error: argument --reference is required

Question

[giuseppacefalu]

Hi Michael,

I am running the command below and I get the error that follows. Any hints?

Thanks,

Giuseppa

gcefalu@ubuntu:~$ cwl-runner BWA-INDEX.cwl index-input.yml --debug
/usr/local/bin/cwl-runner 1.0.20160901133827
usage: BWA-INDEX.cwl [-h] --reference REFERENCE [job_order]
BWA-INDEX.cwl: error: argument --reference is required

BWA-INDEX.cwl contains:
#!/usr/bin/env cwltool
cwlVersion: v1.0
class: CommandLineTool
hints:
  DockerRequirement:
    dockerPull: biodckr/bwa
baseCommand: [bwa, index]
arguments:
  - {prefix: "-p" , valueFrom: $(runtime.cores)}
  - {prefix: "-a", valueFrom: "\tis"}
inputs:
  reference:
    type: File
    inputBinding:
      position: 1
      valueFrom: $(self.dirname)/$(self.nameroot)

stdout: $(inputs.reference.nameroot).bwt
stdout: $(inputs.reference.nameroot).amb
stdout: $(inputs.reference.nameroot).ann
stdout: $(inputs.reference.nameroot).pac
stdout: $(inputs.reference.nameroot).sa

outputs:
  index_files:
    type: stdout       

index-input.yml contains:
!/usr/bin/env cwltool
cwl:tool: BWA-INDEX.cwl
reference:
  class: File
  location: ref.fa

[Ram]

Hi Michael

Who's Michael?

[Chris Fields]

It's a CWL file, so maybe Michael Crusoe?

[Ram]

Could be him - was the first Michael to cross my mind. What's a CWL file by the way?

[Chris Fields]

Common Workflow Language.

[giuseppacefalu]

I have modified BWA-INDEX.cwl, but can not figure out how to get rid of the error.

!/usr/bin/env cwltool

cwlVersion: v1.0 class: CommandLineTool

hints: DockerRequirement: dockerPull: biodckr/bwa

baseCommand: [bwa, index]

arguments: - {prefix: "-p", valueFrom: $(runtime.cores)} - {prefix: "-a", valueFrom: "\tis"}

inputs: reference: type: File inputBinding: position: 1 valueFrom: $(self.dirname)/$(self.nameroot) outputs: output: type: File # format: http://edamontology.org/format_1929 # FASTA secondaryFiles: - '^.bai' - '^.amb' - '^.ann' - '^.bwt' - '^.pac' - '^.sa' outputBinding: glob: $(inputs.reference.basename)

[Michael R. Crusoe]

FYI, To get full debugging output pass --debug immediately after cwltool or cwl-runner (though the later isn't guaranteed to work with other implementations)

Have you tried the existing BWA index description? https://github.com/common-workflow-language/workflows/blob/master/tools/bwa-index.cwl