name: dragmap_align
description: Performs fastq alignment to a reference using DRAGMAP
keywords:
    - alignment
    - map
    - fastq
    - bam
    - sam
tools:
    - dragmap:
        description: Dragmap is the Dragen mapper/aligner Open Source Software.
        homepage: https://github.com/Illumina/dragmap
        documentation: https://github.com/Illumina/dragmap
        tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage
        doi: ""
        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.
    - hashmap:
        type: file
        description: DRAGMAP hash table
        pattern: "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}"
output:
    - bam:
        type: file
        description: Output BAM file containing read alignments
        pattern: "*.{bam}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
  - "@Emiller88"