CWL Argument Error

Question

[StarCute]

I have a cwl file:

cwlVersion: cwl:draft-3
class: CommandLineTool
baseCommand: [bwa, mem]
inputs:
  - id: reference
    type: File
    inputBinding:
      position: 1
  - id: forward
    type: File
    inputBinding:
      position: 2
  - id: sam
    type: string
    inputBinding:
      position: 3
      prefix: ">"
outputs: []

And a yml file:

reference:
  class: File
  path: ref.fa
forward:
  class: File
  path: lane1.fa
sam: res.sam

When I run the command:

cwl-runner bwa.cwl bwa.yml --debug

I get the following error message:

usage: bwa.cwl [-h] --reference REFERENCE --forward FORWARD --sam SAM
           [job_order]
bwa.cwl: error: argument --reference is required

Both ref.fa and lane1.fa are in my current working directory. Any advice?

Answer 1

[karl.nordstrom]

The problem is with the placement of the --debug flag

The command should be:

cwl-runner --debug bwa.cwl bwa.yml