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download_and_compress_pipeline.cwl

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    download_and_compress_pipeline.cwl 1.81 KiB
    class: Workflow
    cwlVersion: v1.1
    id: compress_pipeline_cwl
    label: compress_pipeline.cwl
    inputs:
      - id: flag_autocorrelation
        type: boolean?
      - id: surls
        type: 'string[]'
    outputs:
      - id: compressed
        outputSource:
          - compress/compressed
        type: File[]
      - id: logfile
        outputSource:
          - compress/logfile
        type:
          type: array
          items:
            type: array
            items: File
      - id: ingest
        outputSource:
          - compress/ingest
        type: Any[]
      - id: quality
        type: Any
        outputSource:
          - format_quality_metrics/formatted_quality
      - id: inspect
        type: File
        outputSource:
          - combine/inspect_file
    steps:
      - id: fetch_data
        in:
          - id: surl_link
            source: surls
        out:
          - id: uncompressed
        run: steps/fetch_data.cwl
        label: fetch_data
        scatter:
          - surl_link
      - id: compress
        in:
          - id: msin
            source: fetch_data/uncompressed
          - id: flag_autocorrelation
            source: flag_autocorrelation
        scatter:
          - msin
        out:
          - id: compressed
          - id: inspect
          - id: logfile
          - id: ingest
        run: ./compress_pipeline.cwl
      - id: combine
        in:
        - id: inputs
          source: compress/inspect
        out:
        - inspect_file
        run: steps/combine_inspect_dataset.cwl
      - id: extract_metrics
        in: 
        - id: inspect
          source: combine/inspect_file
        out:
        - id: plots
        - id: quality
        run: steps/extract_quality_metrics.cwl
      - id: format_quality_metrics
        in: 
        - id: plots
          source: extract_metrics/plots
        - id: quality
          source: extract_metrics/quality
        run: steps/format_metrics.cwl
        out:
        - formatted_quality
    requirements:
      - class: ScatterFeatureRequirement
      - class: SubworkflowFeatureRequirement
      - class: StepInputExpressionRequirement
      - class: InlineJavascriptRequirement