name: bbmap_bbduk
description: Adapter and quality trimming of sequencing reads
keywords:
  - trimming
  - adapter trimming
  - quality trimming
tools:
  - bbmap:
      description: BBMap is a short read aligner, as well as various other bioinformatic tools.
      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
      tool_dev_url: None
      doi: ""
      licence: ['UC-LBL license (see package)']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
        type: file
        description: |
          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
          respectively.
  - contaminants:
        type: file
        description: |
          Reference files containing adapter and/or contaminant sequences for sequence kmer matching

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: The trimmed/modified fastq reads
      pattern: "*fastq.gz"
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - log:
      type: file
      description: Bbduk log file
      pattern: "*bbduk.log"

authors:
  - "@MGordon09"