Nextflow Registry | nf-core/picard/collectvariantcallingmetrics@0.0.0-0c7146d

nf-core/picard/collectvariantcallingmetrics @ 0.0.0-0c7146d

Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file

vcf metrics variant calling statistics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @georgiakes

Maintainers: @georgiakes

Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file

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

include { PICARD_COLLECTVARIANTCALLINGMETRICS } from 'nf-core/picard/collectvariantcallingmetrics'

MIT License

Process

`Name`	`PICARD_COLLECTVARIANTCALLINGMETRICS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`vcf` file	Input VCF file for analysis `*.{vcf,vcf.gz}`
`index` file	Index file for the input VCF file `*.{idx,tbi}`
`intervals_file` file	Optional BED file specifying target intervals `*.{bed,bed.gz,intervals_list}`
`fasta` file	Reference sequence file `*.{fasta,fa,fasta.gz,fa.gz}`
`dict` file	Reference sequence dictionary file `*.{dict}`
`dbsnp` file	Reference dbSNP file in dbSNP or VCF format `*.{vcf,vcf.gz}`
`dbsnp_index` file	Reference dbSNP file in dbSNP or VCF format `*.{idx,tbi}`

Output 3 channels

#1 detail_metrics tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.variant_calling_detail_metrics` file	Detailed variant calling metrics file `*.variant_calling_detail_metrics`

#2 summary_metrics tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.variant_calling_summary_metrics` file	Summary variant calling metrics file `*.variant_calling_summary_metrics`

#3 versions_picard tuple

`${task.process}` string	The process the versions were collected from
`picard` string	The tool name
`picard CollectVariantCallingMetrics --version 2>&1 \| sed -n 's/.*Version://p'` string	The command used to generate the version of the tool

Tool	Description	Homepage
picard	A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.	https://broadinstitute.github.io/picard/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:02:35 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcollectvariantcallingmetrics/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/picard/collectvariantcallingmetrics/blobs/sha256:caaba49aa5b3f553f2797092281f52d12ef6a6e053a901e87938f1f6b6e86cb6
Size	3.2 KB
Checksum	sha256:caaba49aa5b3f553f2797092281f52d12ef6a6e053a901e87938f1f6b6e86cb6
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:02:35 (UTC)		1	3.2 KB	-