name: antismash_antismashlite description: | antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. keywords: - secondary metabolites - BGC - biosynthetic gene cluster - genome mining - NRPS - RiPP - antibiotics - prokaryotes - bacteria - eukaryotes - fungi - antismash tools: - antismashlite: description: "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell" homepage: "https://docs.antismash.secondarymetabolites.org" documentation: "https://docs.antismash.secondarymetabolites.org" tool_dev_url: "https://github.com/antismash/antismash" doi: "10.1093/nar/gkab335" licence: "['AGPL v3']" input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - sequence_input: type: file description: nucleotide sequence file (annotated) pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}" - gff: type: file description: GFF3 file to extract annotated features from (only needed if sequence_input is in FASTA format) pattern: "*.{gff, GFF}" - databases: type: directory description: downloaded AntiSMASH databases e.g. data/databases pattern: "*/" - antismash_dir: type: directory description: | A local copy of an AntiSMASH installation folder. This is required when running with docker and singularity (not required for conda), due to attempted 'modifications' of files during database checks in the installation directory, something that cannot be done in immutable docker/singularity containers. Therefore, a local installation directory needs to be mounted (including all modified files from the downloading step) to the container as a workaround. pattern: "*" 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" - clusterblast_file: type: file description: Output of ClusterBlast algorithm pattern: "clusterblast/*_c*.txt" - css_file: type: file description: Style sheet containing the formatting of HTML output pattern: "css/*.css" - image_directory: type: directory description: image files for web view of antiSMASH results pattern: "images" - javascript: type: file description: JavaScript files pattern: "js/*.js" - knownclusterblast_html: type: file description: Tables with MIBiG hits in HTML format pattern: "knownclusterblast/region*/ctg*.html" - knownclusterblast_txt: type: file description: Tables with MIBiG hits pattern: "knownclusterblast/*_c*.txt" - svg_files_clusterblast: type: file description: SVG images showing the % identity of the aligned hits against their queries pattern: "svg/clusterblast*.svg" - svg_files_knownclusterblast: type: file description: SVG images showing the % identity of the aligned hits against their queries pattern: "svg/knownclusterblast*.svg" - gbk_input: type: file description: Nucleotide sequence + annotations in GenBank format; converted from input file pattern: "*.gbk" - json_results: type: file description: Nucleotide sequence + annotations in JSON format; converted from GenBank file (gbk_input) pattern: "*.json" - log: type: file description: Contains all the logging output that antiSMASH produced during its run pattern: "*.log" - zip: type: file description: Contains a compressed version of the output folder in zip format pattern: "*.zip" - gbk_results: type: file description: Nucleotide sequence + annotations in GenBank format; one file per antiSMASH hit pattern: "*region*.gbk" - clusterblastoutput: type: file description: Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm pattern: "clusterblastoutput.txt" - html: type: file description: Graphical web view of results in HTML format patterN: "index.html" - knownclusterblastoutput: type: file description: Raw BLAST output of known clusters of the MIBiG database pattern: "knownclusterblastoutput.txt" - json_sideloading: type: file description: Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation "Annotation sideloading") pattern: "regions.js" authors: - "@jasmezz"