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Support cwl File contents loading in parameter references #9

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eleftherioszisis opened this issue May 31, 2024 · 0 comments
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@eleftherioszisis
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eleftherioszisis commented May 31, 2024

In certain cases the output to one file needs to be loaded and passed as a string argument to a task downstream.

For example stage below converts the region id to its respective acronym and saves it as a region_file txt. init_cells needs to load the contents of that file, i.e. the acronym to pass it as a command argument.

steps:
  - id: stage
    run: ./stage.cwl
    in:
      region_id: region_id
    out:
      - region_file
  
  - id: init_cells
    run: ./init_cells
    in:
      region:
        source: stage/region_file
        valueFrom: $(self.contents)
    out:
      - nodes_file

See the spec for more details: https://www.commonwl.org/v1.1/Workflow.html#File

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