name: bamutil_trimbam
description: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping
keywords:
  - bam
  - trim
  - clipping
  - bamUtil
  - trimBam
tools:
  - bamutil:
      description: Programs that perform operations on SAM/BAM files, all built into a single executable, bam.
      homepage: https://genome.sph.umich.edu/wiki/BamUtil
      documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
      tool_dev_url: https://github.com/statgen/bamUtil
      doi: "10.1101/gr.176552.114"
      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 file
      pattern: "*.bam"
  - trim_left:
      type: integer
      description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
  - trim_right:
      type: integer
      description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - bam:
      type: file
      description: Trimmed but unsorted BAM file
      pattern: "*.bam"

authors:
  - "@jfy133"