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

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

Condenses homRef blocks in a single-sample GVCF

gatk4 gvcf reblockgvcf

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Condenses homRef blocks in a single-sample GVCF

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

include { GATK4_REBLOCKGVCF } from 'nf-core/gatk4/reblockgvcf'

MIT License

Process

`Name`	`GATK4_REBLOCKGVCF`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`gvcf` file	GVCF file created using HaplotypeCaller using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode `*.{vcf,gvcf}.gz`
`tbi` file	Index of the GVCF file `*.tbi`
`intervals` file	Bed file with the genomic regions included in the library (optional)

`fasta` file	The reference fasta file `*.fasta`

`fai` file	Index of reference fasta file `fasta.fai`

`dict` file	GATK sequence dictionary `*.dict`

`dbsnp` file	VCF file containing known sites (optional)

`dbsnp_tbi` file	VCF index of dbsnp (optional)

Output 2 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.rb.g.vcf.gz` file	The reblocked GVCF file `*.rb.g.vcf.gz`
`*.tbi` file	Index of the reblocked GVCF file `*.tbi`

#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

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 18:42:59 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Freblockgvcf/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/reblockgvcf/blobs/sha256:b1cc974c2aa13edece85c1c78ff77a7b5aead3f663d918949aa2b7d7e7efc272
Size	3.1 KB
Checksum	sha256:b1cc974c2aa13edece85c1c78ff77a7b5aead3f663d918949aa2b7d7e7efc272
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:42:59 (UTC)		1	3.1 KB	-