cwl stderr management: Not all output in my outfile.

Question

[sebastien.letort]

Hi, it's a noob question.

I'm practicing cwl with Nucmer software http://mummer.sourceforge.net/manual/#nucmer.

I have described only the help and version argument with :

cwlVersion: v1.0
class: CommandLineTool
baseCommand: nucmer
inputs:
    help:
        type: "null"
        inputBinding:
            prefix: -h
    version:
        type: "null"
        inputBinding:
            prefix: -V
outputs:
    err_msg:
        type: stderr

stderr: output.err

but when running with cwltool ( with help or version arg.) the output.err file only contains :

USAGE: nucmer  [options]  <Reference>  <Query>

Try '/home/sletort/logiciels/MUMmer3.23/nucmer -h' for more information.

Is it a wanted behaviour, is my description incomplete ?

=> nucmer outputs help and version on stderr.

... The output is a general output in case of error. So the command line ran is not well formatted.

Answer 1

[Michael R. Crusoe]

Hello sebastien.letort,

When describing a command line tool in CWL I suggest focusing on a particular way of using that tool instead of immediately trying to describe every possible flag or parameter.

For example, I would describe the default usage of nucmer first, and then add any other flags as needed:

cwlVersion: v1.0
class: CommandLineTool

inputs:
  reference:
    type: File
    inputBinding:
      position: 1
  query:
    type: File
    inputBinding:
      position: 2

baseCommand: nucmer

outputs:
  delta:
    type: File
    outputBinding:
      glob: "out.delta"

Answer 2

[sebastien.letort]

I'll accept the answer as it provided valuable clue to start a description. But I mention that this description (or my use of it !) leads to another error : workflowException: 'location'