name: "gecco_run" description: GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs). keywords: - bgc - detection - metagenomics - contigs tools: - "gecco": description: "Biosynthetic Gene Cluster prediction with Conditional Random Fields." homepage: "https://gecco.embl.de" documentation: "https://gecco.embl.de" tool_dev_url: "https://github.com/zellerlab/GECCO" doi: "10.1101/2021.05.03.442509" licence: "['GPL v3']" input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - input: type: file description: A genomic file containing one or more sequences as input. Input type is any supported by Biopython (fasta, gbk, etc.) pattern: "*" - hmm: file: file description: Alternative HMM file(s) to use in HMMER format pattern: "*.hmm" - model_dir: file: directory description: Path to an alternative CRF (Conditional Random Fields) module to use 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" - genes: type: file description: TSV file containing detected/predicted genes with BGC probability scores pattern: "*.genes.tsv" - features: type: file description: TSV file containing identified domains pattern: "*.features.tsv" - clusters: type: file description: TSV file containing coordinates of predicted clusters and BGC types pattern: "*.clusters.tsv" - gbk: type: file description: Per cluster GenBank file (if found) containing sequence with annotations pattern: "*.gbk" - json: type: file description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied pattern: "*.gbk" authors: - "@jfy133"