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.
  - meta2:
      type: map
      description: |
        Groovy Map containing reference/index information
        e.g. [ id:'test' ]
  - 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:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - 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"
