name: "rtgtools_vcfeval" description: The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set keywords: - benchmarking - vcf - rtg-tools tools: - "rtgtools": description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" doi: "" licence: "['BSD']" input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - truth_vcf: type: file description: A standard VCF to compare against pattern: "*.{vcf,vcf.gz}" - truth_vcf_index: type: file description: The index of the standard VCF (optional) pattern: "*.tbi" - query_vcf: type: file description: A VCF with called variants to benchmark against the standard pattern: "*.{vcf,vcf.gz}" - query_vcf_index: type: file description: The index of the called VCF (optional) pattern: "*.tbi" - bed: type: file description: The BED file of the called VCF pattern: "*.bed" - sdf: type: folder/file description: The SDF (RTG Sequence Data File) of the reference genome. Can be a folder or a tar-zipped folder. pattern: "*.{,tar.gz}" 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" - results: type: file description: A text file containing the results of the benchmark pattern: "*.txt" authors: - "@nvnieuwk"