Nextflow Registry | nf-core/gatk/indelrealigner@0.0.0-6c4ed3a

nf-core/gatk/indelrealigner @ 0.0.0-6c4ed3a

Performs local realignment around indels to correct for mapping errors

bam vcf variant calling indel realignment

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @jfy133

Maintainers: @jfy133

Performs local realignment around indels to correct for mapping errors

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

include { GATK_INDELREALIGNER } from 'nf-core/gatk/indelrealigner'

MIT License

Process

`Name`	`GATK_INDELREALIGNER`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	Sorted and indexed BAM file `*.bam`
`bai` file	BAM index file `*.bai`
`intervals` file	Intervals file created by gatk3 RealignerTargetCreator `*.{intervals,list}`

#2 tuple

`meta2` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`fasta` file	Reference file used to generate BAM file `.{fasta,fa,fna}`

#3 tuple

`meta3` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`fai` file	Index of reference file used to generate BAM file `.fai`

#4 tuple

`meta4` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`dict` file	GATK dict file for reference `.dict`

#5 tuple

`meta5` map	Groovy Map containing file meta-information for known_vcf. e.g. [ id:'test', single_end:false ]
`known_vcf` file	Optional input VCF file(s) with known indels `.vcf`

Output 2 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bam` file	Sorted and indexed BAM file with local realignment around variants `*.bam`
`*.bai` file	Sorted and indexed BAM file with local realignment around variants `*.bam`

#2 versions_gatk tuple

`${task.process}` string	The name of the process
`gatk` string	The name of the tool
`gatk3 --version` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gatk	The full Genome Analysis Toolkit (GATK) framework, license restricted.	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:18:13 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk%2Findelrealigner/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk/indelrealigner/blobs/sha256:fa77a8fb249925b84a1ccbebdda1ade5b63cac29176f3a3da41757168482ab46
Size	3.2 KB
Checksum	sha256:fa77a8fb249925b84a1ccbebdda1ade5b63cac29176f3a3da41757168482ab46
Downloads	3

Version	Date	Status	Downloads	Size