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nf-core/strelka/somatic @ 0.0.0-6c4ed3a

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs

variant calling germline wgs vcf variants
Latest version: 0.0.0-6c4ed3a
Total downloads: 3
Source: nf-core/modules
Authors: @drpatelh
Maintainers: @drpatelh

Summary

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs

Get started

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

include { STRELKA_SOMATIC } from 'nf-core/strelka/somatic'

License

MIT License

Process
Name STRELKA_SOMATIC
Input 3 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
input_normal file

BAM/CRAM/SAM file

 *.{bam,cram,sam}
input_index_normal file

BAM/CRAM/SAM index file

 *.{bai,crai,sai}
input_tumor file

BAM/CRAM/SAM file

 *.{bam,cram,sam}
input_index_tumor file

BAM/CRAM/SAM index file

 *.{bai,crai,sai}
manta_candidate_small_indels file

VCF.gz file

 *.{vcf.gz}
manta_candidate_small_indels_tbi file

VCF.gz index file

 *.tbi
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_snvs tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.somatic_snvs.vcf.gz file

Gzipped VCF file containing variants

 *.{vcf.gz}
#2 versions
versions.yml file

File containing software versions

 versions.yml
#3 vcf_indels tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.somatic_indels.vcf.gz file

Gzipped VCF file containing variants

 *.{vcf.gz}
#4 vcf_snvs_tbi tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.somatic_snvs.vcf.gz.tbi file

Index for gzipped VCF file containing variants

 *.{vcf.gz.tbi}
#5 vcf_indels_tbi tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.somatic_indels.vcf.gz.tbi file

Index for gzipped VCF file containing variants

 *.{vcf.gz.tbi}
Tool Description Homepage
strelka Strelka calls somatic and germline small variants from mapped sequencing reads https://github.com/Illumina/strelka
Version 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:47:42 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fstrelka%2Fsomatic/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/strelka/somatic/blobs/sha256:36b73e555db862ed5b6e65013e8a2b2b93d6c84a558f15f8e0783df767e453fc