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

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

Denoises read counts to produce denoised copy ratios

copyratios denoisereadcounts gatk4

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ramprasadn

Maintainers: @ramprasadn

Denoises read counts to produce denoised copy ratios

Add the following snippet to your workflow script to include this module.

include { GATK4_DENOISEREADCOUNTS } from 'nf-core/gatk4/denoisereadcounts'

MIT License

Process

`Name`	`GATK4_DENOISEREADCOUNTS`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`counts` file	Read counts in hdf5 or tsv format. `*.{hdf5,tsv}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`pon` file	Panel of normals file hdf5 or tsv format. `*.{hdf5}`

Output 3 channels

#1 denoised tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*_denoisedCR.tsv` file	Denoised copy ratios file `*.{tsv}`

#2 standardized tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*_standardizedCR.tsv` file	Standardized copy ratios file. `*.{tsv}`

#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 18:41:34 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fdenoisereadcounts/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/denoisereadcounts/blobs/sha256:cf3b7d01d1ba0189f3818df61754d2c14ef1a1a550b873c71c91528d52ce0f12
Size	3.3 KB
Checksum	sha256:cf3b7d01d1ba0189f3818df61754d2c14ef1a1a550b873c71c91528d52ce0f12
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:41:34 (UTC)		1	3.3 KB	-