nf-core_modules/modules/bwa/aln/meta.yml

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-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.
  - 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 ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - sai:
      type: file
      description: Single or paired SA coordinate files
      pattern: "*.sai"

authors:
  - "@jfy133"