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

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

add replace read-group picard gatk
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @sateeshperi @mjcipriano @hseabolt @cmatKhan @muffato
Maintainers: @sateeshperi @mjcipriano @hseabolt @cmatKhan @muffato

Summary

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

Get started

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

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

License

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 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:40:52 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Faddorreplacereadgroups/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/addorreplacereadgroups/blobs/sha256:4a4f2c177fec8107696fa6d0d7a5ad5ff44fc5f6e8b0836579963fc498a6c561
Size 3.4 KB
Checksum sha256:4a4f2c177fec8107696fa6d0d7a5ad5ff44fc5f6e8b0836579963fc498a6c561
Downloads 1
Version Date Status Downloads Size Diff
0.0.0-0c7146d