name: "trimmomatic"
description: Performs quality and adapter trimming on paired end and single end reads
keywords:
  - trimming
  - adapter trimming
  - quality trimming

tools:
  - "trimmomatic":
      description: "A flexible read trimming tool for Illumina NGS data"
      homepage: "http://www.usadellab.org/cms/?page=trimmomatic"
      documentation: "https://github.com/usadellab/Trimmomatic"
      tool_dev_url: "None"
      doi: "10.1093/bioinformatics/btu170"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively.
      pattern: "*.fastq.gz"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - trimmed_reads:
      type: file
      description: The trimmed/modified paired end fastq reads
      pattern: "*.paired.trim*.fastq.gz"
  - unpaired_reads:
      type: file
      description: The trimmed/modified unpaired end fastq reads
      pattern: "*.unpaired.trim_*.fastq.gz"
  - log:
      type: file
      description: trimmomatic log file
      pattern: "*.log"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@alyssa-ab"