nf-core/gatk4/createsomaticpanelofnormals @ 0.0.0-0c7146d
Summary
Create a panel of normals constraining germline and artifactual sites for use with mutect2.
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4_CREATESOMATICPANELOFNORMALS } from 'nf-core/gatk4/createsomaticpanelofnormals'
License
MIT License
Process
Name
|
GATK4_CREATESOMATICPANELOFNORMALS |
|---|
Input
4 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test'] |
|---|---|
genomicsdb
file
|
GenomicsDB database |
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. [ id:'test'] |
|---|---|
fasta
file
|
The reference fasta file *.fasta
|
#3
tuple
meta3
map
|
Groovy Map containing reference information e.g. [ id:'test'] |
|---|---|
fai
file
|
Index of reference fasta file *.fasta.fai
|
#4
tuple
meta4
map
|
Groovy Map containing reference information e.g. [ id:'test'] |
|---|---|
dict
file
|
GATK sequence dictionary *.dict
|
Output
3 channels
#1
tbi
tuple
meta
map
|
A Groovy map containing sample information |
|---|---|
*.tbi
file
|
Tabix index of vcf file *vcf.gz.tbi
|
#2
vcf
tuple
meta
map
|
A Groovy map containing sample information |
|---|---|
*.vcf.gz
file
|
panel of normal as compressed vcf file *.vcf.gz
|
#3
versions_gatk4
tuple
${task.process}
string
|
The name of the process |
|---|---|
gatk4
string
|
The name of the tool |
gatk --version | sed -n '/GATK.*v/s/.*v//p'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| gatk4 | Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. | https://gatk.broadinstitute.org/hc/en-us |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:41:32 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fcreatesomaticpanelofnormals/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/createsomaticpanelofnormals/blobs/sha256:5f9e8ae22e5e8612d56c7fdf31824b684623b2510309ffa5922b9eb72bedfa48 |
| Size | 2.9 KB |
| Checksum | sha256:5f9e8ae22e5e8612d56c7fdf31824b684623b2510309ffa5922b9eb72bedfa48 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:41:32 (UTC) | 1 | 2.9 KB | - |