nf-core_modules/software/bwa/mem/meta.yml

name: bwa_mem
description: Performs fastq alignment to a fasta reference using BWA
keywords:
  - mem
  - bwa
  - alignment
  - map
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://www.htslib.org/doc/samtools.html
      arxiv: arXiv:1303.3997
params:
  - outdir:
      type: string
      description: |
        The pipeline's output directory. By default, the module will
        output files into `$params.outdir/<SOFTWARE>`
  - publish_dir_mode:
      type: string
      description: |
        Value for the Nextflow `publishDir` mode parameter.
        Available: symlink, rellink, link, copy, copyNoFollow, move.
  - conda:
      type: boolean
      description: |
        Run the module with Conda using the software specified
        via the `conda` directive
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: "*.{amb,ann,bwt,pac,sa}"
  - fasta:
      type: file
      description: |
        Input genome fasta file
  - options:
      type: map
      description: |
        Groovy Map containing module options for passing command-line arguments and
        output file paths.
output:
  - bam:
      type: file
      description: Output BAM file containing read alignments
      pattern: "*.bam"
  - version:
      type: file
      description: File containing software version
      pattern: "*.version.txt"
authors:
  - "@drpatelh"
  - "@jeremy1805"