common-workflow-language / common-workflow-language/cwltool

support secondaryFiles for File in CommandInputRecordField

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Python
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376
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2d 7h
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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 ).

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