Nextflow Registry | nf-core/gatk4/svcluster@0.0.0-0c7146d

nf-core/gatk4/svcluster @ 0.0.0-0c7146d

Clusters structural variants based on coordinates, event type, and supporting algorithms

gatk4 structural variants svcluster vcf

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Clusters structural variants based on coordinates, event type, and supporting algorithms

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

include { GATK4_SVCLUSTER } from 'nf-core/gatk4/svcluster'

MIT License

Process

`Name`	`GATK4_SVCLUSTER`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcfs` file	One or more VCF files created with a structural variant caller `*.vcf.gz`
`indices` file	Index files for the VCFs `*.vcf.gz.tbi`

`ploidy_table` file	The sample ploidy table `*.tsv`

`fasta` file	Reference FASTA file needed when the input is a CRAM file `*.{fasta,fa}`

`fasta_fai` file	Index of the reference FASTA file needed when the input is a CRAM file `*.fai`

`dict` file	Sequence dictionary of the reference FASTA file needed when the input is a CRAM file `*.dict`

Output 3 channels

#1 clustered_vcf tuple

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

#2 versions_gatk4 tuple

`${task.process}` string	The name of the process
`gatk4` string	The name of the tool
`gatk --version \| sed -n '/GATK.v/s/.v//p'` eval	The expression to obtain the version of the tool

#3 clustered_vcf_index tuple

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

Tool	Description	Homepage
gatk4	Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:43:18 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fsvcluster/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/svcluster/blobs/sha256:f2361e259a389bac941cbb24996c8d5c521bc7c392345f40e1da2dd20ca35552
Size	3.1 KB
Checksum	sha256:f2361e259a389bac941cbb24996c8d5c521bc7c392345f40e1da2dd20ca35552
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:43:18 (UTC)		1	3.1 KB	-