name: rgi_main description: Predict antibiotic resistance from protein or nucleotide data keywords: - bacteria - fasta - antibiotic resistance tools: - rgi: description: This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website homepage: https://card.mcmaster.ca documentation: https://github.com/arpcard/rgi tool_dev_url: https://github.com/arpcard/rgi doi: "10.1093/nar/gkz935" licence: ['https://card.mcmaster.ca/about'] 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}" 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" - json: type: file description: JSON formatted file with RGI results pattern: "*.{json}" - tsv: type: file description: Tab-delimited file with RGI results pattern: "*.{txt}" authors: - "@rpetit3"