CWL input files as secondaryFiles JS

Question

[cocchi.e89]

I am using CWL, just got a fresh install of cwltool (cwl-runner says its version 2.0) and the way I always used to specify secondaryFiles doesn't work anymore, especially:

inputs:
  - id: reference_fasta
    type: File
    inputBinding:
      position: 1
      prefix: '--reference'
    secondaryFiles:
      - $( inputs.reference_index )
      - $( inputs.reference_dict )
  - id: reference_index
    type: File
  - id: reference_dict
    type: File

does not recognize $( inputs.file ) format anymore, it keeps failing with:

ERROR Workflow error: can only concatenate str (not "dict") to str

Any idea?

[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?