how to make seconaryFiles work for File in CommandInputRecordField

Question

[liuxf09]

I have a input parameter that is an array of records, like the following:

resources:
  type:
    type: array
    items:
    - type: record
      name: resource
      fields:
        - name: resource
          type: File
          inputBinding:
            prefix: --resource
        - name: resource_param
          type: string
          inputBinding:
            prefix: --resource_param

In the record, resource is File object, and will require secondaryFiles. But secondaryFiles is only allowed for CommandInputParameter, and not allowed in CommandInputRecordField. Ideally I want to something like the following to work:

resources:
  type:
    type: array
    items:
    - type: record
      name: resource
      fields:
        - name: resource
          type: File
          secondaryFiles:
            - ".ext"
          inputBinding:
            prefix: --resource
        - name: resource_param
          type: string
          inputBinding:
            prefix: --resource_param

My reason to use array of records here is to combine resource and resource_param together to produce command line like --resource --resource_param --resource --resource_param. I wish there is some other alternative in cwl.

Answer 1

[liuxf09]

My another question is:

Is the support of `seconaryFiles` in `CommandInputRecordField` general enough? Should this be added to cwl standard?

Answer 2

[liuxf09]

If it is going to support secondaryFiles in InputRecordField, the fix is straight foward:

In `schemas/v1.0/Process.yml`, there is a `secondaryFiles` field under `Parameter`. Just copy this field to under InputRecordField after label field.

Answer 3

[liuxf09]

One ticket is filed on github/cwltool ( https://github.com/common-workflow-language/cwltool/issues/480 ).