Nextflow Registry | nf-core/strelka/germline@0.0.0-3fc6d40

nf-core/strelka/germline @ 0.0.0-3fc6d40

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

variantcalling germline wgs vcf variants

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

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	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:32:50 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fstrelka%2Fgermline/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/strelka/germline/blobs/sha256:c324db7e7ba4264a15d4f5f5a53bfdb97534637ff37f7db691b9dcaaf573e517
Size	3.3 KB
Checksum	sha256:c324db7e7ba4264a15d4f5f5a53bfdb97534637ff37f7db691b9dcaaf573e517
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:47:41 (UTC)		3	3.2 KB
0.0.0-3fc6d40	22 Apr 2026 15:32:50 (UTC)