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

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

NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2.

variant vcf mutect2 mutect somatic

Latest version: 0.0.0-0c7146d

Total downloads: 3

Source: nf-core/modules

Authors: @bsiranosian

Maintainers: @famosab

NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2.

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

include { PARABRICKS_MUTECTCALLER } from 'nf-core/parabricks/mutectcaller'

MIT License

Process

`Name`	`PARABRICKS_MUTECTCALLER`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information - tumor_id and normal_id must match read groups for the respective samples. [ id:'test', tumor_id:'tumor', normal_id:'normal' ]
`tumor_bam` file	bam file for tumor sample. `*.bam`
`tumor_bam_index` file	(Optional) bai index corresponding to tumor bam file. Only required if intervals are provided. `*.bam.bai`
`normal_bam` file	(Optional) bam file for normal sample in tumor-vs-normal calling. `*.bam`
`normal_bam_index` file	(Optional) bai index corresponding to normal bam file. Only required if intervals are provided. `*.bam.bai`
`intervals` file	(Optional) file or files containing genomic intervals for use in base quality score recalibration. `*.{bed,interval_list,picard,list,intervals}`

#2 tuple

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

`panel_of_normals` file	(Optional) panel of normals file. `*.vcf.gz`

`panel_of_normals_index` file	(Optional) tbi index corresponding to panel of normals file. `*.tbi`

Output 4 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.vcf.gz` file	Compressed variants file. Will include an annotated vcf file if panel of normals is used. `*.vcf.gz`

#2 stats tuple

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

#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 19:24:11 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fparabricks%2Fmutectcaller/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/parabricks/mutectcaller/blobs/sha256:b9656dbae27367c235a1560a44c01af9a5df6532fb2c22a550a17c9de76c654d
Size	4.5 KB
Checksum	sha256:b9656dbae27367c235a1560a44c01af9a5df6532fb2c22a550a17c9de76c654d