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!
1 answer
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,
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