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CONTRIBUTING.md

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Contributing

Thank you for your interest in contributing. If you have a bug to report or a question about an atomic workflow please create an issue. In the case of a bug report, the issue should contain

  • the command ran,
  • the error message, and
  • the compute environment (package and language versions)

If you'd like to add a workflow, or make modifications to an existing one, please do the following:

  1. Fork the project.
# Press "Fork" at the top right of the GitHub page
  1. Clone the fork and create a branch for your feature
git clone https://github.com/<USERNAME>/atomic-workflows.git
cd atomic-workflows
git checkout -b cool-new-feature
  1. Make changes, add files, and commit
# make changes, add files, and commit them
git add file1.py file2.ipynb
git commit -m "I made these changes"
  1. Push changes to GitHub
git push origin cool-new-feature

  1. Submit a pull request with the following

    • README.md containing

      • Inputs
      • Preprocessing tools
      • Preprocessing steps
      • Outputs
      • Metrics (and their utility)

    • spec.md with the assay sequencing library specification (defined with seqspec)

    • example.ipynb a Google Colab notebook executing the atomic workflow

Note: If you are unfamilar with pull requests, you can find more information on the GitHub help page.