Nextflow Registry | nf-core/bcftools/merge@0.0.0-6c4ed3a

nf-core/bcftools/merge @ 0.0.0-6c4ed3a

Merge VCF files

variant calling merge VCF

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @joseespinosa @drpatelh @nvnieuwk @ramprasadn

Maintainers: @joseespinosa @drpatelh @nvnieuwk @ramprasadn

Merge VCF files

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

include { BCFTOOLS_MERGE } from 'nf-core/bcftools/merge'

MIT License

Process

`Name`	`BCFTOOLS_MERGE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcfs` file	List containing 2 or more vcf files e.g. [ 'file1.vcf', 'file2.vcf' ]
`tbis` file	List containing the tbi index files corresponding to the vcfs input files e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
`bed` file	(Optional) The bed regions to merge on `*.bed`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter) `*.{fasta,fa}`
`fai` file	(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter) `*.fai`

Output 3 channels

#1 vcf tuple

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

#2 index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{csi,tbi}` file	index of merged output `*.{csi,tbi}`

#3 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
merge	Merge VCF files.	http://samtools.github.io/bcftools/bcftools.html

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:04:58 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbcftools%2Fmerge/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bcftools/merge/blobs/sha256:105a0e67fccf0208d5ef6034ae61ce5d3fa793d302723f1f5f400ff1d4ec2c92
Size	4.3 KB
Checksum	sha256:105a0e67fccf0208d5ef6034ae61ce5d3fa793d302723f1f5f400ff1d4ec2c92
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:04:58 (UTC)		3	4.3 KB
0.0.0-0c7146d	08 Apr 2026 18:45:57 (UTC)		4	4.3 KB