Dependent inputs in a workflow

CWL Questions
1

Alright, so I have a set of dependent inputs for a command line tool:

dependentForward:
type:
  type: record
  name: dependentForward
  fields:
    forwardInFastq:
      type: File
      inputBinding:
        position: 16
      doc: |
        Single end or forward reads of paired reads
    forwardAdapter:
      type: string
      inputBinding:
        position: 1
        prefix: "--adapter"
      doc: |
        Sequence of an adapter ligated to the 3' end (paired
        data: of the first read). The adapter and subsequent
        bases are trimmed. If a '$' character is appended
        ('anchoring'), the adapter is only found if it is a
        suffix of the read.
    forwardOutFastq:
      type: File
      inputBinding:
        position: 12
        prefix: "--output"
      doc: |
        Write trimmed reads to FILE. FASTQ or FASTA format is
        chosen depending on input. Summary report is sent to
        standard output. Use '{name}' for demultiplexing (see
        docs). Default: write to standard output

I am trying to figure out what the syntax for filling the fields of this record is in a workflow.

What I have so far:

cutadapt:
run: ../commandLineTools/cutadapt.cwl
in:
  dependentForward:
    forwardInFastq:
      source: pairedEndFastqsIn
      valueFrom: $(self.forwardFastq)
    forwardAdapter:
      source: forwardAdapter
    forwardOutFastq:
      source: pairedEndFastqsIn
      valueFrom: $(self.forwardFastq.nameroot)_trimmed.fastq

The benten language server doesn’t think this is correct.

Any help would be appreciated!

2

Hi @DiDeoxy, could you please try with the latest master for Benten? I put in a fix for a problem that looks a bit like this. Thanks!