Nextflow Registry | nf-core/gatk4spark/applybqsr@0.0.0-0c7146d

nf-core/gatk4spark/applybqsr @ 0.0.0-0c7146d

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

bam base quality score recalibration bqsr cram gatk4spark

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:43:28 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4spark%2Fapplybqsr/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4spark/applybqsr/blobs/sha256:caaa7d91e4f2ca1456aa5cbe7ded247bf83077a3356c0f3070e381254be60289
Size	3.8 KB
Checksum	sha256:caaa7d91e4f2ca1456aa5cbe7ded247bf83077a3356c0f3070e381254be60289
Downloads	1

Version	Date	Status	Downloads	Size