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How to convert File to array of File? Type mismatch between source and sink, File to array

I wonder how I convert a File to an array of files? This might be a completely trivial question, but I have a hard time solving it.

Below is a summary of my problem:

I have a small pipeline (trimming ==> mapping ==> sorting). Sorting is done with picardtools, which allows for multiple input files. Below is the section in the tool description file:

     inputs:
     ...
       - id: "inputFileName_mergedSam"
         type:
           type: array
           items: File
           streamable: true
           inputBinding: { prefix: "INPUT=" }
         inputBinding: { position: 5 }
     ...

My problem is that the mapping step before returns a single file. Connecting the two steps in a workflow fails:

steps:
...
  - id: alignment
    ...
    outputs:
      - id: alignment

  - id: sort
    inputs:
      - id: inputFileName_mergedSam
        source: "#alignment/alignment"
...

The error thrown is a mismatch between source (File) and sink ({'items': 'File', 'streamable': True, 'inputBinding': {'prefix': 'INPUT='}, 'type': 'array'}).

How do I convert the File output from the alignment step to an array?

common-workflow-language cwl
• 2,531 views • link
updated by Ram Ram • written by karl.nordstrom karl.nordstrom

1 answer

Hello Karl,

The following hack should work; a future version of the standard should make this easier.

  1. Add StepInputExpressionRequirement & InlineJavascriptRequirement to your requirements list

  2. Use valueFrom to wrap the single item into an array

All together

requirements:
  - class: StepInputExpressionRequirement
  - class: InlineJavascriptRequirement

steps:
...
  - id: alignment
    ...
    outputs:
      - id: alignment

  - id: sort
    inputs:
      - id: inputFileName_mergedSam
        source: "#alignment/alignment
        valueFrom: ${ return [ self ]; }
• 0 views • link
written by Michael R. Crusoe Michael R. Crusoe

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