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Import wdl from GCS

Hello-
I'm trying to a get a pipeline up and running in FC and can't seem to figure out wdl imports. I'd like to have the main method as a simple wdl that imports various other sub-workflows that are commonly used by different pipelines (like QC or format conversions). Rather than copy-pasting the common tasks in every pipeline, they're stored in a google bucket and should simply be imported by some hardcoded url.

When I try to test this locally with test.wdl:

import "http://path/to/wdl.wdl" as subwf

workflow wf {
  call subwf.task1
}

calling :

java -jar wdltool-0.12.jar validate test.wdl

It seems that the url is being interpreted as a local path:

Failed to import workflow http://path/to/wdl.wdl.:
File not found /Users/tmajaria/http://path/to/wdl.wdl

This same problem occurs using the GCS link (gs://path/to/something). So basically, are urls supported in import statements? Or is there another method for importing wdls from some remote repo when running in FC?

Thanks!

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Best Answer

Answers

  • KateNKateN Cambridge, MAMember, Broadie, Moderator

    The developers are currently working on getting import statements in FireCloud. We hope to have it done this quarter, so keep an eye on the release notes for it over the next few months.

  • manidrmanidr Cambridge, MAMember

    Are both WDL file imports and URL imports being currently implemented? The WDL documentation seems to state that WDL file imports are "Cromwell supported" while URL imports are "Coming soon in Cromwell". I am trying to implement a 2-level scatter, and using a sub-workflow via WDL file import seems to be the only way ...

  • KateNKateN Cambridge, MAMember, Broadie, Moderator
    edited October 2017

    Only WDL URL imports will be implemented with the above-mentioned FireCloud update. File imports will be implemented at a later date.

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