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

      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.
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test', single_end:false ]
  - 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"
