Importing nextflow pipeline to the project

Iman Nazari

Dear UKB-RAP team, 

I would appreciate it if you help let me know GUI to add nextflow pipeline is available on UKB-RAP? or the only way is to use dx-toolkit?    

 

Thanks

Iman

Comments

2 comments

Date Votes
  • Comment author
    Dr. Mc. Ninja

    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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  • Comment author
    Iman Nazari

    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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