name: "stecfinder"
description: Serotype STEC samples from paired-end reads or assemblies
keywords:
  - serotype
  - Escherichia coli
  - fastq
  - fasta
tools:
  - "stecfinder":
      description: "Cluster informed Shigatoxin producing E. coli (STEC) serotyping tool from Illumina reads and assemblies"
      homepage: "https://github.com/LanLab/STECFinder"
      documentation: "https://github.com/LanLab/STECFinder"
      tool_dev_url: "https://github.com/LanLab/STECFinder"
      doi: "10.3389/fcimb.2021.772574"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - seqs:
      type: file
      description: Illumina paired-end reads or an assembly
      pattern: "*.{fastq.gz,fasta.gz,fna.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 tab-delimited report of results
      pattern: "*.tsv"

authors:
  - "@rpetit3"
