Finding the workflow (method) you need (and its JSON) in the Methods Repository

Allie Hajian
  • Updated

Many workflows already exist in Terra to help carry out different steps in your research journey. Below is a step-by-step outline for finding workflows in the Broad Methods Repository. 

FireCloud "methods" are called "workflows" in Terra

1. Click on "Workflows" in the main drop-down menu at the top left on any page in Terra:

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2. Here you'll find the Terra workflows library, which features GATK4 Best Practices WDLs front and center:

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3. If the workflow you need is not there, you can find additional workflows in Dockstore or the Broad Methods Repository by selecting one of these options in the menu on the right side of the page:

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4. The Broad Methods Repository link will take you to the legacy Methods repository, where you can browse and search public and featured workflows/methods: 

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5. To export the workflow or for more information, click on the workflow name (a link in the "Method" column).

You will be taken to the workflow page, which will include a summary description as well as configuration and snapshot options (if available).

You can export the workflow to your workspace by clicking the Export button (arrow at right in the screenshot) or clone it by selecting the "Clone" button (circled at left in the screenshot below) :

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A copy of the workflow will now be in the Workflows tab of your workspace, ready for you to use for bulk analysis!

 

 

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