Writing WDL Workflows in Terra (The Course)
Free!
Minimum price
$19.00
Minimum paid price

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

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.

Share

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

Instructors

The Leanpub 60 Day 100% Happiness Guarantee

Within 60 days of purchase you can get a 100% refund on any Leanpub purchase, in two clicks.

Now, this is technically risky for us, since you'll have the book or course files either way. But we're so confident in our products and services, and in our authors and readers, that we're happy to offer a full money back guarantee for everything we sell.

You can only find out how good something is by trying it, and because of our 100% money back guarantee there's literally no risk to do so!

So, there's no reason not to click the Add to Cart button, is there?

See full terms...

Earn $8 on a $10 Purchase, and $16 on a $20 Purchase

We pay 80% royalties on purchases of $7.99 or more, and 80% royalties minus a 50 cent flat fee on purchases between $0.99 and $7.98. You earn $8 on a $10 sale, and $16 on a $20 sale. So, if we sell 5000 non-refunded copies of your book for $20, you'll earn $80,000.

(Yes, some authors have already earned much more than that on Leanpub.)

In fact, authors have earnedover $13 millionwriting, publishing and selling on Leanpub.

Learn more about writing on Leanpub

Free Updates. DRM Free.

If you buy a Leanpub book, you get free updates for as long as the author updates the book! Many authors use Leanpub to publish their books in-progress, while they are writing them. All readers get free updates, regardless of when they bought the book or how much they paid (including free).

Most Leanpub books are available in PDF (for computers) and EPUB (for phones, tablets and Kindle). The formats that a book includes are shown at the top right corner of this page.

Finally, Leanpub books don't have any DRM copy-protection nonsense, so you can easily read them on any supported device.

Learn more about Leanpub's ebook formats and where to read them

Write and Publish on Leanpub

You can use Leanpub to easily write, publish and sell in-progress and completed ebooks and online courses!

Leanpub is a powerful platform for serious authors, combining a simple, elegant writing and publishing workflow with a store focused on selling in-progress ebooks.

Leanpub is a magical typewriter for authors: just write in plain text, and to publish your ebook, just click a button. (Or, if you are producing your ebook your own way, you can even upload your own PDF and/or EPUB files and then publish with one click!) It really is that easy.

Learn more about writing on Leanpub