Nextflow Registry | nf-core/glimpse2/chunk@0.0.0-0c7146d

nf-core/glimpse2/chunk @ 0.0.0-0c7146d

Defines chunks where to run imputation

chunk low-coverage imputation glimpse

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @louislenezet

Maintainers: @louislenezet

Defines chunks where to run imputation

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

include { GLIMPSE2_CHUNK } from 'nf-core/glimpse2/chunk'

MIT License

Process

`Name`	`GLIMPSE2_CHUNK`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	Target dataset in VCF/BCF format defined at all variable positions. The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). `*.{vcf,bcf,vcf.gz,bcf.gz}`
`input_index` file	Index file of the input VCF/BCF file containing genotype likelihoods. `*.{vcf.gz.csi,bcf.gz.csi}`
`region` string	Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.
`map` file	File containing the genetic map. `*.gmap`

`model` string	Algorithm model to use: "recursive": Recursive algorithm "sequential": Sequential algorithm (Recommended) "uniform-number-variants": Experimental. Uniform the number of variants in the sequential algorithm `{recursive,sequential,uniform-number-variants}`

Output 2 channels

#1 chunk_chr tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.txt` file	Tab delimited output txt file containing buffer and imputation regions. `*.{txt}`

#2 versions_glimpse2 tuple

`${task.process}` string	The name of the process
`glimpse2` string	The name of the tool
`GLIMPSE2_chunk --help \| grep -oE 'v[0-9.]+' \| cut -c2-` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
glimpse2	GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.	https://odelaneau.github.io/GLIMPSE

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:44:48 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fglimpse2%2Fchunk/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/glimpse2/chunk/blobs/sha256:5f04475f2cba4eeec90d2e405e0774ddeb6c036246e0e137a28d78666cd46376
Size	3.1 KB
Checksum	sha256:5f04475f2cba4eeec90d2e405e0774ddeb6c036246e0e137a28d78666cd46376
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:44:48 (UTC)		1	3.1 KB	-