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Contributing

Contributions are welcome when they improve reproducibility, correctness, portability, or documentation.

Development setup

git clone https://github.com/Ekin-Kahraman/rnaseq-nextflow-pipeline.git
cd rnaseq-nextflow-pipeline
python test/create_test_data.py
nextflow run main.nf -profile test,docker --outdir test_results
python scripts/validate_outputs.py test_results

Use -profile test for pull requests. It builds a tiny synthetic reference and verifies the full software path without downloading controlled or patient-derived data.

Pull request checklist

  • The test profile completes locally.
  • python scripts/validate_outputs.py <outdir> passes.
  • New parameters are documented in README.md and nextflow.config.
  • Changes affecting cloud execution update docs/cloud.md.
  • Output layout changes are reflected in the README output tree.

Scope

Preferred contributions:

  • Additional aligner or quantifier options with tests
  • More robust schema validation
  • Cloud execution improvements
  • Documentation for real datasets
  • Bug fixes in output validation

Out of scope:

  • Committing real FASTQ files, large references, or private metadata
  • Unpinned custom containers without a clear reason
  • Changes that silently alter biological interpretation without documenting the effect

Licence

By contributing, you agree that your contributions are licensed under the MIT licence.