name: "seroba_run"
description: Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
keywords:
  - fastq
  - serotype
  - Streptococcus pneumoniae
tools:
  - "seroba":
      description: "SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references."
      homepage: "https://sanger-pathogens.github.io/seroba/"
      documentation: "https://sanger-pathogens.github.io/seroba/"
      tool_dev_url: "https://github.com/sanger-pathogens/seroba"
      doi: "10.1099/mgen.0.000186"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: Input Illunina paired-end FASTQ files
      pattern: "*.{fq.gz,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: The predicted serotype in tab-delimited format
      pattern: "*.tsv"
  - txt:
      type: file
      description: A detailed description of the predicted serotype
      pattern: "*.txt"

authors:
  - "@rpetit3"