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Description
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 ).