Difficulty using fgbio with CWL

CWL Questions
1

I’m trying to write a tool for running fgbio ExtractUmisFromBam and am having some difficulty with a particular argument. The molecular_index_tags argument expects a string of SAM tags of any length. When I provide a string I receive the error Error: SAM tags must be of length two so I have tried instead to have my tool accept an array of strings, but that also fails with the same error. When running fgbio manually without using CWL I do not encounter this issue. Clearly I am not providing the input string properly in CWL, but I’m at a loss as to what else to do. Any help would be appreciated.

My tool so far is:

cwlVersion: v1.2
class: CommandLineTool

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/fgbio

baseCommand: ["fgbio", "ExtractUmisFromBam"]

arguments:
  - prefix: "--output"
    valueFrom: $(inputs.sampleID).fgbio.bam

inputs:
  input:
    type: File
    inputBinding:
      position: 1
      prefix: "--input"
  sampleID:
    type: string
  read_structure:
    type: string
    inputBinding:
      position: 2
      prefix: "--read-structure"
  molecular_index_tags:
    type: string[]
    inputBinding:
      position: 3
      itemSeparator: ' '
      shellQuote: false
      prefix: "--molecular-index-tags"
  single_tag:
    type: string
    inputBinding:
      position: 4
      prefix: "--single-tag"

outputs:
  output_bam:
    type: File
    outputBinding:
      glob: "*.fgbio.bam"

My input is structured like so

input:
    class: File
    format: edam:format_2572
    path: ./test_files/input.bam
sampleID: "test_sample"
read_structure: "8M143T 8M143T"
molecular_index_tags:
    - "ZA"
    - "ZB"
single_tag: "RX"

The error I’m receiving is

Exception: ValidationException
Error: SAM tags must be of length two: ZA ZB
2

This is very interesting, can you try using the --debug parameter for cwltool to see what the actual shell script command is underneath?

3

From the array inputs guide, the most appropriate solution should just be to mimic the filesA input in the guide

  molecular_index_tags:
    type: string[]
    inputBinding:
      prefix: "--molecular-index-tags"