Nextflow Registry | nf-core/gatk4/analyzecovariates@0.0.0-0c7146d

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

Evaluate and compare base quality score recalibration (BQSR) tables

bqsr gatk4 genomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @thomasisensee

Maintainers: @thomasisensee

Evaluate and compare base quality score recalibration (BQSR) tables

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

include { GATK4_ANALYZECOVARIATES } from 'nf-core/gatk4/analyzecovariates'

MIT License

Process

`Name`	`GATK4_ANALYZECOVARIATES`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`before_table` file	Base quality score recalibration (BQSR) table before recalibration `*.table`
`after_table` file	Base quality score recalibration (BQSR) table after recalibration `*.table`
`additional_table` file	An additional base quality score recalibration (BQSR) table to be included in the comparison (optional) `*.table`

Output 3 channels

#1 data tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.csv` file	CSV file containing the data generated by AnalyzeCovariates `*.csv`

#2 plots tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.pdf` file	PDF file containing the plots generated by AnalyzeCovariates `*.pdf`

#3 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 18:40:54 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fanalyzecovariates/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/analyzecovariates/blobs/sha256:42a5c6fc12ea26f3ecf3ea303865ba93d7eaa9ca14eb13801e184883007a765f
Size	2.9 KB
Checksum	sha256:42a5c6fc12ea26f3ecf3ea303865ba93d7eaa9ca14eb13801e184883007a765f
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:40:54 (UTC)		1	2.9 KB	-