nf-core_modules/modules/rtgtools/vcfeval/meta.yml
Nicolas Vannieuwkerke ef4857ec54 Updated meta.yml
2022-05-10 12:20:01 +02:00

83 lines
2.7 KiB
YAML

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"
- truth_regions:
type: file
description: A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional)
pattern: "*.bed"
- evaluation_regions:
type: file
description: A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional)
pattern: "*.bed"
- sdf:
type: file
description: The SDF (RTG Sequence Data File) folder of the reference genome
pattern: "*"
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"
- logging:
type: file
description: Files containing logging from vcfeval
pattern: "*{done,progress,.log}"
- vcf:
type: file
description: VCF files containing the false negatives, false positives and true positives with their index files
pattern: "*.vcf{.gz,.gz.tbi}"
- roc:
type: file
description: TSV files containing ROC data for the evaluated variants
pattern: "*.tsv.gz"
- summary:
type: file
description: A TXT file containing the summary of the evaluation
pattern: "summary.txt"
- phasing:
type: file
description: A TXT file containing the data on the phasing
pattern: "phasing.txt"
authors:
- "@nvnieuwk"