstr "" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 -#: 80c49ed168b14d25b2f09b3b0186b44f +#: ../../src/topics/inputs.md:289 bf9750d215be4294b1cf1e0490a0796a msgid "" "To correct it, you must remember to use an or operator in your JavaScript " "expression when using exclusive parameters, or any parameter that allows " @@ -2857,12 +2500,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 71628ebe908b4cd28dd1fa17e3d2e2fb +#: 612f9efa0ed04559a174c37958def6f7 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 f123ca244c23413c91405a4b84887525 +#: 57eb990c11f044dfb60c012a92a30eb1 msgid "" "Implementation extensions not required for correct execution (for example, " "fields related to GUI presentation) and metadata about the tool or workflow " @@ -2877,7 +2520,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b 23299ae1bec94b00a32a8af7eeac350f +#: a6e6155cb8ff40fb9d8b1fff3e94fb02 msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to cite " @@ -2885,17 +2528,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 2495a9f2032a47c188338cb81ba429eb +#: 063c28fc9e654dfd91c66da164ac1d3d msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 3fd2f3cf7bdf44089df2ce3122534801 +#: 8fcd2ae1ce8d4c7f951281ced81ab32d msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 d5a5b8b490b640439db92da949266e4e +#: 639533652456427480fa311da7beb4f0 msgid "" "For those that are highly motivated, it is also possible to annotate your " "tool with a much larger amount of metadata. This example includes EDAM " @@ -2905,17 +2548,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e 5935ed94331d4b2f8ce597f31edea843 +#: 266808daf2004bbd9830045fbc67a541 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f -#: 5feb559552194ba58da7206c601292fe +#: ../../src/topics/operations.md:1 fd9b715bfa3243b19a919ad19843232d msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 -#: b7124ba4df9042baadc1641ee09545d6 +#: ../../src/topics/operations.md:3 fb568063fa7a4cbe83c271772d3d62bc msgid "" "An Operation is a type of CWL process, just like a workflow, a command-line " "tool, or an expression tool. It is a step of a workflow that specifies " @@ -2923,66 +2564,56 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d -#: d34b698c62114041a64e0abce25ca935 +#: ../../src/topics/operations.md:7 981486166754435cbcd8152e93679405 msgid "" "You can create operations to visualize a workflow during development, before " "you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf -#: cba2c31262bd450cbafc7ca77f4fb8fa +#: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 -#: b01be5f632104096b5af6193aab34d90 +#: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like a " "command line tool or an expression. You can also plot it with the CWL Viewer " "or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 -#: 60a6a02c1367403db6df3ec10f75eb69 +#: ../../src/topics/operations.md:24 02c372245dc9453ea0841026335e405b msgid "" "The output of the command above can be rendered with a Graphviz renderer. " "The following image is rendered with the Sphinx Graphviz directive (this " "user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 -#: 314ea7bc35154f41b2af5fa6683ca389 +#: ../../src/topics/operations.md:55 d331327285d1434e8c17187737345919 msgid "" "If you try running it with `cwltool`, the command will fail since `cwltool` " "does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb -#: d81e679b13474f74bc5e1ce1e31c2bc6 +#: ../../src/topics/operations.md:58 72705f8940bb4194bc5554fcc29eed49 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f -#: d7fb27131ee44bfc82f698ee44b2bae0 +#: ../../src/topics/operations.md:66 76b7c63107e94323859904415d07d31c msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A " "CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de -#: b8ef11eafd1d46e088f1277f4ac372bc +#: ../../src/topics/outputs.md:1 ebf56d267612461799bf801136e61b69 msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d -#: d2382ed1f644459594655d5b5b4d838a +#: ../../src/topics/outputs.md:3 f9cff6b272a24ef6ada90e263c1b1784 msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 -#: 6651632d977b44479b721174fffeda2d +#: ../../src/topics/outputs.md:5 e482821911004cdd8c3ff1539c69368a msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name of " @@ -2990,8 +2621,7 @@ msgid "" "parameter." msgstr "" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 -#: bee5f532554241088764ac9e56abbe85 +#: ../../src/topics/outputs.md:10 e11fcfe1e84b476ea879810b76ff2cb8 msgid "" "When a tool runs under CWL, the starting working directory is the designated " "output directory. The underlying tool or script must record its results in " @@ -3000,20 +2630,17 @@ msgid "" "from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 -#: 0c7c506f38be421399073871f64e99b0 +#: ../../src/topics/outputs.md:16 65c73a37f06a4782bf43f4acf4f1c77e msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 -#: 8b60286e56cc42a8ab5f751a97adf771 +#: ../../src/topics/outputs.md:19 e172dde545164fefac826d910ddd399e msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c -#: fa0ad674f15348339a1eee771a6ba9e2 +#: ../../src/topics/outputs.md:21 225f4d04c28149898f06bd771f741358 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -3021,85 +2648,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f -#: 177b5f1b95a34fb9b2eb42f733d79ac8 +#: ../../src/topics/outputs.md:26 14e9e446768a454ea786b3256b49632e msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a -#: a08a6d8aca8e490482e127a8fd5e650e +#: ../../src/topics/outputs.md:32 4bd659cee1904868a7c33345f94f1300 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 -#: c2c60f68b1e045f88844076e191fda9b +#: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb -#: 6d939f62526e4e6d95acb57d72f60a84 +#: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 msgid "" "And now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d -#: c48edd9034364b81ad42540a98b51d91 +#: ../../src/topics/outputs.md:51 44cdca5b777441baa246c87940df7264 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 -#: 9ebe0186a7124dfaa30e558e8f59653a +#: ../../src/topics/outputs.md:62 edb34af3b22d418d9a6178c0ecbb8b80 msgid "" "The `glob` field consists of the name of a file in the output directory. If " "you don't know name of the file in advance, you can use a wildcard pattern " "like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 -#: 9381b7d7c9904df0a5e16dac29c2e08f +#: ../../src/topics/outputs.md:65 10e68fad866f4187981f0b365b957b03 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 -#: 2aa9c6916e3546b7b92fa64bb83275d1 +#: ../../src/topics/outputs.md:67 77e1261484964ba9ac67d9fc9139a1d6 msgid "" "To capture a tool's standard output stream, add the `stdout` field with the " "name of the file where the output stream should go. Then add `type: stdout` " "on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 -#: 63afb7a597fc4e459b6a7dbd40bbf6ff +#: ../../src/topics/outputs.md:71 c66bd08354d54ccb9e3e1da89634a816 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 -#: 7418915470f041c9af5bd39ea652de36 +#: ../../src/topics/outputs.md:89 7d4056355da1451dbed6733fba8c3c38 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d -#: f82db001b58c4969b2d8bc1dcbd7cf8a +#: ../../src/topics/outputs.md:91 8fed80f9633a4e87a67c651dc3160ce6 msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 -#: 26d9f0b28d384617a8e490c1f8e26e52 +#: ../../src/topics/outputs.md:93 6cba36e037d54f93add05fb16d2359bd msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae -#: cf46c971b31b4e10bf0fefb4cd028c2f +#: ../../src/topics/outputs.md:99 08862892ecf849a1ba2f25ecc9e98227 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 -#: a4347983fb9945a4a2773af88e426dc9 +#: ../../src/topics/outputs.md:112 c5dcc68bb28041b3b96ac1af716b0db8 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -3107,13 +2720,11 @@ msgid "" "mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 -#: c5489e0633114372b273098ee2c9ffd9 +#: ../../src/topics/parameter-references.md:1 53b95fd10d61462daf153d45e5517dad msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 -#: 75de9fd63393429daf1ca10a85339aa7 +#: ../../src/topics/parameter-references.md:3 0702e71de81e493dac08a91d667569e3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file we " @@ -3126,47 +2737,40 @@ msgid "" "specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 -#: 8b5d0ada32d645be9359f43a431f5f91 +#: ../../src/topics/parameter-references.md:13 a1703da32ad64fd2b8bdd423605b50bd msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 -#: 2ed93dc8778e44209194f41b9ad193d5 +#: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 -#: a80dd6d9920540e9880514e04035af86 +#: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 msgid "" "Create your input files and invoke `cwltool` with the tool description and " "the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 -#: 9de300f7b9da49f59d1c9fd96dec4a8b +#: ../../src/topics/parameter-references.md:36 1bcdd99111bd4bc5b75a8297bb61d9bb msgid "" "Certain fields permit parameter references which are enclosed in `$(...)`. " "These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 -#: a61f52d3c1024c3692899e05fcea4bee +#: ../../src/topics/parameter-references.md:47 32eae36c593e43a9a6b4e103a0c2028a msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" -"$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 -#: dafc9ba578c14fd79d075160e6b7bd6b +#: ../../src/topics/parameter-references.md:51 1d785e8a450140a982142aa0fa906257 msgid "" "The value of the \"inputs\" variable is the input object provided when the " "CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 -#: 28ca6cae42904559bcec98fb9d2b07cb +#: ../../src/topics/parameter-references.md:54 e862bb8bc3e84e24a2aa5ec34298cfd5 msgid "" "Note that because `File` parameters are objects, to get the path to an input " "file you must reference the path field on a file object; to reference the " @@ -3174,112 +2778,101 @@ msgid "" "path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 -#: 616c9ff9fcae489285f0bbbc67f07d29 +#: ../../src/topics/parameter-references.md:59 46ffaab11be040cea96a294d9a814738 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad -#: ac17acd83ddb43dc9fb7a5e595ab1153 +#: ../../src/topics/parameter-references.md:61 890d619c415741179c83ffcd56833fbe msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 -#: 156573324cde41ee8b3c47deabf43db8 +#: ../../src/topics/parameter-references.md:63 373e1847d9f745d7a749928642c8e0e3 msgid "" "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 -#: c9725be01e8a401fb3ad9ff01339f81e +#: ../../src/topics/parameter-references.md:69 90d3624e062c41c7a6d1a9824515d0df msgid "" "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 -#: 6797335256e2412cbbe7636507931455 +#: ../../src/topics/parameter-references.md:72 76d09490bd464b708c28991dbff0104e msgid "" "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f -#: 05a5f0fcb7454cb697e3d810d55fac26 +#: ../../src/topics/parameter-references.md:74 f33c76e590dd4feaac1e3cf568069d33 msgid "" "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 -#: 406e68280b5c4ee494632f94b635b7ad +#: ../../src/topics/parameter-references.md:77 74ed4a06c1984c58826ddceb1a45a4ea msgid "" "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 -#: 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: ../../src/topics/parameter-references.md:81 eba3362d34354daa89dc516722c6fbd0 msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" "v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 -#: e71a974b29624210a107fc2d097d4196 +#: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd msgid "" "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 -#: b59df98754e24654bfef0b1fe1d91660 +#: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." "org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c -#: d2bccbff1ce646348fe38c776ad183e1 +#: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 msgid "" "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 943ba46512ce48fe8c5b62327734c503 +#: 2fad0c2bc2834350826b22c454d33cf0 msgid "" "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 bbcd43d5af7d44108aeb65075a6bd2be +#: 9e303aa89a9b4447b0dbdc5ac0a0eb9e msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 834295755af841a78e466eea43864861 +#: 7a4eb47c25a54d11a00eb73e9333ad1c msgid "" "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae a6b626489bfa468e8f059ab3aa669201 +#: 8a957bc8e577476bb59647661b3c0990 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 e1dbea105aa845c38cb1f90b43847271 +#: 2b31f1dec3f5498e9e363a4f1f50dc8d msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb e9640f47d40e45bca184eb30700df648 +#: 5a5f84ecc2f449bf9f037dc9da0ac670 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -3289,14 +2882,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 0456efb3718b4356ad2b277ee16de967 +#: ee89f1526c1f4452b4e36ba67bb59747 msgid "" "In this example, the software requirement being described is InterProScan " "version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 f7e97f926505407f8f8e9a427e055e43 +#: c76cec44f5424f6087df28aa33c521a2 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -3305,7 +2898,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 ec597ff8f6ee47bc815b069335869f1f +#: 072d7b3ce3284ed994ff0736b43bbb86 msgid "" "As well as a version number, a unique resource identifier (URI) for the tool " "is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " @@ -3320,13 +2913,11 @@ msgid "" "main tool citation and the URL to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 -#: 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: ../../src/topics/staging-input-files.md:1 395d611104604a28b78e11b112a95027 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 -#: 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: ../../src/topics/staging-input-files.md:3 811b4db0b1794fa89dc870f6cb59a3cd msgid "" "Normally, input files are located in a read-only directory separate from the " "output directory. This causes problems if the underlying tool expects to " @@ -3336,31 +2927,26 @@ msgid "" "base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 -#: a03372581fa44f9b8e3e088a4099cdd9 +#: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 -#: 36e082be73464be0ad5d0b681cc510da +#: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 -#: 4464455b51ad4873ac13c4a63ee5fb54 +#: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 msgid "" "In this section you will find ways to troubleshoot when you have problems " "executing CWL. We focus on `cwltool` here but some of these techniques may " "apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da -#: ed7ff0753d1743a995f4cfedd6e5dcc2 +#: ../../src/topics/troubleshooting.md:6 6db8a02139644598894220d538c590b9 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 -#: 4c2dd10dd66446058477a52fb8d2c602 +#: ../../src/topics/troubleshooting.md:8 f0da0f6283d44bcc95224eb9fe2d1764 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor output " @@ -3369,8 +2955,7 @@ msgid "" "directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b -#: 978b6a5fd5fa425fa9a18d9f0e8788da +#: ../../src/topics/troubleshooting.md:14 e2fc28b44ffe4254892a7c7973dc80c4 msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " @@ -3379,20 +2964,17 @@ msgid "" "of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b -#: 000c0d6ae8bf414d9293b9f13fd2e448 +#: ../../src/topics/troubleshooting.md:20 505c7cf9ee9c4af1aeed29002eed1b33 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f -#: 7e91b8811be14f8e80df39ac4c5bd316 +#: ../../src/topics/troubleshooting.md:27 4c31fd11a28943538690d04baa2b5dd0 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " "(`cwltool` will create the directory for you if it does not exist already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac -#: d42799cc5bd4484bb6beb309a61e103e +#: ../../src/topics/troubleshooting.md:35 a8532ac700014db4bd8ef690a27fb844 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -3400,8 +2982,7 @@ msgid "" "can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 -#: 48bb0f6666ac48648c7d969608b3bd48 +#: ../../src/topics/troubleshooting.md:44 94a6148512b24b90b87fd1312a926d75 msgid "" "Each workflow step has received a unique ID (the long value that looks like " "a hash). The `${HASH}.status` files display the status of each step executed " @@ -3409,8 +2990,7 @@ msgid "" "output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 -#: f8876044db184cbaaca56579d0c773df +#: ../../src/topics/troubleshooting.md:48 ec4165b7c25c449db6a8804161805e80 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " "the `step_b`). After fixing the typo, when you execute `cwltool` with the " @@ -3420,8 +3000,7 @@ msgid "" "now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 -#: a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: ../../src/topics/troubleshooting.md:59 5c0b71a6376848d4aa491854ea2d185d msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had " "been cached, and there was no change in its execution or output. " @@ -3431,18 +3010,15 @@ msgid "" "re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 -#: 4c240a18c4e6441189489011242c1efd +#: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 -#: e37e76ef376a4ee695e600998906ec1c +#: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 -#: 51a307b0ba7c4c1d89309ba8d2250471 +#: ../../src/topics/using-containers.md:5 2420b16855cf4b25af5bcb87413f6dd9 msgid "" "[Docker][docker] containers simplify software installation by providing a " "complete known-good runtime for software and its dependencies. However, " @@ -3455,40 +3031,34 @@ msgid "" "containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 -#: 13cc38d72d34468fa4eb6d91f23ff105 +#: ../../src/topics/using-containers.md:15 f5266ee2c2b34170bc89cb501b869893 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the container." msgstr "" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a -#: 42a48398d3ef4b03bd7395120f2cfb42 +#: ../../src/topics/using-containers.md:18 728166bf41504e1d89b755400742a1b4 msgid "" "This example runs a simple Node.js script inside a Docker container which " "will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 -#: d59387b433bc4ecfaf7e72026624db02 +#: ../../src/topics/using-containers.md:21 104351ac29d247cb8e017228e2c9b3d8 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 -#: d963418ccc0b4803bbc758d718ccb5aa +#: ../../src/topics/using-containers.md:27 e11a38bfb30b404c99d223647960cb16 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed -#: a224d1510c9e46aab23d8bdc03c349dd +#: ../../src/topics/using-containers.md:33 7ed0bd21e998417cb02fdcb8e44734b6 msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that is " "really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 -#: 0a82f8a45b0546aaac4c976dcc98014a +#: ../../src/topics/using-containers.md:44 9dcddf6812ba4bc2a7d6c5fcdb978a68 msgid "" "`baseCommand: node` tells CWL that we will be running this command using the " "Node Js runtime that is meant for Javascript files. We then need to specify " @@ -3501,27 +3071,23 @@ msgid "" "called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 -#: bc418a2a535e49359c4cd44b373bbe02 +#: ../../src/topics/using-containers.md:52 bc1a09475f154562a4db445bf81ac92f msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " "the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 -#: a799fba2322944cea00e413c08066536 +#: ../../src/topics/using-containers.md:55 2e117019ace84604a8ed5a31214c2587 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 -#: 35379c6b972940bd8451f10b74dd793e +#: ../../src/topics/using-containers.md:69 d0d5b2a1a008411e92859a72101088c1 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 -#: 2d5265525ad544a0b64ad2cf07aacc26 +#: ../../src/topics/using-containers.md:72 591d1cd0282b4095a267b44da7d59804 msgid "" "In this example, the path to the script `hello.js` is `/home/me/cwl/" "user_guide/hello.js` outside the container but `/var/lib/cwl/" @@ -3529,51 +3095,43 @@ msgid "" "invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 -#: e2521b89596d42f8a87a3207fd6c32f2 +#: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 -#: 3676f23b63e142cb8e5715ae07216a47 +#: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 -#: 00725aed13a440ca8b3c4f9155fbee99 +#: ../../src/topics/workflows.md:13 7530029ec04746f2a888dcbc10aa5ce4 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 -#: 2e38a4f9072b4ad9bbb74f943d22084d +#: ../../src/topics/workflows.md:41 c1f1d644b37b4f018b87e15249d8758d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier examples." msgstr "" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 -#: 2b9f4035ea864b6db50c861a1819289d +#: ../../src/topics/workflows.md:51 2d07232b7d9c415b8ad971e8cbcd9577 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb -#: 28e9064780e7418a8e02a22f92e34404 +#: ../../src/topics/workflows.md:81 fa1f770ffeba4b74bcb200cd3949e070 msgid "" "A command-line tool or expression tool can also be written directly in the " "same CWL document as the workflow. For example, we can rewrite the `echo-" "uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa -#: 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: ../../src/topics/workflows.md:91 570020792e824c2ba732bcc2c0134aa1 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a -#: 8dc00528c3d2426c8a3492a8191f1d81 +#: ../../src/topics/workflows.md:150 8a50c511004941d0917a8f0d471467f0 msgid "" "Having separate files helps with modularity and code organization. But it " "can be helpful writing everything in a single file for development. There " @@ -3581,39 +3139,33 @@ msgid "" "pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe -#: f9ef5e258f7c4971a8543d1dfed711a8 +#: ../../src/topics/workflows.md:160 4d2bf0341836405d9729c47d8020faea msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this " "user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 -#: 324bc51071d743ea80124c23880ddc0a +#: ../../src/topics/workflows.md:165 dd6fc85f74984517b284853a0d46c122 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c -#: d8c13e01976b43a1af34c11a7bc36897 +#: ../../src/topics/workflows.md:167 f857d80cd5d84622a560c895ab260a92 msgid "" "This workflow extracts a java source file from a tar file and then compiles " "it." msgstr "" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 -#: 43910a8ab4484e529a17df418b1aedbb +#: ../../src/topics/workflows.md:170 02e7e81cdf7e4226973f910cd57b8ccf msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 -#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 +#: 3a88d92f41aa4daaad4f4cc6829184b3 646367f222ea41e5987561941d17c4f9 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 -#: 7ad12d67e815400c94080804b9285629 +#: ../../src/topics/workflows.md:180 aaba75eb272245db82d072fed97b311c msgid "" "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" "github.com/common-workflow-language/user_guide/blob/" @@ -3623,39 +3175,33 @@ msgid "" "_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 -#: 457d5a31c79143acae2683d95d27f7a3 +#: ../../src/topics/workflows.md:183 f8a6e1af5f0349a5a384be0629c37ac8 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a " "run:" msgstr "" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda -#: a2a73901bf634547900d08b9a1ac8889 +#: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 -#: f347d80e62384b14acf6423675e5359a +#: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 -#: 2a845a4f3f98428fb82f3ca7ce038a6e +#: ../../src/topics/workflows.md:205 84293afa7a6c40f2af0b980c89581fc7 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde -#: e2007c74d5f449a882809d6b91c010bf +#: ../../src/topics/workflows.md:212 e66daf8af53849109936c36ca7d2b2c9 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a workflow." msgstr "" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 -#: 7f5e53ee7cf94be2bff45ef64db28a24 +#: ../../src/topics/workflows.md:221 8fbfbb587b264dcf98a3cea16dd36ef3 msgid "" "The `inputs` section describes the inputs of the workflow. This is a list " "of input parameters where each parameter consists of an identifier and a " @@ -3663,8 +3209,7 @@ msgid "" "workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 -#: a0d076b7b8b048478580c99ef0c8429f +#: ../../src/topics/workflows.md:233 5cdbc4771ea841b4960362b930de2af6 msgid "" "The `outputs` section describes the outputs of the workflow. This is a list " "of output parameters where each parameter consists of an identifier and a " @@ -3672,8 +3217,7 @@ msgid "" "the `compile` step to the workflow output parameter `compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 -#: 7fd926c18ad548e98845e9b5134dd6f2 +#: ../../src/topics/workflows.md:248 2e8a41fe43984dc6b4cf430e1ff66b28 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second step " @@ -3684,8 +3228,7 @@ msgid "" "parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 -#: 789fbd47f8564cceb430ef3c0bc90e9b +#: ../../src/topics/workflows.md:256 78c20aa5a5724da6a4c908849c571334 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input " @@ -3693,8 +3236,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 -#: 45c4d0492d6143ca9cebe81e9b2cf3ae +#: ../../src/topics/workflows.md:261 1606a2f059eb4b0c9e90f2f0cbbe779b msgid "" "The ``in`` section of the workflow step connects these two input parameters " "to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " @@ -3703,15 +3245,13 @@ msgid "" "parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea -#: 73bd3da2af8545928d5ea71d0f7454f6 +#: ../../src/topics/workflows.md:267 b456b11e2760479bbf81a773a3e1f8ee msgid "" "The `out` section of the workflow step lists the output parameters that are " "expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed -#: 15ce3d2700424f0fbb280d602ccebcf6 +#: ../../src/topics/workflows.md:278 0fa01fcec32049c989ad1d68841c74de msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3721,13 +3261,11 @@ msgid "" "section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 -#: af4268f19202436eb0a7e8c6bed5e386 +#: ../../src/topics/workflows.md:285 2bc9829f95584a269eb577c610b2a80c msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e -#: 94a4eadca6b949d79de2990a0150eee8 +#: ../../src/topics/workflows.md:287 0e5e6445bfcb42a4bd03612316dd7225 msgid "" "Workflows are ways to combine multiple tools to perform a larger operations. " "We can also think of a workflow as being a tool itself; a CWL workflow can " @@ -3735,20 +3273,17 @@ msgid "" "the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 -#: 09c1619e8cbd4febbb637f7e99ad5890 +#: ../../src/topics/workflows.md:297 0b83c1028b0e43ba972609e4302bc8a2 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 -#: 677ea7a27eb64568ab3689142d6efe70 +#: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 -#: 097e6d47f9394e62b80110700492783a +#: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d msgid "" "This two-step workflow starts with the `create-tar` step which is connected " "to the `compile` step in orange; `compile` is another workflow, diagrammed " @@ -3756,23 +3291,21 @@ msgid "" "supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a -#: e93affce8c104bf6977182047c1f1077 +#: ../../src/topics/workflows.md:314 2e9797fcd4f04f56b5d2b2f1a3e306d5 msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows." +"cwl\">\"Visualization \"Visualization" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 -#: 06c9e04ba890473b851240a0fa9c3b12 +#: ../../src/topics/workflows.md:322 28f4139911b44eeeb7afd31e9f7cae7b msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " "CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3780,8 +3313,7 @@ msgid "" "to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 -#: 0380dc1fe3aa48e4b62283b7b2a611d8 +#: ../../src/topics/workflows.md:336 4a6cb397a20241beab24d956920a8379 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and `*.java` " @@ -3790,8 +3322,7 @@ msgid "" "workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be -#: 49b251f7a313492ea60504b00109e526 +#: ../../src/topics/workflows.md:341 dccb5472a5dc42b7946dd9245a71ecf0 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar " @@ -3800,8 +3331,7 @@ msgid "" "specific input/output names, as those also appear in its usage as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 -#: 7ee55702d7dd4679a24ff052f6f0cbeb +#: ../../src/topics/workflows.md:347 de1e18b69f654cabb75e52b47058030a msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3809,16 +3339,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 -#: 85d7e2e270874aa6b9f477cec0f48154 +#: ../../src/topics/workflows.md:366 b947e62f4b3b4c10b95737f1839bcc5a msgid "" "In this case our step can assume `Hello.java` rather than be parameterized, " "so we can use hardcoded values `hello.tar` and `Hello.java` in a " "`baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 -#: 570e94513c984c09ad6aa255f534216d +#: ../../src/topics/workflows.md:383 2ed0258a3a104ed5ba3b6b95ad998839 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This is " @@ -3827,8 +3355,7 @@ msgid "" "filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 -#: a107258662fb4bd4a9a3d8754e34d1e9 +#: ../../src/topics/workflows.md:389 6584c0995288450b8a01c35fa231afb6 msgid "" "In this example we had to prepare a tar file outside, but only because our " "inner workflow was designed to take that as an input. A better refactoring " @@ -3836,8 +3363,7 @@ msgid "" "which would simplify its usage as a tool step in other workflows." msgstr "" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 -#: fc1a6502d831458ab8371a575cea47e2 +#: ../../src/topics/workflows.md:394 19237513fd134c33801a7af08f74e70c msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL " @@ -3845,13 +3371,11 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 -#: 2d10806bf1ce4e26b92adda61efc0862 +#: ../../src/topics/workflows.md:398 b66e0d0a36994b3182a3784bda8ffc19 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 -#: 046c5e134de94b629cc22d416f3c9182 +#: ../../src/topics/workflows.md:400 3bfb9851302248568bb4535ddc87a27f msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish to " @@ -3862,8 +3386,7 @@ msgid "" "different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 -#: 52fa22d3277940049fbb589a3ea73433 +#: ../../src/topics/workflows.md:411 78a5a600f8cc49ce8055c77a596ad833 msgid "" "The most common reason a new user might want to use scatter is to perform " "the same analysis on different samples. Let's start with a simple workflow " @@ -3871,27 +3394,23 @@ msgid "" "strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd -#: 6043beb96c2c49648011ec556aa9e986 +#: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 -#: 5ac4310515124e2986724425bed5651f +#: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 msgid "" "Aside from the `requirements` section including `ScatterFeatureRequirement`, " "what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c -#: 7958e91d5c2f4046aa9d2070a900f9ae +#: ../../src/topics/workflows.md:429 7ab022708a9642ab8aa2e79ea7810381 msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f -#: 2db234d776fe4fd38bab07245dcb783a +#: ../../src/topics/workflows.md:441 fe144641fc8040b283f15b2b99ecb5a2 msgid "" "Here we've added a new field to the step `echo` called `scatter`. This field " "tells the runner that we'd like to scatter over this input for this " @@ -3899,8 +3418,7 @@ msgid "" "the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d -#: 7cfb17230e284ee7b6e2a00efe8eeb74 +#: ../../src/topics/workflows.md:445 f13d1b071a7f4a75a4cdee40ecef14fa msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if you " @@ -3908,70 +3426,59 @@ msgid "" "to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 -#: 4311ac98544e4fb0b2f4b24985710a01 +#: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be -#: 780f9c72e6c34c39918642c7e2477355 +#: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 -#: cc4a7316db644b438cbaa181ad9ef2d3 +#: ../../src/topics/workflows.md:458 f5b8681b3c3b4890a86d7b9fb812d958 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " "calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f -#: dfc461a03fe8487794837904febb8b63 +#: ../../src/topics/workflows.md:466 74e70fec6d2447bbbd2a5bc8af1fa58c msgid "" "You can see that the workflow calls echo multiple times on each element of " "our `message_array`. Ok, so how about if we want to scatter over two steps " "in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 -#: 1e83485b00b64dfaba897bd8d772e0f0 +#: ../../src/topics/workflows.md:469 76fed9e7ad1d4792b7bb364bb684eeb2 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding the " "following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de -#: d0321d6805ec4d3abf3877d02a0a417f +#: ../../src/topics/workflows.md:472 bef387d9be1f4ca19a97023cfdd1c910 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 -#: d7d77e807b3048c7bdf89558f76804cb +#: ../../src/topics/workflows.md:480 eea1be83da574f39914566d835701b4a msgid "" "And add a second step that uses `wc` to count the characters in each file. " "See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a -#: 8d9b8be147fc4a71922dde858842e543 +#: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b -#: 34b7705416a745a6a42e6d402c0757ed +#: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under each " "step:" msgstr "" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d -#: 257adcee9da64d5c987f3b64efd20ab0 +#: ../../src/topics/workflows.md:491 e6e1a79638d74547b00c64e3c8b05710 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 -#: fa6ed5d0c14f42f4aa3c5144648db22c +#: ../../src/topics/workflows.md:497 03fb16e74bf14c49b43e35ef6cb45030 msgid "" "Here we have placed the scatter field under each step. This is fine for this " "example since it runs quickly, but if you're running many samples for a more " @@ -3988,8 +3495,7 @@ msgid "" "welt!`. You can see how this might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df -#: 333e8ce458d54de394526769f96d12d2 +#: ../../src/topics/workflows.md:509 eca3380c60094df2b91b44b5f7718fae msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can " @@ -3997,45 +3503,38 @@ msgid "" "step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b -#: b819e8a5df6e4fa495924095709669ef +#: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb -#: f1955468a1364d44a930db77c9c4b495 +#: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 msgid "" "Now the scatter acts on a single step, but that step consists of two steps " "so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 -#: 8c3b9b645a204d02b2c73a205e8ec296 +#: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 -#: 4d88b9c186cd4502adbf752e8a70b6ce +#: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 -#: 9927673564024ba5833b5ac271737857 +#: ../../src/topics/workflows.md:527 8f7ee09c9d6b491195e2d80315dae398 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 -#: 84f4ed7ce2004742b8db9087104a469a +#: ../../src/topics/workflows.md:566 966acff0d3d24104ae9673df8a790fb1 msgid "" "The first thing you'll notice is that this workflow is only compatible for " "version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 -#: 2b5f9757adca4490a149c7f45e14fcb5 +#: ../../src/topics/workflows.md:573 d60e1df759654f1b873276cf0296f234 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when` is " @@ -4043,8 +3542,7 @@ msgid "" "from the workflow contains a value `< 1` this step will be executed." msgstr "" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 -#: 0418de720813442f81ecff293c9448b5 +#: ../../src/topics/workflows.md:587 69aa8d3c9d9a4fe4a62875827648d95f msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " "will pass the first conditional step and will therefore be executed and is " @@ -4052,75 +3550,62 @@ msgid "" "skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec -#: 524eec63be8248ae982939c975ef50a2 +#: ../../src/topics/workflows.md:607 fee34c880e964e08b040adf2d3831803 msgid "" "When a value of 3 is given the first conditional step will not be executed " "but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 -#: 5e99f9912cc549a7890e2934425eb943 +#: ../../src/topics/workflows.md:627 cb9e82cf4b484ca7be19612b14fbdf33 msgid "" "If no conditions are met for example when using `--val 2` the workflow will " "raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e -#: b0121ee087d6424fbb0ea5957a7b0b8c +#: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c -#: 49e9f6b3a06840289decf3f557860f87 +#: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers and " "humans. This guide introduces the features of YAML that are relevant when " "writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 -#: ed9eebec0b3d4b72ba65507d37757a37 +#: ../../src/topics/yaml-guide.md:13 2cc21093311548cd837aa7b3f0939093 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea -#: bf9b255a24a84f3ba989a223492b8f41 +#: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee -#: e79fa0b7f8b14810a3a20908ef92bc55 +#: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a -#: 290e2035f903417cbecb5dc5f09d6ebe +#: ../../src/topics/yaml-guide.md:19 179290eee12343dd9aa4d49207cf7c68 msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c -#: d420730151534f1a89076588a3358f09 +#: ../../src/topics/yaml-guide.md:20 7880db40e98e4aaabdc96def3d9f515d msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc -#: a6b5378bbe1e4bee9e37a765bddf75f7 +#: ../../src/topics/yaml-guide.md:21 75f3b499494b445f9f9a532d178cbc10 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 -#: 6e4d9465dc2b454d96b02d7ad1817795 +#: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 -#: a649d4af5f434dac9395e013ec4836bb +#: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 -#: 446190a298834b73bda068286e8490cf +#: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the `:` " @@ -4130,8 +3615,7 @@ msgid "" "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b -#: 2f35c012ff174721bffe66a3f58a804f +#: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 msgid "" "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " "and `home` - with their four respective values. Values can be character " @@ -4139,8 +3623,7 @@ msgid "" "Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 -#: 43127c98c9d94aedac61cee67929c1a6 +#: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c msgid "" "Values may be wrapped in quotation marks, but be aware that this may change " "the way that they are interpreted i.e. `\"1234\"` will be treated as a " @@ -4151,33 +3634,28 @@ msgid "" "numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 -#: dc4fe561203c4c38a9caea5bd6eff2cd +#: ../../src/topics/yaml-guide.md:61 d18c1f5ef55d4bb6b8334438fcbc96b8 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 -#: f924e4896db2424d99ce8c9da14c599a +#: ../../src/topics/yaml-guide.md:63 dc6869049fc143b4af91d172a419a125 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program interpreting " "the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d -#: bf7646f5f925485c842a6d34140e40b8 +#: ../../src/topics/yaml-guide.md:76 c3c7f5ecfedb4884ad5e91bb79ba2a7c msgid "" "If there is anything on the line before the comment, be sure to add at least " "one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf -#: c483e61dec8949fa96bb893d422888a0 +#: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 -#: 85fcb523d0e34a499eae04d304887f7b +#: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, these " @@ -4188,8 +3666,7 @@ msgid "" "are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 -#: 83d47c8736a34f3cbf09e3997845e4f4 +#: ../../src/topics/yaml-guide.md:104 ce790af50da540eb9108ad89eae037cf msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -4201,13 +3678,11 @@ msgid "" "graphical representation of the `inputs` object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 -#: c698fb3d37bc403e9aeb679b8fc0e15e +#: ../../src/topics/yaml-guide.md:127 c3c9ef616b5d472a894ad6330267bcd2 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 -#: ae8af2f0eeda4aec97201211dfa965c7 +#: ../../src/topics/yaml-guide.md:129 b8a7360f6e0640aa9a2c4907c1ba3fe8 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) section " @@ -4217,30 +3692,25 @@ msgid "" "where each value is defined on its own line and preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 -#: 2ee87aa465cd41fda16a61e242f8c9d0 +#: ../../src/topics/yaml-guide.md:146 363da878600a4d229efe0ba79835d73c msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d -#: 0a6fd4469ff24b61b3ad001b09eead18 +#: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d -#: b96ba19bce9341d39c46054e1f10fe8f +#: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " "can also be defined in YAML using the native JSON syntax. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc -#: 903f30af3d0c45cfb61063936a8097a7 +#: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 -#: ede8db7c0a58432e8a1c416e937a06d2 +#: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd msgid "" "Native JSON can be useful in indicating where a field is intentionally left " "empty (such as `[]` for an empty array), as well as where it makes more " @@ -4250,130 +3720,50 @@ msgid "" "file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d -#: c8b53615476a4a1fbef2420d93bac94e +#: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 -#: ea03cb5525cc491f9feb5c4780b38fee +#: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " "while we wrote this guide, though it also covers features that are not valid " "in CWL." msgstr "" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 -#: 92fd3a5e31714eab859dd630af2e78cf +#: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 -#: de660ecdb5b44c97a0e519d00b232497 +#: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to the " "list." msgstr "" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c -#: 5afc1e1288e74ed0985e61e5164479c7 +#: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 -#: 862dc7ac81e54b1fb3d4c2f961b8810e +#: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b msgid "" "[Introduction to Workflows with Common Workflow Language: For Contributors.]" "(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f -#: e2c94c0e1c7048d38cd7aa2c465a859d +#: ../../src/tutorials.md:11 3505468d39c34a20bc55f431a3c697f7 msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f -#: b63253780f51467a95207d820d13ac39 +#: ../../src/tutorials.md:13 e5731a11b89e492d8d751100a46c5226 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f -#: 6d06ca7ed5df4560aaed286f4fe33928 +#: ../../src/tutorials.md:15 cdfeabb88f6245d9a687197d242ed3f9 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 -#: 5448df4a6a8f431d80e269bcd480e19e +#: ../../src/tutorials.md:17 997679b781a84add9b6d8b1900deec35 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" - -#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the `Creative Commons " -"Attribution license `_. The following is a human-readable " -"summary of (and not a substitute for) the `full legal text of the CC BY 4.0 " -"license `_." -msgstr "" -"Todo o material instrucional do projeto Common Workflow Language e " -"alterações na estrutura também são disponibilizados sob a `licença Creative " -"Commons Attribution `_. O seguinte é um resumo legível por " -"humanos de (e não um substituto para) o `texto legal completo da licença CC " -"BY 4.0 `_." - -#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 -msgid "to **Share**—copy and redistribute the material in any medium or format" -msgstr "" -"**Compartilhar**—copiar e redistribuir o material em qualquer suporte ou " -"formato" - -#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 -msgid "to **Adapt**—remix, transform, and build upon the material" -msgstr "**Adaptar**—remixar, transformar, e criar a partir do material" - -#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 -msgid "" -"**Attribution**—You must give appropriate credit (mentioning that your work " -"is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a `link to the license `_, and indicate if changes " -"were made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." -msgstr "" -"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " -"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " -"Language project», e, quando prático, criar uma ligação para https://www." -"commonwl.org/ ), fornecer um `link para a licença `_, e " -"indicar se foram feitas alterações. Você pode fazê-lo de qualquer forma " -"razoável, mas não de uma forma que sugira que o licenciante o apoia ou " -"aprova o seu uso." - -#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 -msgid "" -"**No additional restrictions**—You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" -msgstr "" -"**Sem restrições adicionais**—Você não pode aplicar termos jurídicos ou " -"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " -"algo que a licença permita. Com o entendimento de que:" - -#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"`OSI`_-approved `Apache 2.0 license `_." -msgstr "" -"Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " -"`licença Apache 2.0 `_ aprovada pela `OSI`_." - -#: ../../LICENSE.rst:50 9c4d58a1129a4d4eb4db1bfabbeddb6e -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." -msgstr "" From 6b74133f5986eb2364e88ee9642d688ca4a98d49 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 16:17:18 +0100 Subject: [PATCH 49/49] add command to update translations --- Makefile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/Makefile b/Makefile index c549b172..c4627689 100644 --- a/Makefile +++ b/Makefile @@ -42,6 +42,10 @@ check-json: container-pull: for container in $$(git grep dockerPull $$(git ls-files *.cwl) | awk '-F: ' '{print $$3}'); do docker pull $${container}; done +update_translations: gettext + sphinx-intl update -p _build/gettext + + .PHONY: help clean watch unittest-examples check-json Makefile # Catch-all target : route all unknown targets to Sphinx using the new