Dear All,

I have a CWL script to run a python script. The commad line tool version of CWL is as following,

cwlVersion: v1.0
class: CommandLineTool
doc: Spladder

baseCommand: [python, sladder.py]

requirements:
 - class: InlineJavascriptRequirement
 - class: InitialWorkDirRequirement
   listing: 
    - entry: "$({class: 'Directory', listing: []})"
      entryname: $(inputs.spladder_outDir)
      writable: true

inputs:
 spladder_gtf: 
  type: File
  inputBinding:
   position: 1
   prefix: -a
 spladder_bams: 
  type: File[]
  inputBinding:
   position: 2
   prefix: -b
   itemSeparator: ","
  secondaryFiles: .bai
 spladder_outDir:
  type: string
  inputBinding:
   position: 3
   prefix: -o
 spladder_phase2:
  type: string
  inputBinding:
   position: 4
   prefix: -T
 spladder_confidence:
  type: int
  inputBinding:
   position: 4
   prefix: -c
 spladder_merge_graphs:
  type: string
  inputBinding:
   position: 5
   prefix: -M
 spladder_alt:
  type: string
  inputBinding:
   position: 7
   prefix: -t
 spladder_RL:
  type: int
  inputBinding:
   position: 8
   prefix: -n
 spladder_primary_alignment:
  type: string
  inputBinding:
   position: 9
   prefix: -P


outputs:
 spladder_out_dir1:
  type: Directory
  outputBinding:
   glob: $(inputs.spladder_outDir)/lad
 spladder_out_dir2:
   type: Directory
   outputBinding:
    glob: $(inputs.spladder_outDir)
 spladderFile:
  type: File
  outputBinding:
   glob: $(inputs.spladder_outDir)/lad/genes_graph_conf3.merge_graphs.pickle

And the YML file looks like,

spladder_gtf:
 class: File
 path: /ur/home/gencode.v19.annotation.hs37d5_chr.spladder.gtf
spladder_outDir: ladder_out
spladder_bams: [
 {class: File, path: /cluster/work/sampleA.bam},
 {class: File, path: /cluster/work/sampleB.bam}
]
spladder_confidence: 2
spladder_merge_graphs: merge_graphs
spladder_alt: alt_3prime
spladder_RL: 100
spladder_phase2: y
spladder_primary_alignment: y

I execute the above as following cwltool lad.cwl lad.yml, it is throwing the following error,

lad.cwl:77:4: Did not find output file with glob pattern: '['./ladder_out/lad/genes_graph_conf3.merge_graphs.pickle']'

The directory ladder_out is not existing and the python script create it while executing.