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wtsi-hgi / gatk-cwl-generator

Generates CWL files from the GATK documentation
MIT License
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Add genomicsdb-workspace output for ImportGenomicsDB tool #15

Closed ThomasHickman closed 6 years ago

ThomasHickman commented 6 years ago

ImportGenomicsDB produces a folder referenced to by genomicsdb-workspace-path. This is not specified as an output parameter

sersorrel commented 6 years ago

I think this is now done. This is the extra cwl that now gets inserted:

outputs:
- id: genomicsdb-workspace-path-out
  doc: Resulting GenomicsDB workspace (corresponding to the input genomicsdb-workspace-path).
  type: Directory
  outputBinding:
    glob: $(inputs['genomicsdb-workspace-path'])

The spec isn't too explicit about it, but I think it's allowed to have type: Directory on an output.

sersorrel commented 6 years ago

clarifying globbing behaviour with directories: common-workflow-language/cwl-v1.1#7

mr-c commented 6 years ago

Type: Directory and glob is valid, yes

mr-c commented 6 years ago

It would be better to write $(inputs.genomicsdb-workspace-path) which doesn't require InlineJavascriptRequirement