name: Trim Galore!
description: Trim FastQ files using Trim Galore!
keywords:
    - trimming
    - adapters
    - sequencing adapters
tools:
    - fastqc:
        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:
    -
        - sample_id:
            type: string
            description: Sample identifier
        - reads:
            type: file
            description: Input FastQ file, or pair of files
output:
    -
        - sample_id:
            type: string
            description: Sample identifier
        - trimmed_fastq:
            type: file
            description: Trimmed FastQ files
            pattern: *fq.gz
    -
        - report:
            type: file
            description: Trim Galore! trimming report
            pattern: *trimming_report.txt
    -
        - fastqc_report:
            type: file
            description: FastQC report
            pattern: *_fastqc.{zip,html}
authors:
    - @ewels