name: trimgalore
description: Trim FastQ files using Trim Galore!
keywords:
  - trimming
  - adapters
  - sequencing adapters
  - fastq
tools:
  - trimgalore:
      description: |
        A wrapper tool around Cutadapt and FastQC to consistently apply quality
        and adapter trimming to FastQ files, with some extra functionality for
        MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
      homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
      documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
      licence: ["GPL-3.0-or-later"]
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.
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        List of input adapter trimmed FastQ files of size 1 and 2 for
        single-end and paired-end data, respectively.
      pattern: "*{3prime,5prime,trimmed,val}*.fq.gz"
  - unpaired:
      type: file
      description: |
        FastQ files containing unpaired reads from read 1 or read 2
      pattern: "*unpaired*.fq.gz"
  - html:
      type: file
      description: FastQC report (optional)
      pattern: "*_{fastqc.html}"
  - zip:
      type: file
      description: FastQC report archive (optional)
      pattern: "*_{fastqc.zip}"
  - log:
      type: file
      description: Trim Galore! trimming report
      pattern: "*_{report.txt}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@ewels"
  - "@FelixKrueger"
