name: mobsuite_recon
description: A tool to reconstruct plasmids in bacterial assemblies
keywords:
  - bacteria
  - plasmid
tools:
  - mobsuite:
      description: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
      homepage: https://github.com/phac-nml/mob-suite
      documentation: https://github.com/phac-nml/mob-suite
      tool_dev_url: https://github.com/phac-nml/mob-suite
      doi: "10.1099/mgen.0.000435"
      licence: ["Apache License, Version 2.0"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: A bacterial genome assembly in FASTA format
      pattern: "*.{fasta,fa,fna}"

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"
  - chromosome:
      type: file
      description: FASTA file of all contigs found to belong to the chromosome
      pattern: "chromosome.fasta"
  - contig_report:
      type: file
      description: Assignment of the contig to chromosome or a particular plasmid grouping
      pattern: "contig_report.txt"
  - plasmids:
      type: file
      description: Each plasmid group is written to an individual FASTA
      pattern: "plasmid_*.fasta"
  - mobtyper_results:
      type: file
      description: Aggregate MOB-typer report files for all identified plasmid
      pattern: "mobtyper_results.txt"

authors:
  - "@rpetit3"