name: biobambam_bammerge
description: Merge a list of sorted bam files
keywords:
  - merge
  - bam
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: List containing 1 or more bam files
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: Merged BAM file
      pattern: "*.bam"
  - bam_index:
      type: file
      description: BAM index file
      pattern: "*"
  - checksum:
      type: file
      description: Checksum file
      pattern: "*"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@matthdsm"