mirror of
https://github.com/MillironX/nf-core_modules.git
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95 lines
3.1 KiB
YAML
95 lines
3.1 KiB
YAML
name: "rtgtools_vcfeval"
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description: The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set
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keywords:
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- benchmarking
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- vcf
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- rtg-tools
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tools:
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- "rtgtools":
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description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation"
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homepage: "https://www.realtimegenomics.com/products/rtg-tools"
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documentation: "https://github.com/RealTimeGenomics/rtg-tools"
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tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools"
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doi: ""
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licence: "['BSD']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- truth_vcf:
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type: file
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description: A standard VCF to compare against
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pattern: "*.{vcf,vcf.gz}"
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- truth_vcf_index:
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type: file
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description: The index of the standard VCF (optional)
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pattern: "*.tbi"
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- query_vcf:
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type: file
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description: A VCF with called variants to benchmark against the standard
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pattern: "*.{vcf,vcf.gz}"
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- query_vcf_index:
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type: file
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description: The index of the called VCF (optional)
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pattern: "*.tbi"
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- truth_regions:
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type: file
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description: A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional)
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pattern: "*.bed"
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- evaluation_regions:
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type: file
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description: A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional)
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pattern: "*.bed"
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- sdf:
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type: file
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description: The SDF (RTG Sequence Data File) folder of the reference genome
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pattern: "*"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- logging:
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type: file
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description: Files containing logging from vcfeval
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pattern: "*{done,progress,.log}"
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- tp:
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type: file
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description: A tuple containing the VCF and TBI file for the true positive variants
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pattern: "tp.vcf{.gz,.gz.tbi}"
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- baseline:
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type: file
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description: A tuple containing the VCF and TBI file for the baseline true positive variants
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pattern: "tp-baseline.vcf{.gz,.gz.tbi}"
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- fp:
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type: file
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description: A tuple containing the VCF and TBI file for the false positive variants
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pattern: "fp.vcf{.gz,.gz.tbi}"
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- fn:
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type: file
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description: A tuple containing the VCF and TBI file for the false negative variants
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pattern: "fn.vcf{.gz,.gz.tbi}"
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- roc:
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type: file
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description: TSV files containing ROC data for the evaluated variants
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pattern: "*.tsv.gz"
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- summary:
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type: file
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description: A TXT file containing the summary of the evaluation
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pattern: "summary.txt"
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- phasing:
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type: file
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description: A TXT file containing the data on the phasing
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pattern: "phasing.txt"
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authors:
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- "@nvnieuwk"
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