nf-core/gatk4/learnreadorientationmodel @ 0.0.0-0c7146d
Summary
Uses f1r2 counts collected during mutect2 to Learn the prior probability of read orientation artifacts
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4_LEARNREADORIENTATIONMODEL } from 'nf-core/gatk4/learnreadorientationmodel'
License
MIT License
Process
Name
|
GATK4_LEARNREADORIENTATIONMODEL |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
f1r2
list
|
list of f1r2 files to be used as input. *.f1r2.tar.gz
|
Output
2 channels
#1
artifactprior
tuple
meta
file
|
file containing artifact-priors to be used by filtermutectcalls *.tar.gz
|
|---|---|
*.tar.gz
file
|
file containing artifact-priors to be used by filtermutectcalls *.tar.gz
|
#2
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 18:42:06 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Flearnreadorientationmodel/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/learnreadorientationmodel/blobs/sha256:824c87eea2fe398c860faf791776813cb609c939c9d43df683fbd5eeffda1e23 |
| Size | 3.5 KB |
| Checksum | sha256:824c87eea2fe398c860faf791776813cb609c939c9d43df683fbd5eeffda1e23 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:42:06 (UTC) | 1 | 3.5 KB | - |