name: "from_bd_to_10x_molecular_barcode_tags"
namespace: "convert"
scope: "public"
description: |
  Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format (UB).
authors:
  - __merge__: /src/authors/dries_schaumont.yaml
    roles: [ maintainer ]
arguments:
  - name: "--input"
    alternatives: ["-i"]
    type: file
    must_exist: true
    description: Input SAM or BAM file.
    example: "input.bam"
    direction: input
    required: true
  - name: "--output"
    alternatives: ["-o"]
    type: file
    description: Output alignment file.
    example: "output.bam"
    direction: output
  - name: "--bam"
    type: boolean_true
    description: Output a BAM file.
  - name: "--threads"
    alternatives: ["-t"]
    type: integer
    description: Number of threads
resources:
  - type: bash_script
    path: script.sh
test_resources:
  - type: bash_script
    path: run_test.sh
  - path: /resources_test/bdrhap_5kjrt/processed/output_raw
engines:
  - type: docker
    image: ubuntu:latest
    setup:
      - type: apt
        packages: [ samtools ]
runners:
  - type: executable
  - type: nextflow
    directives:
      label: [lowmem, singlecpu]
