Nextflow Registry | nf-core/gatk4/calculatecontamination@0.0.0-0c7146d

nf-core/gatk4/calculatecontamination @ 0.0.0-0c7146d

Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.

gatk4 calculatecontamination cross-samplecontamination getpileupsummaries filtermutectcalls

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @GCJMackenzie @maxulysse

Maintainers: @GCJMackenzie @maxulysse

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

Process

`Name`	`GATK4_CALCULATECONTAMINATION`

Input 1 channel

#1 tuple

`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`

Output 3 channels

#1 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`

#2 contamination tuple

`meta` file	File containing the contamination table. `*.contamination.table`
`*.contamination.table` file	File containing the contamination table. `*.contamination.table`

#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 18:41:08 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fcalculatecontamination/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/calculatecontamination/blobs/sha256:0d74fb0364b6c4b76cacfe3a9ab9b69fff8948a7b9c0c03f92cf180a6d7c74ad
Size	3.2 KB
Checksum	sha256:0d74fb0364b6c4b76cacfe3a9ab9b69fff8948a7b9c0c03f92cf180a6d7c74ad
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:41:08 (UTC)		1	3.2 KB	-