name: plasmidid description: assembles bacterial plasmids keywords: - assembly - plasmid - bacterial tools: - plasmidid: description: Pipeline for plasmid identification and reconstruction homepage: https://github.com/BU-ISCIII/plasmidID/wiki documentation: https://github.com/BU-ISCIII/plasmidID#readme tool_dev_url: https://github.com/BU-ISCIII/plasmidID doi: "" licence: ['GPL v3'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - scaffold: type: file description: | Fasta file containing scaffold - fasta: type: file description: FASTA reference file pattern: "*.{fasta,fa}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - html: type: file description: html file with results rendered pattern: "*.{html}" - tab: type: file description: Results in a tabular file pattern: "*.{tab}" - images: type: directory description: Directory containing the images produced by plasmidid pattern: "images" - logs: type: directory description: Directory containing the logs produced by plasmidid pattern: "logs" - data: type: directory description: Directory containing the data produced by plasmidid pattern: "data" - database: type: directory description: Directory containing the database produced by plasmidid pattern: "database" - fasta_files: type: directory description: Directory containing the fasta files produced by plasmidid pattern: "fasta_files" - kmer: type: directory description: Directory containing the kmer files produced by plasmidid pattern: "database" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@joseespinosa" - "@drpatelh"