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
params:
    - outdir:
        type: string
        description: |
            The pipeline's output directory. By default, the module will
            output files into `$params.outdir/<SOFTWARE>`
    - publish_dir_mode:
        type: string
        description: |
            Value for the Nextflow `publishDir` mode parameter.
            Available: symlink, rellink, link, copy, copyNoFollow, move.
    - conda:
        type: boolean
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
    - clip_r1:
        type: integer
        description: |
            Instructs Trim Galore to remove bp from the 5' end of read 1
            (or single-end reads)
    - clip_r2:
        type: integer
        description: |
            Instructs Trim Galore to remove bp from the 5' end of read 2
            (paired-end reads only)
    - three_prime_clip_r1:
        type: integer
        description: |
            Instructs Trim Galore to remove bp from the 3' end of read 1
            AFTER adapter/quality trimming has been performed
    - three_prime_clip_r2:
        type: integer
        description: |
            Instructs Trim Galore to re move bp from the 3' end of read 2
            AFTER adapter/quality trimming has been performed
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.
    - options:
        type: map
        description: |
            Groovy Map containing module options for passing command-line arguments and
            output file paths.
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"