fileContent error for CreateFileRequirement

[kellrott]

I'm trying to do a samtools index step:

class: CommandLineTool
cwlVersion: draft-3

baseCommand: [samtools, index]

requirements:
  - class: InlineJavascriptRequirement
  - class: CreateFileRequirement
    fileDef:
      - fileName: indexed.bam
      - fileContent: $(inputs.in_bam)

inputs:
  - id: in_bam
    type: File
    inputBinding:
      position: 1

outputs:
  - id: out_bam
    type: File
    outputBinding:
      glob: indexed.bam
    secondaryFiles:
      - ".bai"

But I seem to be getting:

Unexpected exception
Traceback (most recent call last):
  File "/home/ubuntu/mc3/venv/local/lib/python2.7/site-packages/cwltool/workflow.py", line 532, in job
    **kwargs):
  File "/home/ubuntu/mc3/venv/local/lib/python2.7/site-packages/cwltool/draft2tool.py", line 273, in job
    j.generatefiles[builder.do_eval(t["filename"])] = copy.deepcopy(builder.do_eval(t["fileContent"]))
KeyError: 'fileContent'
Workflow error, try again with --debug for more information:
  'fileContent'

Am I doing something wrong?

[kellrott]

Got it, the

fileDef:
      - fileName: indexed.bam
      - fileContent: $(inputs.in_bam)

created an array of dicts, rather then a single dict. I was supposed to do:

fileDef:
      - fileName: indexed.bam
        fileContent: $(inputs.in_bam)

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