CWL Support in Terra

Post author
Chris Miller

A large chunk of the cancer genomics community has invested heavily in CWL for developing genomics workflows. Since Cromwell already supports CWL, it would be great to see Terra support it as well.

Comments

9 comments

  • Comment author
    Malachi Griffith

    Specific examples of large scale cancer genomics efforts that are using CWL.

    - The NCI Genomic Data Commons harmonized analyses of TCGA and other large datasets are very widely.  GDC has several CWL pipelines
    - The Pan Cancer Analysis of Whole Genomes, International Cancer Genome Consortium, and Seven Bridges used CWL for variant calling on a large set of whole genomes
    - McDonnell Genome Institute CWL pipelines for alignment, somatic variant calling, germline variant calling, WGBS, bulk RNA-seq, sc-RNA, etc.
    - The Gabriella Miller Kids First Data Resource Center uses CWL for their workflows.
    - bcbio generates CWL workflows
    - The Illumina Connected Analytics service uses CWL definitions.
    - ...

     

    2
  • Comment author
    Jason Cerrato

    Hi Chris and Malachi,

    Thanks so much for this feature request and for these details. We're trying to get a better sense of how much demand there is for CWL support in Terra, so this is helpful information. If any of your colleagues would also like to see this support built into Terra, please refer them to this thread to upvote and comment. We'll be happy to pass these details on to one of our product managers for consideration.

    Kind regards,
    Jason

    2
  • Comment author
    Michelle White

    Hi all,

    There are several members of the Karlsson lab that are also looking for CWL support in Terra. We have collaborators using Seven Bridges and Kids First pipelines referenced above and it would make our work significantly easier and more efficient if we could clone these workflows, adjust them to work for non-human samples, and share those new workflows between institutions.

    Thank you,

    Michelle

    1
  • Comment author
    Malachi Griffith

    Here is another nice example, showing the breadth of researchers using CWL.  

    https://github.com/Duke-GCB/GGR-cwl

    In this case, much of it related to fundamental functional genomics. 

     

    0
  • Comment author
    Jason Cerrato

    Hi Michelle and Malachi,

    Thank you so much for voicing your support here! We're keeping the appropriate team apprised of the ongoing support for this feature, and we'll follow-up in this thread if we hear any updates on CWL support being built into Terra.

    Kind regards,

    Jason

    0
  • Comment author
    Boyang Zhao

    Just furthering the upvote here. We also develop heavily using CWLs all our workflows, for both research and clinical analyses. It would be really great to have CWL support on Terra.

    0
  • Comment author
    Jason Cerrato

    Hi Boyang,

    Thank you for writing in with your support. I will inform our product team so that they are aware.

    Kind regards,

    Jason

    0
  • Comment author
    Andrey Kartashov

    University of Cincinnati and Cincinnati Children's Hospital are using CWL as well. https://github.com/Barski-lab/workflows & https://github.com/Barski-lab/cwl-airflow

    0
  • Comment author
    Emil Furat
    • Edited

    Hi Andrey,

    Thank you for writing in about your support for this feature. I will inform our product team so that they are aware.

    Kind regards,

    Emil

    0

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