Importing nextflow pipeline to the project

• 

  Dr. Mc. Ninja

  • 16 May 2025 08:56

  I got the answer below from my assistant, but when I tried it, I didn't see the option to import pipeline.

  It seems that DNANexus DOES have this feature, but that UKB RAP doesn't have it enabled.

  e.g. 

  https://documentation.dnanexus.com/developer/workflows/importing-workflows

  This clearly shows the ‘Import Pipeline Workflow’ feature that my assistant referenced in her (incorrect) answer below.

   

  Could be worth asking directly if this can be turned on / why it's turned off. Let us know what you find.

   

  Cheers,
  Dan.

   

  INCORRECT ANSWER BASED ON CONFUSING GENERIC DNANEXUS INFO WITH UKB RAP SPECIFIC FEATURES…

  Yes — the DNAnexus/UKB-RAP interface does give you a point-and-click way to bring in a Nextflow pipeline.

  • Web-GUI import: In any project’s Manage tab choose Add → Import Pipeline / Workflow.
    The dialog lets you paste the public Git URL (or DNAnexus file link) of the external workflow and pick the destination folder; the platform then registers it as a regular workflow object that you can edit and launch from the browser just like any other pipeline .
  • Running it: Once imported the workflow appears in the project list; you can open it, connect inputs graphically and click Start Analysis. If you prefer, you can still execute it from the CLI with dx run <workflow> .
  • CLI / automation options:
    • dx-toolkit — build or update a workflow from a local dxworkflow.json, lock it, version it, etc.
    • Cloud Workstation / Jupyter — run raw nextflow run … commands entirely at the shell or in a notebook when you need full control over Nextflow execution rather than a DNAnexus workflow object .

  So the GUI route is available for adding and running a Nextflow pipeline; the dx-toolkit and workstation/Jupyter methods are alternatives when you need scripting or tighter version control.

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• 

  Iman Nazari

  • 16 May 2025 10:11

  Dear Dan 

   

  Thanks for your comment on this issues, 

  has been a long time i am trying to find someone who did it before and unfortunately i couldn't find any, and also in terms of the GUI  i have faced the same issue.

   

  I am following this issue to see what we need to do at the end, i will keep you updated here.

   

  BW

  Iman

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• 

  Daniil Igumnov

  • 06 July 2025 09:49

  AFAIK there's no support for Nextflow import to UKB RAP. It exists on DNAnexus per se, but there is no such option on RAP unfortunately. We can either import WDL or make a RAP-locked applet (which you won't be able to migrate elsewhere). 

  So I suppose we need to wait for the whole nextflow workflow support…

   

   

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• 

  Tom Willis

  • 22 July 2025 21:52

  Thanks, Daniil, it's helpful to learn that. Very disappointing!

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