name: Bowtie 2 
description: Ultrafast alignment to reference genome
keywords:
    - Alignment
    - Short reads
    - FM Index
tools:
    - fastqc:
        description: |
            Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
            to long reference sequences. It is particularly good at aligning reads of about
            50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively
            long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep
            its memory footprint small: for the human genome, its memory footprint is typically
            around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
        homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
        documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
input:
    -
        - sample_id:
            type: string
            description: Sample identifier
        - reads:
            type: file
            description: Input FastQ file, or pair of files
output:
    -
        - report:
            type: file
            description: mapping statistics report
            pattern: *bowtie2_stats.txt
        - alignment:
            type: file
            description: alignment file in BAM format
            pattern: *bowtie2.bam
authors:
    - @FelixKrueger