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

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

bcftools Haplotype-aware consequence caller

annotation gff gff3 protein functional vcf bcf bcftools

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @lindenb

Maintainers: @lindenb

bcftools Haplotype-aware consequence caller

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

include { BCFTOOLS_CSQ } from 'nf-core/bcftools/csq'

MIT License

Process

`Name`	`BCFTOOLS_CSQ`

Input 4 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing fasta information
`fasta` file	Fasta reference `*.{fasta,fa}`

#3 tuple

`meta3` map	Groovy Map containing fai information
`fai` file	Fasta index `*.{fai}`

#4 tuple

`meta4` map	Groovy Map containing gff3 information
`gff3` file	GFF3 file `*.{gff,gff.gz,gff3,gff3.gz}`

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 ]
`*.${extension}` file	VCF with annotation, bgzipped per default `*.{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
reheader	Haplotype-aware consequence caller	http://samtools.github.io/bcftools/bcftools.html

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:04:54 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbcftools%2Fcsq/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bcftools/csq/blobs/sha256:6c05a900fedb14ae5ca82b84a739de62e27cea53ee74f05595fe17fed929701e
Size	2.9 KB
Checksum	sha256:6c05a900fedb14ae5ca82b84a739de62e27cea53ee74f05595fe17fed929701e
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a