name: bwa_index
description: Create BWA index for reference genome
keywords:
  - index
  - fasta
  - genome
  - reference
tools:
  - bwa:
      description: |
        BWA is a software package for mapping DNA sequences against
        a large reference genome, such as the human genome.
      homepage: http://bio-bwa.sourceforge.net/
      documentation: http://www.htslib.org/doc/samtools.html
      arxiv: arXiv:1303.3997
      licence: ["GPL-3.0-or-later"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing reference information.
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: Input genome fasta file
output:
  - meta:
      type: map
      description: |
        Groovy Map containing reference information.
        e.g. [ id:'test', single_end:false ]
  - index:
      type: file
      description: BWA genome index files
      pattern: "*.{amb,ann,bwt,pac,sa}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@maxulysse"
maintainers:
  - "@drpatelh"
  - "@maxulysse"
  - "@gallvp"
