Skip to content

support secondaryFiles for File in CommandInputRecordField #480

@liuxf09

Description

@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.
One fix is to support secondaryFiles for File in CommandInputRecordField:
"In schemas/v1.0/Process.yml, there is a secondaryFiles field under Parameter. Just copy this field to under InputRecordField after label field. "
This was posted as a question on BioStars ( https://www.biostars.org/p/263577/#263643 ).

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions