Nextflow Registry | nf-core/sentieon/gvcftyper@0.0.0-6c4ed3a

nf-core/sentieon/gvcftyper @ 0.0.0-6c4ed3a

Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.

joint genotyping genotype gvcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @asp8200

Maintainers: @asp8200

Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.

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

include { SENTIEON_GVCFTYPER } from 'nf-core/sentieon/gvcftyper'

MIT License

Process

`Name`	`SENTIEON_GVCFTYPER`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`gvcfs` file	gVCF(.gz) file `*.{vcf,vcf.gz}`
`tbis` file	index of gvcf file `*.tbi`
`intervals` file	Interval file with the genomic regions included in the library (optional)

#2 tuple

`meta1` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Reference fasta file `*.fasta`

#3 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fai` file	Reference fasta index file `*.fai`

#4 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`dbsnp` file	dbSNP VCF file `*.vcf.gz`

#5 tuple

`meta4` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`dbsnp_tbi` file	dbSNP VCF index file `*.tbi`

Output 3 channels

#1 vcf_gz tuple

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

#2 vcf_gz_tbi tuple

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

#3 versions_sentieon tuple

`${task.process}` string	The process the versions were collected from
`sentieon` string	The tool name
`sentieon driver --version \| sed "s/.*-//g"` string	The command used to generate the version of the tool

Tool	Description	Homepage
sentieon	Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.	https://www.sentieon.com/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:44:01 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Fgvcftyper/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sentieon/gvcftyper/blobs/sha256:ff364a8f86fcb56027226d5e39cdeb768035a49aa7f51d7d9c9ff46e30b19c55
Size	3.6 KB
Checksum	sha256:ff364a8f86fcb56027226d5e39cdeb768035a49aa7f51d7d9c9ff46e30b19c55