Nextflow Registry | nf-core/sentieon/collectvcmetrics@0.0.0-6c4ed3a

nf-core/sentieon/collectvcmetrics @ 0.0.0-6c4ed3a

Accelerated implementation of the Picard CollectVariantCallingMetrics tool.

vcf sentieon genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @adamrtalbot

Maintainers: @adamrtalbot

Accelerated implementation of the Picard CollectVariantCallingMetrics tool.

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

include { SENTIEON_COLLECTVCMETRICS } from 'nf-core/sentieon/collectvcmetrics'

MIT License

Process

`Name`	`SENTIEON_COLLECTVCMETRICS`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`vcf` file	Sorted VCF file [required] `*.vcf`
`tbi` file	VCF index file [required] `*.vcf{,.gz}.tbi`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`dbsnp` file	dbsnp VCF file [required] `*.vcf{,.gz}`
`dbsnp_tbi` file	dbsnp VCF index file [required] `*.vcf{,.gz}.tbi`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`fasta` file	Genome fasta file [required] `*.{fa,fasta}`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`fai` file	Index of the genome fasta file [required] `*.fai`

#5 tuple

`meta5` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`interval` file	BED file of genome regions to draw coverage from `*.bed`

Output 3 channels

#1 metrics tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.variant_calling_detail_metrics` file	Metrics file from VCF `*.variant_calling_detail_metrics`

#2 summary tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.variant_calling_summary_metrics` file	Summary of VCF metrics `*.collectvcmetrics.txt`

#3 versions_sentieon tuple

`${task.process}` string	The process the versions were collected from
`sentieon` string	The tool name
`sentieon driver --version \| sed "s/.*-//g"` string	The command used to generate the version of the tool

Tool	Description	Homepage
sentieon	Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.	https://www.sentieon.com/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:43:54 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Fcollectvcmetrics/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sentieon/collectvcmetrics/blobs/sha256:12a7a7772b4bc84741a5ca8a0d8670e60723ab9d1a3ed9312ef5da6f50df246f
Size	3.5 KB