Getting Involved

GenPipes bioinformatics pipelines were originally developed at the Canadian Centre for Computational Genomics (C3G), as part of the GenAP project. These, are now available for public use. GenPipes includes a wide array of pipelines, including RNA-Seq, ChIP-Seq, WGS, exome sequencing, Bisulfite sequencing, Hi-C, capture Hi-C, metagenomics and the latest SARS-CoV-2 genome sequencing pipeline.

Contributing to GenPipes

We love your input!

The objective of this document is to make contributing to GenPipes as easy and transparent as possible, for any of the following types of contributions from the wider community:

  1. Reporting a bug or issue

  2. Submitting a fix

  3. Proposing new features

  4. Discussing code optimizations

  5. Becoming a maintainer

Tracking GenPipes Issues and Feature Requests

GenPipes uses Bitbucket to host its source code, track issues and feature requests, as well as pull requests.

Pull requests are the best way to propose changes to the code base. Please ensure that you follow the following process as GenPipes is complex and requires careful validation of any updates. Also, you may need computational resources as GenPipes is demanding in terms of compute resources.

  • Fork the repo and create your branch from master.

  • If you have added code that should be tested, add tests.

  • If applicable, update the documentation.

  • Ensure the test suite passes.

  • Make sure your code lints.

  • Issue that pull request!


GenPipes is available under the LGPL license. Any contributions you make will be under the LGPLv3 license.

Reporting a bug or issue

You can report a bug or an issue related to GenPipes using the following template:

  • Single line summary briefly describing the issue

  • Steps to reproduce
    • Specific instructions

    • If required, provided commands and code that caused the issue

    • Make sure you specify GenPipes version number, deployment type

  • What was expected and what actually happened

  • Other insights or logs that can help debug the issue.

This guide is adapted from FaceBook Draft.js Guide.