Welcome to Choppy

Choppy: reproducible omics pipeline

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:

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.

API Reference

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