name: scoary description: Use pangenome outputs for GWAS keywords: - gwas - pangenome - prokaryote tools: - scoary: description: Microbial pan-GWAS using the output from Roary homepage: https://github.com/AdmiralenOla/Scoary documentation: https://github.com/AdmiralenOla/Scoary tool_dev_url: https://github.com/AdmiralenOla/Scoary doi: "10.1186/s13059-016-1108-8" licence: ["GPL v3"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - genes: type: file description: A presence/absence matrix of genes in the pan-genome pattern: "*.csv" - traits: type: file description: A CSV file containing trait information per-sample pattern: "*.csv" - tree: type: file description: A Newick formtted tree for phylogenetic analyses pattern: "*.{dnd,nwk,treefile}" 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" - csv: type: file description: Gene associations in a CSV file per trait pattern: "*.csv" authors: - "@rpetit3"