name: abricate_summary description: Screen assemblies for antimicrobial resistance against multiple databases keywords: - bacteria - assembly - antimicrobial reistance tools: - abricate: description: Mass screening of contigs for antibiotic resistance genes homepage: https://github.com/tseemann/abricate documentation: https://github.com/tseemann/abricate tool_dev_url: https://github.com/tseemann/abricate doi: "" licence: ["GPL v2", "GPL v2"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - assembly: type: file description: FASTA, GenBank or EMBL formatted file pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.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" - summary: type: file description: Tab-delimited report of aggregated results pattern: "*.{txt}" authors: - "@rpetit3"