Nextflow Registry | nf-core/expansionhunter@0.0.0-6c4ed3a

nf-core/expansionhunter @ 0.0.0-6c4ed3a

Estimate repeat sizes using NGS data

STR repeat_expansions bam cram vcf json

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @jemten

Maintainers: @jemten

Estimate repeat sizes using NGS data

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

include { EXPANSIONHUNTER } from 'nf-core/expansionhunter'

MIT License

Process

`Name`	`EXPANSIONHUNTER`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	BAM/CRAM file `*.{bam,cram}`
`bai` file	Index of BAM/CRAM file `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fasta` file	Reference genome `*.{fna,fa,fasta}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fasta_fai` file	Reference genome index `*.fai`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'test' ]
`variant_catalog` file	JSON file with repeat expansion sites to genotype `*.json`

Output 5 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', gender:'female' ]
`*_realigned.bam` file	BAM/CRAM file `*.{bam,cram}`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', gender:'female' ]
`*.vcf.gz` file	VCF with repeat expansions `*.vcf.gz`

#3 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', gender:'female' ]
`*.json.gz` file	JSON with repeat expansions `*.json.gz`

#4 versions_bgzip tuple

`${task.process}` string	The process the versions were collected from
`bgzip` string	The tool name
`bgzip --version \| sed '1!d;s/.* //'` eval	The expression to obtain the version of the tool

#5 versions_expansionhunter tuple

`${task.process}` string	The process the versions were collected from
`expansionhunter` string	The tool name
`ExpansionHunter --version \| head -1 \| sed -n 's/^.*ExpansionHunter v//; s/]//p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
expansionhunter	A tool for estimating repeat sizes	https://github.com/Illumina/ExpansionHunter

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:15:09 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fexpansionhunter/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/expansionhunter/blobs/sha256:4fbda5bbf1dc12f46