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Outputting and inputting a directory

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6 comments

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    Jason Cerrato

    Hi Alex,

    Can you share the workspace where you're running this with GROUP_FireCloud-Support@firecloud.org so we can take a closer look at the job? Please also share the workflow with jcerrato@broadinstitute.org if it's not publicly available.

    Many thanks,

    Jason

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    Alex O

    Shared

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    Jason Cerrato

    Hi Alex,

    Can you also share the workflow with jcerrato@broadinstitute.org so I can take a closer look at the WDL itself?

     

    Many thanks,

    Jason

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    Alex O

    Added, but versions 3 and 5 were edits I made to try to get it to work. The one that gave me the error originally was v2. Thanks!

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    Jason Cerrato

    Hi Alex,

    It looks like the root of the issue is the trying to delocalize a directory, which is not something you can do. However, you have a couple options.

    You can’t delocalize a directory as a File, but an array of files can technically delocalize the directory contents with a glob():
    output {
    Array[File] directoryContents = glob("myDir/*")
    }
    Then you can use the array of files elsewhere, but the array is technically not the same as a “directory”. See the docs here: https://github.com/openwdl/wdl/blob/master/versions/1.0/SPEC.md#globs
     
    The other way to "delocalize directories” is to tar the contents using something like tar czf myDir.tgz myDir then
    output {
    File myDirTgz = "myDir.tgz"
    }
    Then the next steps can untar the previous output.
     

    I hope that makes sense. If you have any questions, please let us know.

    Kind regards,

    Jason

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    Alex O

    Awesome, thank you so much!

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