Auto-casting single item to array fails

Input

  inputFileName_markDups:
    type: File[]?
    inputBinding:
      position: 4
      prefix: INPUT=

The call uses a single BAM file from a previous step, not an array.

Causes the following error:

Workflow error, try again with --debug for more information:
  Type mismatch between source 'file:///home/ubuntu/gitroot/common-workflow-language/workflows/workflows/GATK/GATK-complete-Workflow-h3abionet.cwl#samtools-sort/sorted' (File) and sink 'file:///home/ubuntu/gitroot/common-workflow-language/workflows/workflows/GATK/GATK-complete-Workflow-h3abionet.cwl#MarkDuplicates/inputFileName_markDups' ([u'null', {u'items': 'File', u'type': u'array'}])

But it works fine when markdup’s input is:

  inputFileName_markDups:
    type: File[]
    inputBinding:
      position: 4
      prefix: INPUT=

[briandoconnor]

Workaround with javascript:

      inputFileName_markDups:
        source: samtools-sort/sorted
        valueFrom: ${return [ self ];}

[tetron]

Try this:

     inputFileName_markDups: [samtools-sort/sorted]