Welcome to Choppy

Welcome to Choppy’s documentation. Get started with Installation and then get an overview with the Quickstart. There is also a more detailed tutorial that shows how to analyze omics data with Choppy. The rest of the docs describe each component of Choppy in detail, with a full reference in the api section.

Choppy depends on the Cromwell Workflow Management System and the WDL Workflow Definition Language. The documentation for these libraries can be found at:

• Cromwell documentation

• WDL documentation

User’s Guide

This part of the documentation, which is mostly prose, begins with some background information about Choppy, then focuses on step-by-step instructions for Reproducible Omics Pipeline with Choppy.

• Installation
  • Python Version
• Quickstart
  • RNA-Seq Example

API Reference

If you are looking for information on a specific function, class or method, this part of the documentation is for you.

Additional Notes

Design notes, legal information and changelog are here for the interested.

• Upgrading to Newer Releases
• Choppy Changelog
  • Version 0.3.8
• License
  • Authors
  • General License Definitions
  • Choppy License
• How to contribute to Choppy
  • Support questions
  • Reporting issues
  • Submitting choppy app