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63 lines
1.8 KiB
YAML
63 lines
1.8 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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- bed:
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type: file
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description: The BED file of the called VCF
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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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- results:
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type: file
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description: A text file containing the results of the benchmark
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pattern: "*.txt"
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authors:
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- "@nvnieuwk"
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