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 Quiz
3 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 Quiz
3 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 Quiz
3 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 Quiz
3 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 Quiz
3 attempts allowed
Chapter 5 Quiz review
Next: Course wrapup
Course Conclusion
Course survey
Getting help
Writing WDL Workflows in Terra
Writing WDL Workflows in Terra
This course provides you with the tools to write and run workflows on Terra. Hands-on exercises guide you through writing basic WDL scripts, pre-configuring workflows, and customizing your workflow's Docker containers.
The instructors are letting you choose the price you pay for this course!
The instructors are letting you choose the price you pay for this course!
This course provides you with the tools to write and run workflows on Terra. Hands-on exercises guide you through writing basic WDL scripts, pre-configuring workflows, and customizing your workflow's Docker containers.
About
About the Course
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.
Price
Course Price
Minimum price
Free!
$19.00
You pay
$0.00Instructors
About the Instructors
Leyla Tarhan
Frederick Tan
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.
Anton Kovalsky
Material
Course Material
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