name: biobambam_bammarkduplicates2
description: Locate and tag duplicate reads in a BAM file
keywords:
  - markduplicates
  - bam
  - cram
tools:
  - biobambam:
      description: |
        biobambam is a set of tools for early stage alignment file processing.
      homepage: https://gitlab.com/german.tischler/biobambam2
      documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
      doi: 10.1186/1751-0473-9-13
      licence: ["GPL v3"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM/CRAM file
      pattern: "*.{bam,cram}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM file with duplicate reads marked/removed
      pattern: "*.{bam}"
  - metrics:
      type: file
      description: Duplicate metrics file generated by biobambam
      pattern: "*.{metrics.txt}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@muffato"