CWL: Array of strings in workflow

Question

[mkher]

I have a command line tool that expect an input that is an array of strings.

 programs:
    type:
      type: array
      items: string
      inputBinding: {prefix: PROGRAM=, separate: false}
    inputBinding:
      position: 10

I can run this with a job yaml file:

programs: ["CollectAlignmentSummaryMetrics"]

Now I'm trying to use this tool in a workflow and I can't figure out how to pass that value. It is not an input to the workflow. I always want to pass the same value to the tool, when called from this particular workflow. I'm probably missing something obvious.

Thank you. Manisha

Answer 1

[Tom]

You can tackle this at tool-level, by adding this as an argument to your CommandLineTool (see field arguments here)

arguments:
  - valueFrom: ["CollectAlignmentSummaryMetrics"]
    prefix: PROGRAM=
    separate: false
    position: 10

Alternatively, use StepInputExpressionRequirement to define a static WorkflowStepInput using valueFrom. Something like this:

step-giraffe-collect:
  run: giraffe.cwl
  in:
    [...]
    programs:
      valueFrom: ["CollectAlignmentSummaryMetrics"]
  out: [...]

*edit: Added example for the step input expression variant.

Answer 2

[mkher]

Thank you, but that is not what I want to do. The tool is used in multiple contexts and the list of programs varies in each context. In my workflow there's a step where I call it with programs set to [CollectAlignementSummaryMetrics] and another step which calls the same tool with programs set to [MeanQualityByCycle, QualityScoreDistribution].

I have tested the steps individually and they work. In the process, I learned that I don't need the quotes to mark the values as strings. My difficulty is in passing the value from the workflow to the step at the above steps.

[Tom]

I'm not sure i understand. If the arrays are not inputs to the workflow but different for different steps, then you want to hard-code them into the workflow, right? Shouldn't a StepInputExpression be what you are looking for? (I have added an example to my suggestion from yesterday to make it more clear.)

If hard-coding them like this is not sufficient, please explain in more detail what is supposed to happen in the workflow.

Best Regards, Tom

[mkher]

I'm sorry, my mistake. I missed your second suggestion of adding StepInputExpressionRequirement. That looks like exactly what I'm missing.

[Tom]

Great, glad i could help! Feel free to ask if there is any problem implementing this. When first using StepInputExpressionRequirement i struggled for quite a while.

If you were successful, please remember to mark the thread as solved by clicking on the appropriate button next to an answer that solved it.

Cheers,

Tom