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Is there a way to repeat a prefix for an input that is an array of strings?

With this input parameter:

fci__rf: [FailsVendorQualityCheck, BadMate, UnmappedRead, BadCigar]

I would like this:

read_filters:
  type: string[]
  inputBinding:
    prefix: --read_filter

To result in this:

java
-jar GenomeAnalysisTK.jar
-T
FindCoveredIntervals
--input_file
sample.bam
--reference_sequence ref.fasta
--read_filter FailsVendorQualityCheck
--read_filter BadMate
--read_filter UnmappedRead
--read_filter BadCigar

Do I need to use shellQuote? Or perhaps I need to use a string input instead of an array?

cwl
• 1,688 views • link
updated by bogdan.gavrilovic bogdan.gavrilovic • written by ionox0 ionox0

1 answer

Please check out this page http://www.commonwl.org/user_guide/09-array-inputs/

In your case this definition will do the job:

inputs:
  read_filters:
    type:
      type: array
      items: string
      inputBinding:
        prefix: --read_filter
    inputBinding:
      position: 1
• 0 views • link
written by bogdan.gavrilovic bogdan.gavrilovic

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