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

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

Generate recalibration table for Base Quality Score Recalibration (BQSR)

base quality score recalibration table bqsr gatk4 sort

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @yocra3 @FriederikeHanssen @maxulysse

Maintainers: @yocra3 @FriederikeHanssen @maxulysse

Generate recalibration table for Base Quality Score Recalibration (BQSR)

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

include { GATK4_BASERECALIBRATOR } from 'nf-core/gatk4/baserecalibrator'

MIT License

Process

`Name`	`GATK4_BASERECALIBRATOR`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM file from alignment `*.{bam,cram}`
`input_index` file	BAI/CRAI file from alignment `*.{bai,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:'genome']
`fasta` file	The reference fasta file `*.fasta`

#3 tuple

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

#4 tuple

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

#5 tuple

`meta5` map	Groovy Map containing reference information e.g. [ id:'genome']
`known_sites` file	VCF files with known sites for indels / snps `*.vcf.gz`

#6 tuple

`meta6` map	Groovy Map containing reference information e.g. [ id:'genome']
`known_sites_tbi` file	Tabix index of the known_sites `*.vcf.gz.tbi`

Output 2 channels

#1 table tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.table` file	Recalibration table from BaseRecalibrator `*.{table}`

#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 15:18:24 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fbaserecalibrator/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/baserecalibrator/blobs/sha256:8e8f1a677fdd0a391d050a394d6c12127c486d13f514e32ae3fb663a132e4dc9