name: bismark_genomepreparation
description: |
  Converts a specified reference genome into two different bisulfite
  converted versions and indexes them for alignments.
keywords:
  - bismark
  - 3-letter genome
  - index
  - methylation
  - 5mC
  - methylseq
  - bisulphite
  - bisulfite
  - fasta
tools:
  - bismark:
      description: |
        Bismark is a tool to map bisulfite treated sequencing reads
        and perform methylation calling in a quick and easy-to-use fashion.
      homepage: https://github.com/FelixKrueger/Bismark
      documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
      doi: 10.1093/bioinformatics/btr167
      licence: ["GPL-3.0-or-later"]
input:
  - fasta:
      type: file
      description: Input genome fasta file
output:
  - index:
      type: dir
      description: Bismark genome index directory
      pattern: "BismarkIndex"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@phue"
