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fix: add guidelines to PRs and issues
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.github/CONTRIBUTING.md
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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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.github/ISSUE_TEMPLATE/bug_report.md
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---
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name: Bug report
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about: Report something that is broken or incorrect
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title: "[BUG]"
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---
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<!--
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# nf-core/module bug report
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Hi there!
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Thanks for telling us about a problem with the modules.
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Please delete this text and anything that's not relevant from the template below:
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-->
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## Check Documentation
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I have checked the following places for your error:
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- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
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- [ ] [nf-core/module documentation](https://github.com/nf-core/modules/blob/master/README.md)
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## Description of the bug
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<!-- A clear and concise description of what the bug is. -->
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## Steps to reproduce
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Steps to reproduce the behaviour:
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1. Command line: <!-- [e.g. `nextflow run ...`] -->
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2. See error: <!-- [Please provide your error message] -->
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## Expected behaviour
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<!-- A clear and concise description of what you expected to happen. -->
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## Log files
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Have you provided the following extra information/files:
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- [ ] The command used to run the module
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- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the module -->
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## System
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- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
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- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
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- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
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- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
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## Nextflow Installation
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- Version: <!-- [e.g. 19.10.0] -->
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## Container engine
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- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
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- version: <!-- [e.g. 1.0.0] -->
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- Image tag: <!-- [e.g. nfcore/module:2.6] -->
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## Additional context
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<!-- Add any other context about the problem here. -->
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blank_issues_enabled: false
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contact_links:
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- name: Join nf-core
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url: https://nf-co.re/join
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about: Please join the nf-core community here
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- name: "Slack #modules channel"
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url: https://nfcore.slack.com/channels/modules
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about: Discussion about nf-core/modules
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.github/ISSUE_TEMPLATE/feature_request.md
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---
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name: Feature request
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about: Suggest an idea for nf-core/modules
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title: "[FEATURE]"
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---
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<!--
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# nf-core/modules feature request
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Hi there!
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Thanks for suggesting a new feature for the modules!
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Please delete this text and anything that's not relevant from the template below:
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-->
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## Is your feature request related to a problem? Please describe
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<!-- A clear and concise description of what the problem is. -->
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<!-- e.g. [I'm always frustrated when ...] -->
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## Describe the solution you'd like
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<!-- A clear and concise description of what you want to happen. -->
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## Describe alternatives you've considered
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<!-- A clear and concise description of any alternative solutions or features you've considered. -->
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## Additional context
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<!-- Add any other context about the feature request here. -->
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<!--
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# nf-core/modules pull request
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Many thanks for contributing to nf-core/modules!
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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 master branch.
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Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/modules/tree/master/.github/CONTRIBUTING.md)
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-->
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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 module conventions in the [contribution docs](https://github.com/nf-core/modules/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, include test data in your PR.
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- [ ] Remove all TODO statements.
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- [ ] Emit the `<SOFTWARE>.version.txt` file.
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- [ ] Follow the naming conventions.
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- [ ] Follow the parameters requirements.
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- [ ] Follow the input/output options guidelines.
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- [ ] Add a resource `label`
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- [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
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- [ ] Ensure that the test works (`PROFILE=docker pytest --tag <MODULE> --symlink --wt 2 --keep-workflow-wd`)
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