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"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - log:
      type: file
      description: Bbduk log file
      pattern: "*bbduk.log"

authors:
  - "@MGordon09"