name: bowtie_align
description: Align reads to a reference genome using bowtie
keywords:
  - align
  - map
  - fastq
  - fasta
  - genome
  - reference
tools:
  - bowtie:
      description: |
        bowtie is a software package for mapping DNA sequences against
        a large reference genome, such as the human genome.
      homepage: http://bowtie-bio.sourceforge.net/index.shtml
      documentation: http://bowtie-bio.sourceforge.net/manual.shtml
      arxiv: arXiv:1303.3997
      licence: ["Artistic-2.0"]
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: file
      description: Bowtie genome index files
      pattern: "*.ebwt"
output:
  - bam:
      type: file
      description: Output BAM file containing read alignments
      pattern: "*.{bam}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - fastq:
      type: file
      description: Unaligned FastQ files
      pattern: "*.fastq.gz"
authors:
  - "@kevinmenden"