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
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: "*.{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}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@drpatelh"
    - "@ewels"
    - "@FelixKrueger"