Workflows

Terra uses pipelines (workflows) in Workflow Description Language (WDLs) for batch processing genomics data. This section includes documentation on how to set up and run WDLS workflows using sample or your own data in a Google Cloud bucket and additional WDLs resources.

Sections

• Workflows setup
  • Workflow setup: Configuring inputs
  • Workflow setup: Writing outputs to the data table
  • Workflow setup: VM and other options
  • Selecting the root entity type
  • When to use a set table for a workflow
• WDLs Resources
  • Overview: Getting started with WDL

Articles

• Get started running workflows
• Getting started with GATK workflows in the cloud FAQs
• Finding the workflow (method) you need (and its JSON) in the Methods Repository
• Import a workflow and its parameter file from Dockstore into Terra
• What happens when you launch a workflow?
• Monitor and troubleshoot in the Job History tab
• Getting workflows up and running faster with a JSON file
• Scaling your workflow submissions
• Create, edit, and share a new workflow
• Creating a list file of reads for input to a workflow
• How to test workflows locally
• Manage data/automate workflows with the FISS API
• Deeper dive: WDLs, workflows, tasks
• Accessing archived workflow details