name: bwameth_align
description: Performs alignment of BS-Seq reads using bwameth
keywords:
  - bwameth
  - alignment
  - 3-letter genome
  - map
  - methylation
  - 5mC
  - methylseq
  - bisulphite
  - fastq
  - bam
tools:
  - bwameth:
      description: |
        Fast and accurate alignment of BS-Seq reads
        using bwa-mem and a 3-letter genome.
      homepage: https://github.com/brentp/bwa-meth
      documentation: https://github.com/brentp/bwa-meth
      arxiv: arXiv:1401.1129
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively.
  - index:
      type: dir
      description: Directory containing bwameth genome index
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: Output BAM file containing read alignments
      pattern: "*.{bam}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@phue"