nf-core/varscan/somatic @ 0.0.0-0c7146d
Summary
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.
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. |
|---|---|
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. |
|---|---|
*.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. |
|---|---|
*.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 | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:21:26 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvarscan%2Fsomatic/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/varscan/somatic/blobs/sha256:cc9a68f97702791e8d3c66f73f453fe78350e32efcbb38aaea89a2d96f47ef21 |
| Size | 2.8 KB |
| Checksum | sha256:cc9a68f97702791e8d3c66f73f453fe78350e32efcbb38aaea89a2d96f47ef21 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:21:26 (UTC) | 1 | 2.8 KB | - |