cwltool and cwlexec not scattering jobs in same way

I have a simple workflow in which I have 2 inputs, one is type: File, and the other is an array of files. I want to run a command in which each of the files in the array are used against the single input file from input1. When I run cwltool it performs as expected. It runs in serial each file in the array against the single input1. When I run cwlexec it gives me no errors or message, and the job immediately terminates.

the tool is:


cwlVersion: v1.0
class: CommandLineTool

hints:
  SoftwareRequirement:
    packages:
      bedtools:
        version: [ "2.25.0" ]

inputs:
  outputGenomeCov:
    type: File
    inputBinding:
      position: 1
      prefix: -a

  regionsBedFile:
    type: File
    inputBinding:
      position: 2
      prefix: -b

  allPositions:
    type: string
    default: "-c"
    inputBinding:
      position: 3
      prefix: -c

outputs:
  allDepthOutput:
    type: File
    outputBinding: {glob: $(inputs.regionsBedFile.basename)_AtoB.txt}

stdout: $(inputs.regionsBedFile.basename)_AtoB.txt

baseCommand: [bedtools, intersect]

And the workflow is:


cwlVersion: v1.0
class: Workflow

requirements:
 - class: ScatterFeatureRequirement

inputs:
  outputGenomeCov: File
  regionsBedFile: File[]

outputs:
  intersectAB:
    type: File[]
    outputSource: intersect/allDepthOutput

steps:
  intersect:
    run: 2_bedtoolsIntersect.cwl
    scatter: regionsBedFile
    in:
      outputGenomeCov: outputGenomeCov
      regionsBedFile: regionsBedFile
    out: [allDepthOutput]

The .yml file:

outputGenomeCov:
  class: File
  path: /path/to/input.txt

regionsBedFile:
 - {class: File, path: /path/to/bedfile1.bed}
 - {class: File, path: /path/to/bedfile2.bed}
 - {class: File, path: /path/to/bedfile3.bed}

I have another workflow that has designated output files created from the program, but bedtools prints its outputs to stdout. The other workflow works well, but this fails. Thanks, Dennis

yuch7 / cwlexec

cwltool and cwlexec not scattering jobs in same way #4