nf-core/gatk4/calculatecontamination @ 0.0.0-0c7146d
Summary
Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4_CALCULATECONTAMINATION } from 'nf-core/gatk4/calculatecontamination'
License
MIT License
Name
|
GATK4_CALCULATECONTAMINATION |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
pileup
file
|
File containing the pileups summary table of a tumor sample to be used to calculate contamination. *.pileups.table
|
matched
file
|
File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input. *.pileups.table
|
segmentation
tuple
meta
file
|
File containing the contamination table. *.contamination.table
|
|---|---|
*.segmentation.table
file
|
output table containing segmentation of tumor minor allele fractions (optional) *.segmentation.table
|
contamination
tuple
meta
file
|
File containing the contamination table. *.contamination.table
|
|---|---|
*.contamination.table
file
|
File containing the contamination table. *.contamination.table
|
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 | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:02:40 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fcalculatecontamination/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/calculatecontamination/blobs/sha256:c3209f19bdbf0cd2cc797ad6253235b6dd4816af2d6ad002164dd9b0952afdd8 |
| Size | 3.2 KB |
| Checksum | sha256:c3209f19bdbf0cd2cc797ad6253235b6dd4816af2d6ad002164dd9b0952afdd8 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:18:27 (UTC) | 4 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:02:40 (UTC) | 3 | 3.2 KB |