name: bowtie2_build
description: Builds bowtie index for reference genome
keywords:
  - build
  - index
  - fasta
  - genome
  - reference
tools:
  - bowtie2:
      description: |
        Bowtie 2 is an ultrafast and memory-efficient tool for aligning
        sequencing reads to long reference sequences.
      homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
      documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
      doi: 10.1038/nmeth.1923
      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: Bowtie2 genome index files
      pattern: "*.bt2"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@joseespinosa"
  - "@drpatelh"