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concat.cwl

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  • Forked from ResearchAndDevelopment / LINC
    773 commits behind, 437 commits ahead of the upstream repository.
    Alexander Drabent's avatar
    alex authored
    72bb624b
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    concat.cwl 2.49 KiB
    class: Workflow
    cwlVersion: v1.0
    id: concat
    label: concat
    $namespaces:
      sbg: 'https://www.sevenbridges.com/'
    inputs:
      - id: msin
        type: 'Directory[]'
        'sbg:x': -1000
        'sbg:y': -300
      - id: group_id
        type: string
        'sbg:x': -1000
        'sbg:y': -200
      - id: groups_specification
        type: File
        'sbg:x': -1000
        'sbg:y': -100
      - id: filter_baselines
        type: string
        'sbg:x': -1000
        'sbg:y': 0
      - id: avg_timeresolution_concat
        type: int
        'sbg:x': -1000
        'sbg:y': 100
      - id: avg_freqresolution_concat
        type: string
        'sbg:x': -1000
        'sbg:y': 200
      - id: min_unflagged_fraction
        type: float
        'sbg:x': -1000
        'sbg:y': 300
    outputs:
      - id: msout
        outputSource:
          - dpppconcat/msout
        type: Directory
        'sbg:x': 1000
        'sbg:y': 0
      - id: dpppconcat.log
        outputSource:
          - concat_logfiles_dpppconcat/output
        type: File
        'sbg:x': 1000
        'sbg:y': 100
    steps:
      - id: filter_ms_group
        in:
          - id: group_id
            source: group_id
          - id: groups_specification
            source: groups_specification
          - id: measurement_sets
            source:
              - msin
        out:
          - id: output
          - id: selected_ms
        run: ../steps/filter_ms_group.cwl
        label: filter_ms_group
        'sbg:x': -500
        'sbg:y': 0
      - id: dpppconcat
        in:
          - id: msin
            source:
              - msin
          - id: msin_fname
            source: filter_ms_group/selected_ms
          - id: msout_name
            source: group_id
          - id: msin_datacolumn
            default: DATA
          - id: msout_datacolumn
            default: DATA
          - id: filter_baselines
            source: filter_baselines
          - id: filter_remove
            default: true
          - id: overwrite
            default: false
          - id: storagemanager
            default: Dysco
          - id: databitrate
            default: 0
          - id: missingdata
            default: true
          - id: baseline
            source: filter_baselines
          - id: avg_timeresolution
            source: avg_timeresolution_concat
          - id: avg_freqresolution
            source: avg_freqresolution_concat
        out:
          - id: msout
          - id: logfile
        run: ../lofar-cwl/steps/dpppconcat.cwl
        label: dpppconcat
        'sbg:x': -200
        'sbg:y': 0
      - id: concat_logfiles_dpppconcat
        in:
          - id: file_list
            source:
              - dpppconcat/logfile
          - id: file_prefix
            default: dpppconcat
        out:
          - id: output
        run: ../steps/concatenate_files.cwl
        label: concat_logfiles_dpppconcat
        'sbg:x': 600
        'sbg:y': 200
    
    requirements: []