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Contributing to lantern-gwas

Thank you for your interest in contributing to this project. This repository accompanies a peer-reviewed manuscript and is primarily maintained as a reproducibility resource. We welcome contributions that improve usability, fix bugs, or extend the pipeline to new conditions or datasets.

Ways to Contribute

Bug Reports

If you find a bug — incorrect output, a script that fails to run, or behavior that doesn't match the documentation — please open a GitHub Issue with:

  • A clear description of the problem
  • The script name and relevant section
  • The error message or unexpected output
  • Your Hail version and All of Us dataset version (if applicable)

Code Improvements

We welcome pull requests for:

  • Bug fixes
  • Improved error handling or logging
  • Documentation improvements
  • Performance optimizations
  • Support for new All of Us dataset versions (e.g. v9+)

Extending the Pipeline

If you have adapted this pipeline for a related condition or dataset and would like to contribute your extensions, please open an Issue first to discuss before submitting a pull request. We are particularly interested in extensions to:

  • Additional lymphatic or adipose conditions
  • Other large EHR-linked biobanks (UK Biobank, BioMe, etc.)
  • Updated Hail versions

Getting Started

  1. Fork the repository on GitHub
  2. Clone your fork locally
  3. Create a feature branch: git checkout -b fix/your-fix-name
  4. Make your changes
  5. Test your changes in an All of Us Workbench environment if possible
  6. Commit with a clear message (see below)
  7. Push to your fork and open a Pull Request

Commit Message Format

Please use clear, descriptive commit messages. We loosely follow the conventional commits format:

fix: correct chrX PAR filter ordering in lipedema pipeline
feat: add support for Hail v0.2.x annotation API
docs: update cluster configuration for AoU v9
refactor: consolidate QC thresholds into shared config module

Code Style

  • Python 3.10+
  • Follow PEP 8 conventions
  • Use descriptive variable names — this is scientific code that others will need to read and audit
  • Include docstrings on all functions
  • Comment any Hail-specific workarounds or non-obvious implementation choices (see the chrX PAR fix in gwas_lipedema_v2.py as an example)
  • Do not hardcode bucket paths, person IDs, or any workspace-specific identifiers — use os.environ["WORKSPACE_BUCKET"] or equivalent

Data and Privacy

Never commit individual-level data. This includes:

  • CSV files containing person IDs or phenotype data
  • GWAS summary statistics with small cell sizes
  • Any file that could be used to re-identify participants

The .gitignore is configured to exclude common data file types. If you are unsure whether a file is safe to commit, do not commit it.

All contributors are expected to comply with the All of Us Data Use Agreement when working with or extending this pipeline.

Questions

For questions about the scientific methods, please open a GitHub Issue or contact the Ndhlovu Lab at Weill Cornell Medicine.

For questions about All of Us data access, see: All of Us Support