CWL workflow - nested_crossproduct output

Question

[cocchi.e89]

I am working on some GATK gCNV calls through CWL. I am wondering how I can pass a scattered group in the script. I have:

  CollectReadCounts:
    run: CollectReadCounts.v0.cwl
    in:
      interval_list: PreprocessIntervals/PreprocessIntervals_OUT
      reference_fasta: reference_fasta
      reference_index: reference_index
      reference_dict: reference_dict
      bam_file: bam_file_array
      coresMin: coresMin
      ramMin: ramMin
    scatter: [ interval_list, bam_file ]
    scatterMethod: nested_crossproduct
    out: [ CollectReadCounts_OUT ]

but I can't get the ouput:

outputs:
  CollectReadCounts_OUT:
    type:
      type: array
      items: File
    outputSource: CollectReadCounts/CollectReadCounts_OUT

cause it keeps failing with:

gCNV-CHR-workflow.wFILTER_INTERVALS.v0.cwl:53:12: Source 'CollectReadCounts_OUT' of type {"items": {"items": "File", "type": "array"}, "type": "array"} is incompatible
gCNV-CHR-workflow.wFILTER_INTERVALS.v0.cwl:86:5:   with sink 'CollectReadCounts_OUT' of type {"type": "array", "items": "File"}

What is the correct way to specify a nested_crossproduct output??

[Michael R. Crusoe]

Hello, sorry for just now seeing this. Support for CWL and the CWL reference runner has moved from biostars to https://cwl.discourse.group/ ; can you post your question there?