name: amrfinderplus_run
description: Identify antimicrobial resistance in gene or protein sequences
keywords:
  - bacteria
  - fasta
  - antibiotic resistance
tools:
  - amrfinderplus:
      description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
      homepage: https://github.com/ncbi/amr/wiki
      documentation: https://github.com/ncbi/amr/wiki
      tool_dev_url: https://github.com/ncbi/amr
      doi: "10.1038/s41598-021-91456-0"
      licence: ["Public Domain"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: Nucleotide or protein sequences in FASTA format
      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
  - db:
      type: file
      description: A compressed tarball of the AMRFinderPlus database to query
      pattern: "*.tar.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"
  - report:
      type: file
      description: AMRFinder+ final report
      pattern: "*.tsv"
  - mutation_report:
      type: file
      description: Report of organism-specific point-mutations
      pattern: "*-mutations.tsv"
  - tool_version:
      type: string
      description: The version of the tool in string format (useful for downstream tools such as hAMRronization)
  - db_version:
      type: string
      description: The version of the used database in string format (useful for downstream tools such as hAMRronization)

authors:
  - "@rpetit3"
  - "@louperelo"
  - "@jfy133"