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

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

Splits reads that contain Ns in their cigar string

gatk4 merge vcf

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @kevinmenden

Maintainers: @kevinmenden

Splits reads that contain Ns in their cigar string

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

include { GATK4_SPLITNCIGARREADS } from 'nf-core/gatk4/splitncigarreads'

MIT License

Process

`Name`	`GATK4_SPLITNCIGARREADS`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`bam` list	BAM/SAM/CRAM file containing reads `*.{bam,sam,cram}`
`bai` list	BAI/SAI/CRAI index file (optional) `*.{bai,sai,crai}`
`intervals` file	Bed file with the genomic regions included in the library (optional)

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'reference' ]
`fasta` file	The reference fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'reference' ]
`fai` file	Index of reference fasta file `*.fasta.fai`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'reference' ]
`dict` file	GATK sequence dictionary `*.dict`

Output 2 channels

#1 bam tuple

`meta` file	Output file with split reads (BAM/SAM/CRAM) `*.{bam,sam,cram}`
`*.bam` file	Output file with split reads (BAM/SAM/CRAM) `*.{bam,sam,cram}`

#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 18:43:15 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fsplitncigarreads/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/splitncigarreads/blobs/sha256:469c878c7307bd75e72a3024ffed1c91402824412c8fed29dffc0117519f37b7
Size	2.9 KB
Checksum	sha256:469c878c7307bd75e72a3024ffed1c91402824412c8fed29dffc0117519f37b7
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:43:15 (UTC)		1	2.9 KB	-