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CONTRIBUTING.md

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Contributing to CoVigator pipeline

We love your input! We want to make contributing to this project as easy and transparent as possible, whether it's:

  • Reporting a bug
  • Discussing the current state of the code
  • Submitting a fix
  • Proposing new features
  • Becoming a maintainer

We Develop with Github

We use github to host code, to track issues and feature requests, as well as accept pull requests.

We Use Github Flow, So All Code Changes Happen Through Pull Requests

Pull requests are the best way to propose changes to the codebase (we use Github Flow). We actively welcome your pull requests:

  1. Fork the repo and create your branch from master.
  2. If you've added code that should be tested, add tests.
  3. If you've changed pipeline or the interface, update the documentation.
  4. Ensure the test suite passes.
  5. Issue that pull request!

Repository overview

The repository is organized as follows:

  • main.nf holds all the Nextflow code
  • environment-yml defines all conda dependencies
  • nextflow.config contains the nextflow configuration
  • bin folder contains the Python code for the variant calling over the FASTA file. Any other custom code shall be added here.
  • reference folder contains all reference files for SARS-CoV-2 which are used by default. To use CoVigator pipeline for a different organism these resources will need to be provided.

Run the tests

Execute the following to run the tests:

make

All test data is in the repository, but you will need Nextflow and conda installed.

These tests are automated in a private Gitlab instance, we may migrate this to GitHub CI system in the future.

Any contributions you make will be under the MIT Software License

In short, when you submit code changes, your submissions are understood to be under the same MIT License that covers the project. Feel free to contact the maintainers if that's a concern.

Report bugs using Github's issues

We use GitHub issues to track public bugs. Report a bug by opening a new issue; it's that easy!

Write bug reports with detail, background, and sample code

This is an example of a bug report I wrote, and I think it's not a bad model. Here's another example from Craig Hockenberry, an app developer whom I greatly respect.

Great Bug Reports tend to have:

  • A quick summary and/or background
  • Steps to reproduce
    • Be specific!
    • Give sample code if you can. My stackoverflow question includes sample code that anyone with a base R setup can run to reproduce what I was seeing
  • What you expected would happen
  • What actually happens
  • Notes (possibly including why you think this might be happening, or stuff you tried that didn't work)

License

By contributing, you agree that your contributions will be licensed under its MIT License.

References

This document was adapted from https://gist.github.com/briandk/3d2e8b3ec8daf5a27a62