Nextflow Registry | nf-core/htsnimtools/vcfcheck@0.0.0-0c7146d

nf-core/htsnimtools/vcfcheck @ 0.0.0-0c7146d

This tools takes a background VCF, such as gnomad, that has full genome (though in some cases, users will instead want whole exome) coverage and uses that as an expectation of variants.

validation check variation

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Summary

This tools takes a background VCF, such as gnomad, that has full genome (though in some cases, users will instead want whole exome) coverage and uses that as an expectation of variants.

Get started

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

include { HTSNIMTOOLS_VCFCHECK } from 'nf-core/htsnimtools/vcfcheck'

License

MIT License

Process

`Name`	`HTSNIMTOOLS_VCFCHECK`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`vcf` file	The query VCF file `*.{vcf,vcf.gz,bcf}`
`tbi` file	The index of the query VCF file `*.{tbi}`

#2 tuple

`meta2` map	Groovy Map containing background VCF information e.g. `[ id:'sample1', single_end:false ]`
`background_vcf` file	The background VCF file `*.{vcf,vcf.gz,bcf}`
`background_tbi` file	The index of the background VCF file `*.{tbi}`

Output 2 channels

#1 tsv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.tsv` file	A tab-delimited file comparing the variant count of each region in the query VCF and background VCF `*.tsv`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
htsnimtools	useful command-line tools written to show-case hts-nim	https://github.com/brentp/hts-nim-tools

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:48:25 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fhtsnimtools%2Fvcfcheck/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/htsnimtools/vcfcheck/blobs/sha256:a55e269484960bcdc4e5f02822e8eb04a50b944e85a0ee50b169bffa066ddc1f
Size	2.5 KB
Checksum	sha256:a55e269484960bcdc4e5f02822e8eb04a50b944e85a0ee50b169bffa066ddc1f
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:48:25 (UTC)		1	2.5 KB	-