cwltool throws validation errors despite consistent type declarations

[adrabent]

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Expected Behavior

cwltool --validate should not show any warnings

Actual Behavior

cwltool throws a workflow checker warning, although all types are chosen consistently. The warning output complain about "incompatibility" although both source and sink are of the same type.

Workflow Code

minimal_workflow.cwl:

class: Workflow
cwlVersion: v1.2
id: minimal_example
label: minimal_example
inputs:
  - id: msin
    type: File
outputs:
  - id: msout
    outputSource:
        - subworkflow_1/msout
        - subworkflow_2/msout
    type: File[]?
    linkMerge: merge_flattened
steps:
  - id: subworkflow_1
    in:
      - id: msin
        source: msin
    out:
      - id: msout
    run: subworkflow.cwl
  - id: subworkflow_2
    in:
      - id: msin
        source: msin
    out:
      - id: msout
    run: subworkflow.cwl
requirements:
  - class: SubworkflowFeatureRequirement

subworkflow.cwl:

class: Workflow
cwlVersion: v1.2
id: subworkflow
label: subworkflow
inputs:
  - id: msin
    type: File
outputs:
  - id: msout
    outputSource:
        - msin
    type: File[]?
    linkMerge: merge_nested
steps:
  - id: pass
    in:
      - id: msin
        source: msin
    out:
      - id: msout
    run: pass.cwl

pass.cwl ("do nothing"):

class: CommandLineTool
cwlVersion: v1.2
id: pass
baseCommand: echo
inputs:
  - id: msin
    type: File
outputs:
  - id: msout
    type: File?
    outputBinding:
      outputEval: $(inputs.msin)
requirements:
  - class: DockerRequirement
    dockerPull: ubuntu:22.04

I call the command like this:

cwltool --validate minimal_workflow.cwl

Full Traceback

INFO /usr/local/conda/envs/cwl/bin/cwltool 3.1.20250110105449
INFO Resolved 'minimal_workflow.cwl' to 'file:///home/alex/debug/minimal_workflow.cwl'
WARNING Workflow checker warning:
minimal_workflow.cwl:21:9: Source 'msout' of type ["null", {"type": "array", "items": "File"}] may
                           be incompatible
minimal_workflow.cwl:13:5:   with sink 'msout' of type ["null", {"type": "array", "items":
                             "File"}]
minimal_workflow.cwl:9:5:    source has linkMerge method merge_flattened
minimal_workflow.cwl:28:9: Source 'msout' of type ["null", {"type": "array", "items": "File"}] may
                           be incompatible
minimal_workflow.cwl:13:5:   with sink 'msout' of type ["null", {"type": "array", "items":
                             "File"}]
minimal_workflow.cwl:9:5:    source has linkMerge method merge_flattened
minimal_workflow.cwl is valid CWL.

Your Environment

• cwltool version: 3.1.20250110105449

What works

• Change all types to non-null types: File? --> File and File[]? --> File[]