Writing WDL Workflows in Terra (The Course)
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:
- Understand when WDL Workflows are the right tool
- Run a Workflow on Terra
- Write a WDL using Broad Methods Repository
- Bring your own data to analyze
- Customize your Docker environment
- Find additional support resources
Pre-requisites:
- 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
- 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
- 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
- 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
- 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
- Chapter 5 Quiz3 attempts allowed
- Chapter 5 Quiz review
- Next: Course wrapup
- Course Conclusion
- Course survey
- Getting help
Instructors
Frederick Tan is on the Bioinformatics Research Faculty at Carnegie Institution, Department of Embryology, and an Adjunct Assistant Research Scientist at Johns Hopkins University, Department of Biology. His educational activities include the Practical Genomics Workshop, Quantitative Biology Bootcamp, C-MOOR, and AnVIL Outreach.
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