name: yara_mapper
description: Align reads to a reference genome using YARA
keywords:
  - align
  - genome
  - reference
tools:
  - yara:
      description: Yara is an exact tool for aligning DNA sequencing reads to reference genomes.
      homepage: https://github.com/seqan/seqan
      documentation: https://github.com/seqan/seqan
      tool_dev_url: https://github.com/seqan/seqan
      doi: ""
      licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"]

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: YARA genome index files

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"
  - bam:
      type: file
      description: Sorted BAM file
      pattern: "*.{bam}"
  - bai:
      type: file
      description: Sorted BAM file index
      pattern: "*.{bai}"

authors:
  - "@apeltzer"
