Writing WDL Workflows in Terra (The Course)
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Course Info

This course includes 1 attempt.

This course introduces WDL Workflows on Terra. After introducing several concepts, including basic WDL syntax, we present hands-on exercises to run a workflow, write a WDL, localize a file, and customize a Docker image.

By the end of this course, you will be able to:

  1. Understand when WDL Workflows are the right tool
  2. Run a Workflow on Terra
  3. Write a WDL using Broad Methods Repository
  4. Bring your own data to analyze
  5. Customize your Docker environment
  6. Find additional support resources


  • You should have a Terra account and be at least somewhat familiar with Terra. If you're not already familiar with Terra, take the Intro to Terra course.
  • You do not need to install any software.
  • You do not need any prior knowledge of genetics or programming.

It should take approximately 1.5-2 hours to complete this course, including hands-on exercises.


Course Material

  • Overview
  • Skills level
  • Course goals
  • Timing
  • Branding
  • Acknowledgements
  • Next: Leanpub logistics
  • Leanpub logistics
  • Course materials
  • Course discussion
  • Chapter 1: Review Workflows on Terra
  • 1.1 Optional: What is a workflow?
  • 1.2 Optional: Running a workflow in Terra
  • Chapter 1 Quiz
  • icon/quiz Created with Sketch.
    Chapter 1 Quiz3 attempts allowed
  • Chapter 1 quiz review
  • Next: Import and configure a workflow
  • Chapter 2: Import and Configure Workflows
  • 2.1 Importing workflows into Terra
  • 2.2 Configuring workflows with JSON files
  • 2.3 Further reading
  • Chapter 2 Quiz
  • icon/quiz Created with Sketch.
    Chapter 2 Quiz3 attempts allowed
  • Chapter 2 quiz review
  • Next: Write an introductory WDL
  • Chapter 3: Write an Introductory WDL
  • 3.1 Access Broad Methods Respository
  • 3.2 WDL script structure
  • 3.3 Write a hello-input WDL
  • 3.4 Export to Terra and run
  • Chapter 3 Quiz
  • icon/quiz Created with Sketch.
    Chapter 3 Quiz3 attempts allowed
  • Chapter 3 quiz review
  • Next: Write a WDL to calculate idxstats on multiple files
  • Chapter 4: Calculate Idxstats on Multiple Files
  • 4.1 Clone data workspace
  • 4.2 Write an idxstats WDL
  • 4.3 Optional: Run idxstats WDL on multiple .bam files
  • 4.4 Customize your workflow’s setup with WDL
  • Chapter 4 Quiz
  • icon/quiz Created with Sketch.
    Chapter 4 Quiz3 attempts allowed
  • Chapter 4 quiz review
  • Next: Customize Docker
  • Chapter 5: Customize Docker
  • 5.1 Prerequisites
  • 5.2 Containerization with Docker
  • 5.3 Using a published Docker image out of the box
  • 5.4 Configure GitHub Actions
  • 5.5 Build Docker image
  • 5.6 Use your image with the idxstats WDL
  • 5.7 Run idxstats workflow
  • 5.8 Best practices for using Docker
  • Further reading
  • Chapter 5 Quiz
  • icon/quiz Created with Sketch.
    Chapter 5 Quiz3 attempts allowed
  • Chapter 5 Quiz review
  • Next: Course wrapup
  • Course Conclusion
  • Course survey
  • Getting help


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