CODEWITHSUNDEEP
pythonamazon-web-servicesbioinformaticsgenomicswdl
Avery85
Avery85

Reputation: 133

How to collapse/un-nest an Array[File] output in WDL workflow?

I am running a WDL workflow. Here is the output block in the main workflow

    output {
        Array[File] out_foos = some_task.foos
    }

Let's say that array had three elements. The output files would then look like this:

/path/to/out/out_foos/00/fooA.txt
/path/to/out/out_foos/01/fooB.txt
/path/to/out/out_foos/02/fooC.txt

How do I change it so that the output is less nested so it instead looks like this:

/path/to/out/out_foos/fooA.txt
/path/to/out/out_foos/fooB.txt
/path/to/out/out_foos/fooC.txt

My preference is to make this happen with the workflow. I would also be open, however, to just moving the files after the workflow finishes, but this workflow is being submitted to aws with aws omics start-run so it's not clear to me how to do that either

Upvotes: 0

Views: 43

Answers (0)

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