Nextflow Registry | nf-core/htsnimtools/vcfcheck@0.0.0-6c4ed3a

nf-core/htsnimtools/vcfcheck @ 0.0.0-6c4ed3a

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: 0.0.0-6c4ed3a

Total downloads: 11

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:24:43 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fhtsnimtools%2Fvcfcheck/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/htsnimtools/vcfcheck/blobs/sha256:9ae0605e7fbfe71378c95d15a3c8c67fa3879be35c695a0ccf8d2d26e5300a46
Size	2.5 KB
Checksum	sha256:9ae0605e7fbfe71378c95d15a3c8c67fa3879be35c695a0ccf8d2d26e5300a46
Downloads	4

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:24:43 (UTC)	4	2.5 KB
0.0.0-3fc6d40	22 Apr 2026 15:16:42 (UTC)	4	2.5 KB
0.0.0-0c7146d	08 Apr 2026 19:10:13 (UTC)	3	2.5 KB