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

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

Apply a Convolutional Neural Net to filter annotated variants

cnnscorevariants gatk4 variants

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @FriederikeHanssen

Maintainers: @FriederikeHanssen

Apply a Convolutional Neural Net to filter annotated variants

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

include { GATK4_CNNSCOREVARIANTS } from 'nf-core/gatk4/cnnscorevariants'

MIT License

Process

`Name`	`GATK4_CNNSCOREVARIANTS`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcf` file	VCF file `*.vcf.gz`
`tbi` file	VCF index file `*.vcf.gz.tbi`
`aligned_input` file	BAM/CRAM file from alignment (optional) `*.{bam,cram}`
`intervals` file	Bed file with the genomic regions included in the library (optional)

`fasta` file	The reference fasta file `*.fasta`

`fai` file	Index of reference fasta file `*.fasta.fai`

`dict` file	GATK sequence dictionary `*.dict`

`architecture` file	Neural Net architecture configuration json file (optional) `*.json`

`weights` file	Keras model HD5 file with neural net weights. (optional) `*.hd5`

Output 3 channels

#1 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*cnn.vcf.gz.tbi` file	VCF index file `*.vcf.gz.tbi`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*cnn.vcf.gz` file	Annotated VCF file `*.vcf`

#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	4e8e48c04e24c2159a5589a36bae0f038809cd48
Release Date	08 Apr 2026 18:41:12 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fcnnscorevariants/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/cnnscorevariants/blobs/sha256:701914ceb1cc68ffe3653b6b087d186e8ddd31bd00e72743ac0240abdb5211a9
Size	3.3 KB
Checksum	sha256:701914ceb1cc68ffe3653b6b087d186e8ddd31bd00e72743ac0240abdb5211a9
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:41:12 (UTC)		1	3.3 KB	-