Arvados

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
baseCommand: []
requirements:
  InlineJavascriptRequirement: {}
  InitialWorkDirRequirement:
    listing:
      - $(inputs.inputsam)
inputs:
  splitSamIntoChrom:
    type: File
    inputBinding:
      position: 0
  chr-chrom-lst:
    type: File
    inputBinding:
      position: 1
  inputsam:
    type: File
    inputBinding:
      position: 2
      valueFrom: $(self.basename)
outputs:
  output-sam:
    type:
      type: array
      items: File
    outputBinding:
      glob: "*sam" 

arvados-cwl-runner --local splitsam-test.cwl splitsam-test.json 
/usr/local/bin/arvados-cwl-runner 1.0.20160713211920, arvados-python-client 0.1.20160713191718, cwltool 1.0.20160712154127
2016-07-27 19:11:13 arvados.cwl-runner[64747] INFO: Pipeline instance qr1hi-d1hrv-2fb0mcilpm2ehpf
2016-07-27 19:11:14 arvados.arv-run[64747] INFO: Upload local files: "splitSamIntoChrom.pl" "chr_chrom.lst" 
2016-07-27 19:11:14 arvados.arv-run[64747] INFO: Using collection qr1hi-4zz18-gow6notm9tzd0wa
2016-07-27 19:11:20 arvados.cwl-runner[64747] ERROR: Caught unhandled exception, marking pipeline as failed.  Error was: [Errno 2] No such file or directory: '$(task.outdir)/keep:c00bea363a0770335e81662bb7980051+269668/sample.sam'
Workflow error, try again with --debug for more information:
  Workflow did not return a result.

{
  "splitSamIntoChrom":{
        "class":"File",
        "path":"splitSamIntoChrom.pl" 
  },
  "chr-chrom-lst":{
        "class":"File",
        "path":"chr_chrom.lst" 
  },
  "inputsam":{
        "class":"File",
        "path":"keep:c00bea363a0770335e81662bb7980051+269668/sample.sam" 
  }
}