Nextflow support in Terra

Nextflow is a popular bioinformatics workflow language with a fast-growing community of users. It is technically possible to submit Nextflow workflows from within a notebook in Terra but it would be incredibly valuable to offer a user experience on par with Terra's WDL capabilities.

Comments

13 comments

  • Comment author
    Josh Evans

    Hi Geraldine,

    Thank you for writing in! I've sent this request to our development team for consideration, and I'll be happy to follow up with you if this feature gets built.

    Kind regards,

    Josh​ 

    2
  • Comment author
    Curtis Kapsak

    +1 it would be AMAZING if Nextflow workflows had full-fledged support in the same way that WDL workflows currently run on Terra.

     

    2
  • Comment author
    Josh Evans

    Hi Curtis,

    I've added you to the request, and I'll let you know if this feature gets built.

    Best,

    Josh

    0
  • Comment author
    Curtis Kapsak

    Thanks Josh!

    0
  • Comment author
    Casper Lumby

    Hi Josh,

    If possible, I'd also like to be informed about the status of this request.

    Many thanks!

    1
  • Comment author
    Josh Evans

    Hi Casper,

    Thanks for writing in and it's totally possible for us to keep you informed on this request! I've also added your name to the request.

    I'll let you know if the feature gets built.

    Thanks,

    Josh

    1
  • Comment author
    Casper Lumby

    Excellent, thanks!

    0
  • Comment author
    Kaur Alasoo

    The eQTL Catalogue (https://www.ebi.ac.uk/eqtl/) is also extensively using Nextflow workflows and we would love to be able to run those on Terra. 

    0
  • Comment author
    Josh Evans

    Hi Kaur,

    Thanks for writing in! I've added your name to the request and we'll update you if this feature gets built.

    Please let me know if you have any questions.

    Best,

    Josh

    0
  • Comment author
    Johanna Smith

    Hi I would also like to be updated if this feature gets built! Thanks.

    1
  • Comment author
    Nancy Chow

    Hello! I would like to echo this need. This would be great to move public health pathogen genomics forward. Please keep us updated if this feature gets built. Thank you!

    0
  • Comment author
    Shruti Marwaha

    I also request the support for Nextflow pipelines on Terra (and AnVIL). But may be I am missing something,  is it currently possible to run a nextflow pipeline on Terra? Geraldine's original message said "It is technically possible to submit Nextflow workflows from within a notebook in Terra". Can someone please elaborate?

    Best,
    Shruti

    Shruti Marwaha, PhD.
    Research Engineer,
    Stanford Center for Undiagnosed Diseases
    GREGoR (Genomics Research to Elucidate the Genetics of Rare disease) Stanford Site
    Stanford University

    0
  • Comment author
    Pamela Bretscher

    Hi Shruti,

    I can certainly add your name to this feature request and notify you if it gets built! 

    It is possible to run Nextflow pipelines from within a Jupyter notebook in Terra. This involves spinning up a Jupyter environment. However, running Nextflow pipelines as workflows in Terra is not currently possible but is expected to be supported in the future.

    Kind regards,

    Pamela

    0

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