Chapter 10 Workflows

Workflows allow you to run whole genomic pipelines in Terra. Workflows are written in WDL (Workflow Description Language), which is a human-readable and writable language originally developed for genomic analysis pipelines. Terra on AnVIL is specifically designed to integrate a WDL workflow’s input and output information directly into the platform. This integration allows you to easily configure a workflow from your Workspace. Established workflows help make analyses more reproducible. They also make it easier to configure, launch, and monitor analyses across many samples.

You can access workflows from a Workspace by clicking on the Workflows Tab.

Image shows a screenshot of the Workspace, with the Workflows Tab highlighted.

To run a workflow you can either use a pre-configured workflow, or create your own workflow.

10.0.1 Pre-configured Workflow

You will need to clone a Workspace that contains the workflow you’d like to run. Refer to Terra’s quickstart guide for running a pre-configured workflow. You can browse code and workflows in the AnVIL library here.

10.0.2 Create a Custom Workflow

Custom workflows are written in WDL. Refer to Terra’s “Hello, learn-wdl!” tutorial to learn the basics before fully customizing your analysis pipeline.