nf-core/modules: Contributing Guidelines

Hi there! Many thanks for taking an interest in improving nf-core/modules.

We try to manage the required tasks for nf-core/modules using GitHub issues, you probably came to this page when creating one. Please use the pre-filled template to save time.

However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)

If you need help using or modifying nf-core/modules then the best place to ask is on the nf-core Slack #modules channel (join our Slack here).

Contribution workflow

If you'd like to write some code for nf-core/modules, the standard workflow is as follows:

Check that there isn't already an issue about your idea in the nf-core/modules issues to avoid duplicating work
- If there isn't one already, please create one so that others know you're working on this
Fork the nf-core/modules repository to your GitHub account
Make the necessary changes / additions within your forked repository following Pipeline conventions
When adding a module file, follow the guidelines
Ensure that tests are working locally
Submit a Pull Request against the dev branch and wait for the code to be reviewed and merged

If you're not used to this workflow with git, you can start with some docs from GitHub or even their excellent git resources.

Tests

When you create a pull request with changes, GitHub Actions will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.

Module tests

Each nf-core/module should be set up with a minimal set of test-data. GitHub Actions then runs the module on this data to ensure that it exits successfully. If there are any failures then the automated tests fail. These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code.

Patch

⚠️ Only in the unlikely and regretful event of a release happening with a bug.

On your own fork, make a new branch patch based on upstream/master.
Fix the bug, and bump version (X.Y.Z+1).
A PR should be made on master from patch to directly this particular bug.

Getting help

For further information/help, please consult the nf-core/modules README and don't hesitate to get in touch on the nf-core Slack #modules channel (join our Slack here).

Software version reporting

If you add a new module, please ensure you add the information of the tool.

Add to the script block of the process, something like the following:

<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true

<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true

Images and figures

For overview images and other documents we follow the nf-core style guidelines and examples.

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