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@@ -15,11 +15,11 @@ Contributions to the code are even more welcome ;)
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If you'd like to write some code for nf-core/pangenome, the standard workflow is as follows:
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1. Check that there isn't already an issue about your idea in the [nf-core/pangenome issues](https://github.com/nf-core/pangenome/issues) to avoid duplicating work
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* If there isn't one already, please create one so that others know you're working on this
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1. Check that there isn't already an issue about your idea in the [nf-core/pangenome issues](https://github.com/nf-core/pangenome/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
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2.[Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/pangenome repository](https://github.com/nf-core/pangenome) to your GitHub account
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3. Make the necessary changes / additions within your forked repository
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4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
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3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
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4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
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5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
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If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
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There are typically two types of tests that run:
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### Lint Tests
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### Lint tests
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`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
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To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
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If any failures or warnings are encountered, please follow the listed URL for more documentation.
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### Pipeline Tests
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### Pipeline tests
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Each `nf-core` pipeline should be set up with a minimal set of test-data.
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`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
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## Patch
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:warning: Only in the unlikely and regretful event of a release happening with a bug.
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:warning: Only in the unlikely and regretful event of a release happening with a bug.
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* On your own fork, make a new branch `patch` based on `upstream/master`.
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* Fix the bug, and bump version (X.Y.Z+1).
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* A PR should be made on `master` from patch to directly this particular bug.
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- On your own fork, make a new branch `patch` based on `upstream/master`.
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- Fix the bug, and bump version (X.Y.Z+1).
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- A PR should be made on `master` from patch to directly this particular bug.
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## Getting help
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For further information/help, please consult the [nf-core/pangenome documentation](https://nf-co.re/pangenome/docs) and don't hesitate to get in touch on the nf-core Slack [#pangenome](https://nfcore.slack.com/channels/pangenome) channel ([join our Slack here](https://nf-co.re/join/slack)).
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For further information/help, please consult the [nf-core/pangenome documentation](https://nf-co.re/pangenome/usage) and don't hesitate to get in touch on the nf-core Slack [#pangenome](https://nfcore.slack.com/channels/pangenome) channel ([join our Slack here](https://nf-co.re/join/slack)).
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## Pipeline contribution conventions
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To make the nf-core/pangenome code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
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### Adding a new step
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If you wish to contribute a new step, please use the following coding standards:
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1. Define the corresponding input channel into your new process from the expected previous process channel
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2. Write the process block (see below).
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3. Define the output channel if needed (see below).
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4. Add any new parameters to `nextflow.config` with a default (see below).
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5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
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6. Add sanity checks and validation for all relevant parameters.
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7. Perform local tests to validate that the new code works as expected.
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8. If applicable, add a new test command in `.github/workflow/ci.yml`.
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9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
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10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
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### Default values
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Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
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Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
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### Default processes resource requirements
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Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
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The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
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### Naming schemes
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Please use the following naming schemes, to make it easy to understand what is going where.
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- initial process channel: `ch_output_from_<process>`
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- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
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### Nextflow version bumping
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If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
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### Images and figures
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For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
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## GitHub Codespaces
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This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
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To get started:
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- Open the repo in [Codespaces](https://github.com/nf-core/pangenome/codespaces)
description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: command_used
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attributes:
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label: Command used and terminal output
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description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
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render: console
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placeholder: |
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$ nextflow run ...
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Some output where something broke
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- type: textarea
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id: files
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attributes:
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label: Relevant files
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description: |
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Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
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Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
description: Suggest an idea for the nf-core/pangenome pipeline
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labels: enhancement
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body:
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- type: textarea
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id: description
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attributes:
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label: Description of feature
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description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
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