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Copy file name to clipboardExpand all lines: .github/CONTRIBUTING.md
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# nf-core/dragen: Contributing Guidelines
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# `seqeralabs/nf-dragen`: Contributing Guidelines
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Hi there!
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Many thanks for taking an interest in improving nf-core/dragen.
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Many thanks for taking an interest in improving seqeralabs/nf-dragen.
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We try to manage the required tasks for nf-core/dragen using GitHub issues, you probably came to this page when creating one.
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We try to manage the required tasks for seqeralabs/nf-dragen using GitHub issues, you probably came to this page when creating one.
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Please use the pre-filled template to save time.
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However, don't be put off by this template - other more general issues and suggestions are welcome!
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Contributions to the code are even more welcome ;)
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> If you need help using or modifying nf-core/dragen then the best place to ask is on the nf-core Slack [#dragen](https://nfcore.slack.com/channels/dragen) channel ([join our Slack here](https://nf-co.re/join/slack)).
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## Contribution workflow
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If you'd like to write some code for nf-core/dragen, the standard workflow is as follows:
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If you'd like to write some code for seqeralabs/nf-dragen, 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/dragen issues](https://github.com/nf-core/dragen/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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2.[Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/dragen repository](https://github.com/nf-core/dragen) to your GitHub account
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1. Check that there isn't already an issue about your idea in the [seqeralabs/nf-dragen issues](https://github.com/seqeralabs/nf-dragen/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 [seqeralabs/nf-dragen repository](https://github.com/seqeralabs/nf-dragen) to your GitHub account
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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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4. Use `nf-core pipelines 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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## Tests
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You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
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```bash
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nf-test test --profile debug,test,docker --verbose
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```
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When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
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Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
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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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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 pipelines 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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: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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## Getting help
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For further information/help, please consult the [nf-core/dragen documentation](https://nf-co.re/dragen/usage) and don't hesitate to get in touch on the nf-core Slack [#dragen](https://nfcore.slack.com/channels/dragen) channel ([join our Slack here](https://nf-co.re/join/slack)).
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- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
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- Fix the bug, and bump version (X.Y.Z+1).
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- Open a pull-request from `patch` to `main`/`master` with the changes.
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## Pipeline contribution conventions
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To make the nf-core/dragen 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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To make the `seqeralabs/nf-dragen` 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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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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5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines 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.yaml` 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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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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Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
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Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
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Once there, use `nf-core pipelines 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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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/main/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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The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${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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- 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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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 pipelines bump-version --nextflow . [min-nf-version]`
Copy file name to clipboardExpand all lines: .github/PULL_REQUEST_TEMPLATE.md
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<!--
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# nf-core/dragen pull request
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# seqeralabs/dragen pull request
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Many thanks for contributing to nf-core/dragen!
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Many thanks for contributing to seqeralabs/dragen!
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Please fill in the appropriate checklist below (delete whatever is not relevant).
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These are the most common things requested on pull requests (PRs).
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Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
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Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/dragen/tree/master/.github/CONTRIBUTING.md)
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Learn more about contributing: [CONTRIBUTING.md](https://github.com/seqeralabs/dragen/tree/master/.github/CONTRIBUTING.md)
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-->
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<!-- markdownlint-disable ul-indent -->
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## PR checklist
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-[ ] This comment contains a description of changes (with reason).
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-[ ] If you've fixed a bug or added code that should be tested, add tests!
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-[ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/dragen/tree/master/.github/CONTRIBUTING.md)
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-[ ]If necessary, also make a PR on the nf-core/dragen _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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-[ ]Make sure your code lints (`nf-core lint`).
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-[ ]Ensure the test suite passes (`nextflow run . -profile test,docker`).
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-[ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/seqeralabs/dragen/tree/master/.github/CONTRIBUTING.md)
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-[ ]Make sure your code lints (`nf-core pipelines lint`).
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-[ ]Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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-[ ]Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
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-[ ] Usage Documentation in `docs/usage.md` is updated.
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-[ ] Output Documentation in `docs/output.md` is updated.
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