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

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

Prepares bins for coverage collection.

bed gatk4 interval preprocessintervals

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ryanjameskennedy @ViktorHy @ramprasadn

Maintainers: @ryanjameskennedy @ViktorHy @ramprasadn

Prepares bins for coverage collection.

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

include { GATK4_PREPROCESSINTERVALS } from 'nf-core/gatk4/preprocessintervals'

MIT License

Process

`Name`	`GATK4_PREPROCESSINTERVALS`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fasta` file	The reference fasta file `*.fasta`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fai` file	Index of reference fasta file `*.fasta.fai`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'test' ]
`dict` file	GATK sequence dictionary `*.dict`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'test' ]
`intervals` file	Interval file (bed or interval_list) with the genomic regions to be included from the analysis (optional) `*.{bed,interval_list}`

#5 tuple

`meta5` map	Groovy Map containing reference information e.g. [ id:'test' ]
`exclude_intervals` file	Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional) `*.{bed,interval_list}`

Output 2 channels

#1 interval_list tuple

`meta` map	Groovy Map containing reference information e.g. [ id:'test' ]
`${prefix}.interval_list` file	Processed interval list file `*.interval_list`

#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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:42:53 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fpreprocessintervals/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/preprocessintervals/blobs/sha256:ee1478223bc3f154a30a795e6801bff9d65b3ef21fc1243e5d618a8142d9810f
Size	2.9 KB
Checksum	sha256:ee1478223bc3f154a30a795e6801bff9d65b3ef21fc1243e5d618a8142d9810f
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:42:53 (UTC)		1	2.9 KB	-