Nextflow Registry | nf-core/gatk4/splitncigarreads@0.0.0-6c4ed3a

nf-core/gatk4/splitncigarreads @ 0.0.0-6c4ed3a

Splits reads that contain Ns in their cigar string

gatk4 merge vcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:20:37 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fsplitncigarreads/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/splitncigarreads/blobs/sha256:cfac88778db109c38e55bb4a04e302290ac5c129563f4697ee0c88e40cc5d637
Size	2.9 KB
Checksum	sha256:cfac88778db109c38e55bb4a04e302290ac5c129563f4697ee0c88e40cc5d637
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:20:37 (UTC)		4	2.9 KB
0.0.0-0c7146d	08 Apr 2026 19:04:52 (UTC)		4	2.9 KB