name: bwamem2_index
description: Create BWA-mem2 index for reference genome
keywords:
  - index
  - fasta
  - genome
  - reference
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: https://github.com/bwa-mem2/bwa-mem2#usage
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: Input genome fasta file
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - index:
      type: file
      description: BWA genome index files
      pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@maxulysse"