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Importing a workflow that has subworkflows from dockstore to firecloud

bshifawbshifaw Member, Broadie, Moderator admin
edited January 2019 in Ask the FireCloud Team

If i’m importing a workflow from dockstor to FC is there a proper way to import the subworkflows within the workflow?
1. Should i import using github raw file url. This may be the easist way since i don’t need to import the subworkflows to FC. The question here is whether its ok to leave the subworkflows out FC? Users would still be able to view to the subworkflows, but it wont be viewable in the FC method repo.
import "https://raw.githubusercontent.com/gatk-workflows/gatk4-exome-analysis-pipeline/dev/tasks/UnmappedBamToAlignedBam.wdl" as ToBam
2. Should I import the subworkflows into FC first, make sure they are public and use FC’s import url for in the main workflow? This would be elaborate because it would mean importing all workflows to FC, doing them in a particular order to make sure the higher level workflows has the correct snapshot from the FC import url, needing to always update the snapshot url in the main workflow for every update.
import "https://api.firecloud.org/ga4gh/v1/tools/gatk:alignment/versions/4/plain-WDL/descriptor" as Alignment
3. Should i just not try to import from dockstore, instead upload files directly to FC.

I’m leaning towards the first option, I was wondering if anyone sees a major flaw

Best Answer

  • bshifawbshifaw admin
    Accepted Answer

    Dev response:

    • "Importing directly from dockstore (by URL) and therefore bringing in subworkflows with relative paths within dockstore is the eventual future. "
    • "The only problem with 1 is that there will be probably be a period where the main workflow in FC will fail with w/e subworkflows you have on the dev branch of the repo. If you could point the FC workflow to a release version of gatk-workflows or something that would be better I think"

    I'll go ahead with option 1 and make sure the url points to a release tag

Answers

  • bshifawbshifaw Member, Broadie, Moderator admin
    Accepted Answer

    Dev response:

    • "Importing directly from dockstore (by URL) and therefore bringing in subworkflows with relative paths within dockstore is the eventual future. "
    • "The only problem with 1 is that there will be probably be a period where the main workflow in FC will fail with w/e subworkflows you have on the dev branch of the repo. If you could point the FC workflow to a release version of gatk-workflows or something that would be better I think"

    I'll go ahead with option 1 and make sure the url points to a release tag

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