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
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.
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.
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
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
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