gravatar for cole.shaw

2 hours ago by

Hello, I'm new to bioinformatics and the common workflow language. I could not find an answer to this question on the common workflow language user guide nor on this forum, and I appreciate any help or pointers to the right resources.

I'm creating a CWL workflow, and I have some steps that require an array of integer inputs. What is the syntax to specify default values for an array of integers? I have tried several things that all throw exceptions when I use cwltool to validate the workflow definition.

Input definition:

  pcs:
    type:
      type: array
      items: int
      label: 'Principal Components'

The step definition:

      in:
        data: output_data
        pcs:
          - 1
          - 2

Results in an error:

  checking field `in`
      checking object `test.yaml#test/pcs`
                         `source` field is int, expected string, list, or a dict.
                         `source` field is int, expected string, list, or a dict.

I have also tried variants like:

pcs: [1 2 3]

pcs: [1, 2, 3]

 pcs:
   1
   2
   3

 pcs: 1
 pcs: 2
 pcs: 3

All throw errors of some sort. I read this section in the guide on Maps, but that does not seem to help in this case.

Thanks for your help!



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