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CMakeLists.txt

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    identify_issues.cwl 1.23 KiB
    #!/usr/bin/env cwl-runner
    
    cwlVersion: v1.2
    class: CommandLineTool
    label: Identify Known issues
    
    requirements:
    - class: InlineJavascriptRequirement
    - class: InitialWorkDirRequirement
      listing:
      - entryname: $(inputs.msin.basename)
        writable: true
        entry: $(inputs.msin)
    
    inputs:
    - id: msin
      type: Directory
      inputBinding:
        position: 1
    - id: is_long_baseline
      type: boolean?
      inputBinding:
        prefix: --is_long_baseline
        position: 2
    
    outputs:
    - id: issue_list
      type: string[]
      outputBinding:
        glob: output.txt
        outputEval: $(JSON.parse(self[0].contents)['fixable'])
        loadContents: true
    - id: unfixable_issues
      type: string[]
      outputBinding:
        glob: output.txt
        outputEval: $(JSON.parse(self[0].contents)['unfixable_issues'])
        loadContents: true
    - id: is_raw
      type: boolean
      outputBinding:
        glob: output.txt
        outputEval: $(JSON.parse(self[0].contents)['is_raw'])
        loadContents: true
    - id: msout
      type: Directory
      outputBinding:
        glob: $(inputs.msin.basename)
    stdout: output.txt
    
    baseCommand:
    - python3
    - /usr/local/bin/fix_common_ms_issues
    
    hints:
    - class: DockerRequirement
      dockerPull: git.astron.nl:5000/ldv/ldv-images/lofar-legacy:latest
    - class: NetworkAccess
      networkAccess: true
    id: identify_issues