name: bwa_sampe
description: Convert paired-end bwa SA coordinate files to SAM format
keywords:
  - bwa
  - aln
  - short-read
  - align
  - reference
  - fasta
  - map
  - sam
  - bam
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-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: FASTQ files specified alongside meta in input channel.
      pattern: "*.{fastq,fq}.gz"
  - sai:
      type: file
      description: SAI file specified alongside meta and reads in input channel.
      pattern: "*.sai"
  - index:
      type: directory
      description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
      pattern: "bwa/"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - bam:
      type: file
      description: BAM file
      pattern: "*.bam"

authors:
  - "@jfy133"