Nextflow Registry | nf-core/rtgtools/cnveval@0.0.0-6c4ed3a

nf-core/rtgtools/cnveval @ 0.0.0-6c4ed3a

The cnveval tool of RTG tools. It is used to evaluate called CNV regions for agreement with a baseline CNV set.

benchmarking vcf rtg-tools cnv-eval copy-number-variants

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @SevaNur

Maintainers: @SevaNur

The cnveval tool of RTG tools. It is used to evaluate called CNV regions for agreement with a baseline CNV set.

Add the following snippet to your workflow script to include this module.

include { RTGTOOLS_CNVEVAL } from 'nf-core/rtgtools/cnveval'

MIT License

Process

`Name`	`RTGTOOLS_CNVEVAL`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`query_vcf` file	A VCF with called CNV variants to benchmark against the baseline. Records must contain INFO END and INFO SVTYPE (DUP or DEL). `*.{vcf,vcf.gz}`
`query_vcf_tbi` file	The index of the VCF file with called variants `*.{vcf.gz.tbi,vcf.tbi}`
`truth_vcf` file	A baseline VCF containing expected CNV calls. Records must contain INFO END and INFO SVTYPE (DUP or DEL). `*.{vcf,vcf.gz}`
`truth_vcf_tbi` file	The index of the baseline VCF to compare against `*.{vcf.gz.tbi,vcf.tbi}`
`evaluation_regions_bed` file	A BED file containing the regions of interest for evaluation (required). Regions are intersected with truth and calls VCFs to obtain CNV regions. `*.bed`

Output 5 channels

#1 summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.summary.txt` file	A TXT file containing the summary statistics of the evaluation `*.summary.txt`

#2 calls_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.calls.bed.gz` file	A BED file containing called CNV regions with TP/FP status, SVTYPE, the span of the original calls VCF record, and the score value `*.calls.bed.gz`

#3 baseline_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.baseline.bed.gz` file	A BED file containing truth CNV regions with TP/FN status, SVTYPE, and the span of the original truth VCF record `*.baseline.bed.gz`

#4 weighted_roc tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.weighted_roc.tsv.gz` file	TSV file containing weighted ROC data that can be plotted with rocplot `*.weighted_roc.tsv.gz`

#5 versions_rtgtools tuple

`${task.process}` string	The name of the process
`rtgtools` string	The name of the tool
`rtg version \| sed 's/Product: RTG Tools //; q'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
rtgtools	RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation.	https://www.realtimegenomics.com/products/rtg-tools

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:41:25 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Frtgtools%2Fcnveval/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/rtgtools/cnveval/blobs/sha256:d15bde1d57d932ffd3b45bb7d499ae45011057d6d348d00b9f515a734cddeb4d
Size	3.3 KB
Checksum	sha256:d15bde1d57d932ffd3b45bb7d499ae45011057d6d348d00b9f515a734cddeb4d
Downloads	3

Version	Date