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extract_quality_metrics.cwl

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    extract_quality_metrics.cwl 791 B
    cwlVersion: 'v1.2'
    class: CommandLineTool
    baseCommand: 
      - bash
      - script.sh
    
    requirements:
      - class: InlineJavascriptRequirement
      - class: InitialWorkDirRequirement
        listing:
          - entryname: script.sh
            entry: | 
              #!/bin/bash
              inspect_utils.py plot $(inputs.inspect.path) plots
              inspect_utils.py inspect $(inputs.inspect.path) quality.json
    hints:
      - class: DockerRequirement
        dockerPull: git.astron.nl:5000/ldv/imaging_compress_pipeline:v0.5.14
      - class: NetworkAccess
        networkAccess: true
    inputs: 
    - id: inspect
      type: File
    outputs: 
    - id: plots
      type: File[]
      outputBinding: 
        glob: plots/*.png
    - id: quality
      type: Any
      outputBinding:
        glob: quality.json
        loadContents: true
        outputEval: $(JSON.parse(self[0].contents))