Nextflow Registry | nf-core/parabricks/haplotypecaller@0.0.0-0c7146d

nf-core/parabricks/haplotypecaller @ 0.0.0-0c7146d

NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller.

variant vcf haplotypecaller germline

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @bsiranosian

NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller.

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

include { PARABRICKS_HAPLOTYPECALLER } from 'nf-core/parabricks/haplotypecaller'

MIT License

Process

`Name`	`PARABRICKS_HAPLOTYPECALLER`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information. [ id:'test']
`input` file	bam file for sample to be variant called. `*.bam`
`input_index` file	(Optional) bai index corresponding to input bam file. Only necessary when using intervals. `*.bai`
`intervals` file	file or files containing genomic intervals. `*.{bed,interval_list,picard,list,intervals}`

#2 tuple

`ref_meta` map	Groovy Map containing reference information. [ id:'test']
`fasta` file	reference fasta - must be unzipped. `*.fasta`

Output 4 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'test' ]
`*.vcf` file	variant file. `*.vcf`

#2 gvcf tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'test' ]
`*.g.vcf.gz` file	genomic variant file, gzipped. `*.g.vcf.gz`

#3 compatible_versions

`compatible_versions.yml` file	File containing info on compatible CPU-based software versions. `compatible_versions.yml`

#4 versions_parabricks tuple

`${task.process}` string	The process the versions were collected from
`parabricks` string	The tool name
`pbrun version \| grep -m1 '^pbrun:' \| sed 's/^pbrun:[[:space:]]*//'` string	The command used to generate the version of the tool

Tool	Description	Homepage
parabricks	NVIDIA Clara Parabricks GPU-accelerated genomics tools	https://www.nvidia.com/en-us/clara/genomics/

Version	0.0.0-0c7146d
Commit ID	0c7146d85582628b5d1034504702fa808632b1af
Release Date	08 Apr 2026 19:01:09 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fparabricks%2Fhaplotypecaller/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/parabricks/haplotypecaller/blobs/sha256:4e25a6534c45a0d3df2459cae8ad07a9e19d63dbfa359776fa6d48ab806836e9
Size	3.6 KB
Checksum	sha256:4e25a6534c45a0d3df2459cae8ad07a9e19d63dbfa359776fa6d48ab806836e9
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:01:09 (UTC)		1	3.6 KB	-