name: "shigatyper"
description: Determine Shigella serotype from Illumina or Oxford Nanopore reads
keywords:
  - fastq
  - shigella
  - serotype
tools:
  - "shigatyper":
      description: "Typing tool for Shigella spp. from WGS Illumina sequencing"
      homepage: "https://github.com/CFSAN-Biostatistics/shigatyper"
      documentation: "https://github.com/CFSAN-Biostatistics/shigatyper"
      tool_dev_url: "https://github.com/CFSAN-Biostatistics/shigatyper"
      doi: "10.1128/AEM.00165-19"
      licence: "['Public Domain']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false, is_ont:false ]
  - reads:
      type: file
      description: Illumina or Nanopore FASTQ file
      pattern: "*.fastq.gz"

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"
  - tsv:
      type: file
      description: A TSV formatted file with ShigaTyper results
      pattern: "*.tsv"
  - hits:
      type: file
      description: A TSV formatted file with individual gene hits
      pattern: "*-hits.tsv"

authors:
  - "@rpetit3"
