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how to run latest GATK Best Practices workflows

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    Beri Shifaw

    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. 

     

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    Ashish Agarwal

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

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