Nextflow Registry | nf-core/gatk4spark/applybqsr@0.0.0-6c4ed3a

nf-core/gatk4spark/applybqsr @ 0.0.0-6c4ed3a

Apply base quality score recalibration (BQSR) to a bam file

bam base quality score recalibration bqsr cram gatk4spark

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @yocra3 @FriederikeHanssen @maxulysse

Maintainers: @yocra3 @FriederikeHanssen @maxulysse

Apply base quality score recalibration (BQSR) to a bam file

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

include { GATK4SPARK_APPLYBQSR } from 'nf-core/gatk4spark/applybqsr'

MIT License

Process

`Name`	`GATK4SPARK_APPLYBQSR`

Input 4 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}`
`bqsr_table` file	Recalibration table from gatk4_baserecalibrator
`intervals` file	Bed file with the genomic regions included in the library (optional)

`fasta` file	The reference fasta file `*.fasta`

`fai` file	Index of reference fasta file `*.fasta.fai`

`dict` file	GATK sequence dictionary `*.dict`

Output 4 channels

#1 bai tuple

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

#2 bam tuple

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

#3 cram tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.cram` file	Recalibrated CRAM file `${prefix}.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 15:20:46 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4spark%2Fapplybqsr/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4spark/applybqsr/blobs/sha256:81b9eea64f2dd7c828dbf9a3d2f94dd2892760706cf799ced197fec1c94ec7ce
Size	3.8 KB
Checksum	sha256:81b9eea64f2dd7c828dbf9a3d2f94dd2892760706cf799ced197fec1c94ec7ce
Downloads	3

Version	Date	Status	Downloads	Size