Nextflow Registry | nf-core/bcftools/view@0.0.0-0c7146d

nf-core/bcftools/view @ 0.0.0-0c7146d

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

variant calling view bcftools VCF

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @abhi18av

Maintainers: @abhi18av

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

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

include { BCFTOOLS_VIEW } from 'nf-core/bcftools/view'

MIT License

Process

`Name`	`BCFTOOLS_VIEW`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcf` file	The vcf file to be inspected. e.g. 'file.vcf'
`index` file	The tab index for the VCF file to be inspected. e.g. 'file.tbi'

`regions` file	Optionally, restrict the operation to regions listed in this file. e.g. 'file.vcf'

`targets` file	Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) e.g. 'file.vcf'

`samples` file	Optional, file of sample names to be included or excluded. e.g. 'file.tsv'

Output 4 channels

#1 csi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.csi` file	Default VCF file index `*.csi`

#2 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tbi` file	Alternative VCF file index `*.tbi`

#3 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{vcf,vcf.gz,bcf,bcf.gz}` file	VCF normalized output file `*.{vcf,vcf.gz,bcf,bcf.gz}`

#4 versions_bcftools tuple

`${task.process}` string	The process the versions were collected from
`bcftools` string	The tool name
`bcftools --version \| sed '1!d; s/^.*bcftools //'` string	The command used to generate the version of the tool

Tool	Description	Homepage
view	View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF	http://samtools.github.io/bcftools/bcftools.html

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:25:49 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbcftools%2Fview/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bcftools/view/blobs/sha256:2174864bfe105ccbfe119fc58824b3c2976c698ffe014c86eba55502e7351694
Size	3.9 KB
Checksum	sha256:2174864bfe105ccbfe119fc58824b3c2976c698ffe014c86eba55502e7351694
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:25:49 (UTC)		1	3.9 KB	-