Question: CWL 'glob' field not capturing files
0
gravatar for eduardo
18 months ago by
eduardo10
eduardo10 wrote:

In my workflow, I am unable to capture specific files using the 'glob' field from one of the step that outputs an array of files. The glob is ignored and I end up with all files.

I have tried the following:

outputs:
  sss_out:
        # type: File doesn't work. It has to be a file array
        type: File[]
        outputSource: sss/cwl_out
        outputBinding:
            # glob is ignored
            glob: "*.xml.xml"

Example:

cwltool https://raw.githubusercontent.com/esanzgar/gluetools-cwl/master/playground/glob_not_working.cwl

Any ideas on how to grab specific files from one workflow step using a 'glob'?

Thanks!

cwl • 780 views
ADD COMMENTlink modified 18 months ago by Michael R. Crusoe1.4k • written 18 months ago by eduardo10
0
gravatar for Michael R. Crusoe
18 months ago by
Common Workflow Language project
Michael R. Crusoe1.4k wrote:

Hello eduardo,

Sorry for the confusion, the fact that outputBinding is allowed here doesn't make much sense and I've started the process to change/remove that: https://github.com/common-workflow-language/common-workflow-language/issues/543

You'll either need another tool to parse the sss/cwl_out or you can add another output to ncbiblast.cwl with the glob you want. It is no problem in CWL to have multiple overlapping outputs.

Cheers,

ADD COMMENTlink written 18 months ago by Michael R. Crusoe1.4k
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