Path to enable execution of PWD via CWL #90

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1. jan-janssen commented on May 2, 2025

   

   jan-janssen

   on May 2, 2025

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   I had a discussion with @elinscott in MADICES/MADICES-2025#16 about this topic. As you already pointed out the challenging part is the data transfer between the individual tasks. Still I think this is fine as the Python Workflow Definition and CWL address two rather different challenges, CWL is for interoperability of file-based workflow engines and PWD for interoperability of Python based workflow engines. So I would add a comment in the supplementary material but would not make it a part of the main manuscript.
2. GeigerJ2 commented on May 2, 2025

   

   GeigerJ2

   on May 2, 2025

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   Given by Gemini from JSON:

   {
     "nodes": [
       { "id": 0, "type": "function", "value": "workflow.get_prod_and_div" },
       { "id": 1, "type": "function", "value": "workflow.get_sum" },
       { "id": 2, "type": "input", "name": "a", "defaultValue": 1 },
       { "id": 3, "type": "input", "name": "b", "defaultValue": 2 },
       { "id": 4, "type": "output", "name": "c" }
     ],
     "edges": [
       { "target": 0, "targetPort": "x", "source": 2, "sourcePort": null },
       { "target": 0, "targetPort": "y", "source": 3, "sourcePort": null },
       { "target": 1, "targetPort": "x", "source": 0, "sourcePort": "prod" },
       { "target": 1, "targetPort": "y", "source": 0, "sourcePort": "div" },
       { "target": 4, "targetPort": null, "source": 1, "sourcePort": "result" }
     ]
   }

   to CWL:

   cwlVersion: v1.0
   class: Workflow
   id: my_workflow
   
   inputs:
     a:
       type: int
       default: 1
     b:
       type: int
       default: 2
   
   steps:
     get_prod_and_div_step:
       run: "#get_prod_and_div_tool"
       in:
         x: a
         y: b
       out: [prod, div]
   
     get_sum_step:
       run: "#get_sum_tool"
       in:
         x: get_prod_and_div_step/prod
         y: get_prod_and_div_step/div
       out: [result]
   
   outputs:
     c:
       type: int
       outputSource: get_sum_step/result
   
   $schemas:
   - https://raw.githubusercontent.com/common-workflow-language/cwltool/main/schemas/v1.0/CommandLineTool.yml
   
   # Dummy CommandLineTool definitions (replace with actual tool descriptions)
   tools:
     get_prod_and_div_tool:
       id: "#get_prod_and_div_tool"
       class: CommandLineTool
       baseCommand: ["python", "get_prod_and_div.py"]
       inputs:
         x: int
         y: int
       outputs:
         prod:
           type: int
           outputBinding:
             glob: "prod.txt"
         div:
           type: int
           outputBinding:
             glob: "div.txt"
       requirements:
         - class: InlineJavascriptRequirement
   
     get_sum_tool:
       id: "#get_sum_tool"
       class: CommandLineTool
       baseCommand: ["python", "get_sum.py"]
       inputs:
         x: int
         y: int
       outputs:
         result:
           type: int
           outputBinding:
             glob: "result.txt"
       requirements:
         - class: InlineJavascriptRequirement
3. jan-janssen commented on May 15, 2025

   

   jan-janssen

   on May 15, 2025

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   I close this issue as this was implemented in #98
4. jan-janssen

   closed this as completedon May 15, 2025