mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
95 lines
3.1 KiB
YAML
95 lines
3.1 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}"
|
|
- tp:
|
|
type: file
|
|
description: A tuple containing the VCF and TBI file for the true positive variants
|
|
pattern: "tp.vcf{.gz,.gz.tbi}"
|
|
- baseline:
|
|
type: file
|
|
description: A tuple containing the VCF and TBI file for the baseline true positive variants
|
|
pattern: "tp-baseline.vcf{.gz,.gz.tbi}"
|
|
- fp:
|
|
type: file
|
|
description: A tuple containing the VCF and TBI file for the false positive variants
|
|
pattern: "fp.vcf{.gz,.gz.tbi}"
|
|
- fn:
|
|
type: file
|
|
description: A tuple containing the VCF and TBI file for the false negative variants
|
|
pattern: "fn.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"
|