Nextflow Registry | nf-core/varscan/somatic@0.0.0-0c7146d

nf-core/varscan/somatic @ 0.0.0-0c7146d

VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs.

variant calling germline somatic vcf variants genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @vmelichar

Maintainers: @vmelichar

Summary

Get started

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

include { VARSCAN_SOMATIC } from 'nf-core/varscan/somatic'

License

MIT License

Process

`Name`	`VARSCAN_SOMATIC`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`normal_mpileup` file	mpileup file from normal sample `*.mpileup`
`tumour_mpileup` file	mpileup file from tumour sample `*.mpileup`

Output 3 channels

#1 vcf_snvs tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.snvs.vcf.gz` file	VCF file with SNVs `*.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:'sample1' ]`
`*.indels.vcf.gz` file	VCF file with indels `*.vcf.gz`

Tool	Description	Homepage
varscan	variant detection in massively parallel sequencing data	https://github.com/dkoboldt/varscan

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:45:34 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fvarscan%2Fsomatic/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/varscan/somatic/blobs/sha256:8ce32fb20545530e6b6e78099230c2bda73619add7afbcd965201e957f693d30
Size	2.8 KB
Checksum	sha256:8ce32fb20545530e6b6e78099230c2bda73619add7afbcd965201e957f693d30
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:51:54 (UTC)		2	2.8 KB
0.0.0-0c7146d	08 Apr 2026 19:45:34 (UTC)		4	2.8 KB