name: "mykrobe_predict"
description: AMR predictions for supported species
keywords:
  - fastq
  - bam
  - antimicrobial resistance
tools:
  - "mykrobe":
      description: "Antibiotic resistance prediction in minutes"
      homepage: "http://www.mykrobe.com/"
      documentation: "https://github.com/Mykrobe-tools/mykrobe/wiki"
      tool_dev_url: "https://github.com/Mykrobe-tools/mykrobe"
      doi: "10.1038/ncomms10063"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - seqs:
      type: file
      description: BAM or FASTQ file
      pattern: "*.{bam,fastq.gz,fq.gz}"
  - species:
      type: string
      description: Species to make AMR prediction against
      pattern: "*"

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"
  - csv:
      type: file
      description: AMR predictions in CSV format
      pattern: "*.csv"
  - json:
      type: file
      description: AMR predictions in JSON format
      pattern: "*.json"

authors:
  - "@rpetit3"