name: bowtie2_align
description: Align reads to a reference genome using bowtie2
keywords:
  - align
  - map
  - fasta
  - fastq
  - 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 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.
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test', single_end:false ]
  - index:
      type: file
      description: Bowtie2 genome index files
      pattern: "*.ebwt"
  - save_unaligned:
      type: boolean
      description: |
        Save reads that do not map to the reference (true) or discard them (false)
        (default: false)
  - sort_bam:
      type: boolean
      description: use samtools sort (true) or samtools view (false)
      pattern: "true or false"
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"
  - log:
      type: file
      description: Aligment log
      pattern: "*.log"
authors:
  - "@joseespinosa"
  - "@drpatelh"