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
params:
    - outdir:
          type: string
          description: |
              The pipeline's output directory. By default, the module will
              output files into `$params.outdir/<SOFTWARE>`
    - publish_dir_mode:
          type: string
          description: |
              Value for the Nextflow `publishDir` mode parameter.
              Available: symlink, rellink, link, copy, copyNoFollow, move.
    - enable_conda:
          type: boolean
          description: |
              Run the module with Conda using the software specified
              via the `conda` directive
    - singularity_pull_docker_container:
          type: boolean
          description: |
              Instead of directly downloading Singularity images for use with Singularity,
              force the workflow to pull and convert Docker containers instead.
input:
    - fasta:
          type: file
          description: Input genome fasta file
output:
    - index:
          type: file
          description: Bowtie2 genome index files
          pattern: "*.bt2"
    - version:
          type: file
          description: File containing software version
          pattern: "*.{version.txt}"
authors:
    - "@joseespinosa"
    - "drpatelh"