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"]
      identifier: ""
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.
        ontologies: []
output:
  reads:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz":
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
          pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz"
  log:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*report.txt":
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
          pattern: "*_{report.txt}"
  unpaired:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*unpaired{,_1,_2}.fq.gz":
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
          pattern: "*unpaired*.fq.gz"
  html:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.html":
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
          pattern: "*_{fastqc.html}"
  zip:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.zip":
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
          pattern: "*_{fastqc.zip}"
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@drpatelh"
  - "@ewels"
  - "@FelixKrueger"
maintainers:
  - "@drpatelh"
  - "@ewels"
  - "@FelixKrueger"
