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"