name: FastQ Screen
description: Run FastQ Screen on sequenced reads for Species Identification
keywords:
    - Quality Control
    - Species Screen
    - Contamination
tools:
    - fastqc:
        description: |
            FastQ Screen allows you to screen a library of sequences in
            FastQ format against a set of sequence databases so you can
            see if the composition of the library matches with what you expect.
        homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/_build/html/index.html
input:
    -
        - sample_id:
            type: string
            description: Sample identifier
        - reads:
            type: file
            description: Input FastQ file
output:
    -
        - report:
            type: file
            description: FastQ Screen report
            pattern: "*_screen.{txt,html,png}"
            optional_pattern: "*_screen.bisulfite_orientation.png"
authors:
    - "@FelixKrueger"