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: 0.0.0-6c4ed3a

Total downloads: 5

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	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:04:37 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Freblockgvcf/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/reblockgvcf/blobs/sha256:9d1ac2d21bc0495d3c4bb53ce693080dffe60a319c0d821b540fa7d15ed040df
Size	3.0 KB
Checksum	sha256:9d1ac2d21bc0495d3c4bb53ce693080dffe60a319c0d821b540fa7d15ed040df
Downloads	2

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:20:27 (UTC)		3	3.1 KB
0.0.0-0c7146d	08 Apr 2026 19:04:37 (UTC)		2	3.0 KB