CWL input files as secondaryFiles JS
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?
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by
Michael R. Crusoe
•
written
by
cocchi.e89
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cocchi.e89
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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?