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https://github.com/MillironX/nf-core_modules.git
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71 lines
3.6 KiB
Markdown
71 lines
3.6 KiB
Markdown
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# nf-core/modules: Contributing Guidelines
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Hi there!
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Many thanks for taking an interest in improving nf-core/modules.
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We try to manage the required tasks for nf-core/modules 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/modules then the best place to ask is on the nf-core Slack [#modules](https://nfcore.slack.com/channels/modules) 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/modules, 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/modules issues](https://github.com/nf-core/modules/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/modules repository](https://github.com/nf-core/modules) 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. When adding a module file, follow the [guidelines](https://github.com/nf-core/modules#adding-a-new-module-file)
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5. Ensure that [tests are working locally](https://github.com/nf-core/modules#running-tests-locally)
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6. 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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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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### Module tests
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Each `nf-core/module` should be set up with a minimal set of test-data.
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`GitHub Actions` then runs the module on this data to ensure that it exits successfully.
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If there are any failures then the automated tests fail.
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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.
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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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* 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/modules README](https://github.com/nf-core/modules) and don't hesitate to get in touch on the nf-core Slack [#modules](https://nfcore.slack.com/channels/modules) channel ([join our Slack here](https://nf-co.re/join/slack)).
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### Software version reporting
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If you add a new module, please ensure you add the information of the tool.
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Add to the script block of the process, something like the following:
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```bash
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<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
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```
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or
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```bash
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<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
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```
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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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