Nextflow Registry | nf-core/strelka/germline@0.0.0-0c7146d

nf-core/strelka/germline @ 0.0.0-0c7146d

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation

variantcalling germline wgs vcf variants

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @arontommi

Maintainers: @arontommi

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation

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

include { STRELKA_GERMLINE } from 'nf-core/strelka/germline'

MIT License

Process

`Name`	`STRELKA_GERMLINE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`input` file	BAM/CRAM file `*.{bam,cram}`
`input_index` file	BAM/CRAI index file `*.{bai,crai}`
`target_bed` file	BED file containing target regions for variant calling `*.{bed}`
`target_bed_index` file	Index for BED file containing target regions for variant calling `*.{bed.tbi}`

`fasta` file	Genome reference FASTA file `*.{fa,fasta}`

`fai` file	Genome reference FASTA index file `*.{fa.fai,fasta.fai}`

Output 5 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`*variants.vcf.gz` file	gzipped germline variant file `*.{vcf.gz}`

#2 vcf_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`*variants.vcf.gz.tbi` file	index file for the vcf file `*.vcf.gz.tbi`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

#4 genome_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`*genome.vcf.gz` file	variant records and compressed non-variant blocks `*_genome.vcf.gz`

#5 genome_vcf_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`*genome.vcf.gz.tbi` file	index file for the genome_vcf file `*_genome.vcf.gz.tbi`

Tool	Description	Homepage
strelka	Strelka calls somatic and germline small variants from mapped sequencing reads	https://github.com/Illumina/strelka

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:17:00 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fstrelka%2Fgermline/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/strelka/germline/blobs/sha256:42bb18ba341085a76a4bbab8a451755a9bc856ce1b481923acf811f2ce79ef14
Size	3.2 KB
Checksum	sha256:42bb18ba341085a76a4bbab8a451755a9bc856ce1b481923acf811f2ce79ef14
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:17:00 (UTC)		1	3.2 KB	-