Nextflow Registry | nf-core/plink2/vcf2bgen@0.0.0-0c7146d

nf-core/plink2/vcf2bgen @ 0.0.0-0c7146d

Convert from VCF file to BGEN file version 1.2 format preserving dosages.

plink2 bgen file vcf file genotype dosages

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @edg1983

Maintainers: @edg1983

Convert from VCF file to BGEN file version 1.2 format preserving dosages.

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

include { PLINK2_VCF2BGEN } from 'nf-core/plink2/vcf2bgen'

MIT License

Process

`Name`	`PLINK2_VCF2BGEN`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`vcf` file	A vcf or vcf.gz file with genetic variants `*.{vcf,vcf.gz}`
`dosage_field` string	The FORMAT field that contains the dosage information. Set to DS to when a dosage field is not present.
`bgen_reffirst` boolean	Set true to write BGEN file with ref-first flag. With this option the first allele in the BGEN correspond to the REF allele.
`sample_name_mode` string	Option to use to set IID/FID in the BGEN file. Allowed values are double-id, const-fid , or id-delim .

Output 4 channels

#1 log_file tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.log` file	Log file generated by plink2 with information on the process applied `*.log`

#2 versions

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

#3 bgen_file tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.bgen` file	BGEN file version 1.2 `*.bgen`

#4 sample_file tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.sample` file	Sample file defining samples in the BGEN `*.sample`

Tool	Description	Homepage
plink2	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner	http://www.cog-genomics.org/plink/2.0/

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:27:53 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fplink2%2Fvcf2bgen/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/plink2/vcf2bgen/blobs/sha256:3adb35b450f574c77ad0049fcb3f75cc1115c2babb3ce81f3cdc1e363bda92e4
Size	3.1 KB
Checksum	sha256:3adb35b450f574c77ad0049fcb3f75cc1115c2babb3ce81f3cdc1e363bda92e4
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:38:04 (UTC)	3	3.1 KB
0.0.0-3fc6d40	22 Apr 2026 15:27:13 (UTC)	3	3.1 KB
0.0.0-0c7146d	08 Apr 2026 19:27:53 (UTC)	3	3.1 KB