CWL: Make Enum optional (CommandInputEnumSchema)

Question

[eduardo]

Is it possible to make an Enum optional?

  outfmt:
      type:
          type: enum
          symbols:
            - clustal
            - clustal_num
            - fa
            - msf
            - nexus
            - phylip
            - selex
            - stockholm
            - vienna
          inputBinding:
            position: 13
            prefix: --outfmt

I have tried enum? but then it is not recognised as CommandInputEnumSchema.

[kloetzl]

? is just a shorthand for [ <T>, "null"]. Try the latter.

[eduardo]

Could you provide an example? I have tried a few alternatives with null but I couldn't make it work.

Answer 1

[Michael R. Crusoe]

From https://github.com/common-workflow-language/common-workflow-language/issues/392

type:
  - "null"
  -  type: enum
     symbols: [none, apply, calculate]

Or give it a name:

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl/blob/master/tools/InterProScan5.21-60.cwl#L38

[eduardo]

Any idea on how to make the enum an array?

The following breaks:

type:
  - "null"
  - type: enum[]

The only way I found is custom type as the example mentioned by Michael R. Crusoe

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl/blob/master/tools/InterProScan5.21-60.cwl#L38

[Michael R. Crusoe]

type:
  - "null"
  - type: array
    items:
      type: enum
      symbols: [none, apply, calculate]

Yes, as you found, it is easier when we give names to our custom types

[eduardo]

Awesome! Thank you very much!

[eduardo]

https://github.com/common-workflow-language/cwltool/issues/576