name: bwamem2_mem
description: Performs fastq alignment to a fasta reference using BWA
keywords:
    - mem
    - bwa
    - alignment
    - map
    - fastq
    - bam
    - sam
tools:
    - bwa:
        description: |
            BWA-mem2 is a software package for mapping DNA sequences against
            a large reference genome, such as the human genome.
        homepage: https://github.com/bwa-mem2/bwa-mem2
        documentation: http://www.htslib.org/doc/samtools.html
        arxiv: arXiv:1303.3997
        licence: ['MIT']
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.
    - index:
        type: file
        description: BWA genome index files
        pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
    - sort_bam:
        type: boolean
        description: use samtools sort (true) or samtools view (false)
        pattern: "true or false"
output:
    - bam:
        type: file
        description: Output BAM file containing read alignments
        pattern: "*.{bam}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@maxulysse"