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

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

Assigns all the reads in a file to a single new read-group

add replace read-group picard gatk

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @sateeshperi @mjcipriano @hseabolt @cmatKhan @muffato

Maintainers: @sateeshperi @mjcipriano @hseabolt @cmatKhan @muffato

Assigns all the reads in a file to a single new read-group

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

include { GATK4_ADDORREPLACEREADGROUPS } from 'nf-core/gatk4/addorreplacereadgroups'

MIT License

Process

`Name`	`GATK4_ADDORREPLACEREADGROUPS`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	Input BAM file `*.{bam}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Reference genome file `*.{fasta,fa,fasta.gz,fa.gz}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta_index` file	Reference genome index file `*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}`

Output 4 channels

#1 bai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bai` file	An optional BAM index file `*.{bai}`

#2 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bam` file	Output BAM file `*.{bam}`

#3 cram tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cram` file	Output CRAM file `*.{cram}`

#4 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 15:18:17 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Faddorreplacereadgroups/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/addorreplacereadgroups/blobs/sha256:07e603e876c636a8b59a8909832fc17e556b526414f9c614f7d5ef594e90bdee
Size	3.4 KB
Checksum	sha256:07e603e876c636a8b59a8909832fc17e556b526414f9c614f7d5ef594e90bdee
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15