how to run latest GATK Best Practices workflows Pinned Answered

Post author
Ashish Agarwal

I believe the latest implementation of GATK's Best Practices workflows are at How can I run one of the WDL workflows there on Terra? AFAICT, none of the pipelines listed in the Terra library, which is titled "GATK4 Best Practices workflows", corresponds to any of the WDL scripts at 

Conversely, clicking one of the workflows listed in the library redirects to Firecloud, where we can see the WDL for that workflow, for example this one. Where does this WDL come from? Presumably this one is published by the Broad somewhere, but it is not clear which of their github repos it is from, if any. The summary links to dockstore and the gatk repo's script directory, but it is not clear where therein one could find this exact WDL.

Tagging Beri since I believe you manage the workspaces in question. Thank you for any help.



  • Comment author
    • Edited

    Hi Ashish Agarwal

    The easiest place you can access the latest implementation GATK's Best Practices workflows to be run on Terra is GATK Best Practices Workflows collection in Dockstore. Currently the workflows within the collection originate from one of the repositories in the gatk-workflows git organization or GATK git repo

    Yes, the workflows in the Terra library redirects users to the Firecloud repository which have older version of the GATK workflows. Eventually we'd like to replace these with links to direct users to their respective Dockstore location, until then we've added a note to the workflow description pointing to the Dockstore GATK collection.

    You are correct about pre-processing-hg38-gatk4 not being available in the Dockstore collection, I've recently added it to the collection so it should be available now (link). You should be able to find any of the workflows mentioned in the Terra Library in the GATK dockstore collection, if not, inform us and it will be corrected. 


  • Comment author
    Ashish Agarwal

    Beri, thank you for the explanations. I understand better now the different resources.


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