name: bwa_aln
description: Find SA coordinates of the input reads for bwa short-read mapping
keywords:
  - bwa
  - aln
  - short-read
  - align
  - reference
  - fasta
  - map
  - fastq
tools:
    - bwa:
        description: |
            BWA is a software package for mapping DNA sequences against
            a large reference genome, such as the human genome.
        homepage: http://bio-bwa.sourceforge.net/
        documentation: http://bio-bwa.sourceforge.net/
        doi: "10.1093/bioinformatics/btp324"
      licence: ['GPL v3']

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: BWA genome index files
        pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - sai:
      type: file
      description: Single or paired SA coordinate files
      pattern: "*.sai"

authors:
  - "@jfy133"