name: plink_vcf description: Analyses variant calling files using plink keywords: - plink - vcf tools: - plink: description: | Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner homepage: "https://www.cog-genomics.org/plink" documentation: None tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" doi: "" licence: ['GPL'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: type: file description: Variant calling file (vcf) pattern: "*.{vcf}" 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" - bed: type: file description: PLINK binary biallelic genotype table pattern: "*.{bed}" - bim: type: file description: PLINK extended MAP file pattern: "*.{bim}" - fam: type: file description: PLINK sample information file pattern: "*.{fam}" authors: - "@Mxrcon" - "@abhi18av"