CWL 'glob' field not capturing files

Question

[eduardo]

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!

Answer 1

[Michael R. Crusoe]

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,