Common Workflow Language for Bioinformatics

Common Workflow Language (or CWL), is a growing language for defining workflows in a cross-platform and cross-domain manner. In biology in particular, we need workflows to automate complex analyses such as DNA variant calling, RNA sequencing, and genome assembly. CWL provides a simple and well-defined format for automating these analysis by specifying their stages and connections using readable CWL documents.

CWL makes use of a number of existing standards, including support for cluster computing using SLURM or PBS, containerisation using Docker, and deployment using common packaging formats. In addition, the CWL ecosystem has grown to include workflow visualisation tools, graphical workflow editors, libraries for interacting with CWL programatically and tools that convert to and from CWL and other workflow formats.

Learning Objectives

By the end of this workshop will understand the concepts of:

• Wrapping tools using the CWL standard
• Writing CWL workflows
• Running CWL on different computing environments
• Using Docker containers to ensure reproducibility
• Sharing CWL tools and workflows
• Use-cases for CWL in bioinformatics

Requirements

This workshop requires basic Unix command-line experience.

Attendees are required to bring their own laptop computers.