name: nextgenmap
description: Performs fastq alignment to a fasta reference using NextGenMap
keywords:
  - NextGenMap
  - ngm
  - alignment
  - map
  - fastq
  - bam
  - sam
tools:
  - bwa:
      description: |
        NextGenMap is a flexible highly sensitive short read mapping tool that
        handles much higher mismatch rates than comparable algorithms while
        still outperforming them in terms of runtime
      homepage: https://github.com/Cibiv/NextGenMap
      documentation: https://github.com/Cibiv/NextGenMap/wiki
      doi: 10.1093/bioinformatics/btt468
      licence: ["MIT"]
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, if meta.single_end is true, and 2
        if meta.single_end is false.
  - fasta:
      type: file
      description: |
        Genomic reference fasta file
      pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information. First item of tuple with
        bam, below.
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: |
        Output BAM file containing read alignments. Second item of tuple with
        meta, above
      pattern: "*.{bam}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@cmatkhan"