Nextflow Registry | nf-core/glimpse/phase@0.0.0-0c7146d

nf-core/glimpse/phase @ 0.0.0-0c7146d

main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods

phase imputation low-coverage glimpse

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @louislenezet

Maintainers: @louislenezet

main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods

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

include { GLIMPSE_PHASE } from 'nf-core/glimpse/phase'

MIT License

Process

`Name`	`GLIMPSE_PHASE`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	Input VCF/BCF file containing genotype likelihoods. `*.{vcf.gz,bcf.gz}`
`input_index` file	Index file of the input VCF/BCF file containing genotype likelihoods. `*.{vcf.gz.csi,bcf.gz.csi}`
`samples_file` file	File with sample names and ploidy information. One sample per line with a mandatory second column indicating ploidy (1 or 2). Sample names that are not present are assumed to have ploidy 2 (diploids). GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy. `*.{txt,tsv}`
`input_region` string	Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). `chrXX:leftBufferPosition-rightBufferPosition`
`output_region` string	Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). `chrXX:leftBufferPosition-rightBufferPosition`
`reference` file	Reference panel of haplotypes in VCF/BCF format. `*.{vcf.gz,bcf.gz}`
`reference_index` file	Index file of the Reference panel file. `*.{vcf.gz.csi,bcf.gz.csi}`
`map` file	File containing the genetic map. `*.gmap`

Output 2 channels

#1 phased_variants tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{vcf,bcf,vcf.gz,bcf.gz}` file	Output VCF/BCF file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score. `*.{vcf,bcf,vcf.gz,bcf.gz}`

#2 versions_glimpse tuple

`${task.process}` string	The name of the process
`glimpse` string	The name of the tool
`GLIMPSE_phase --help \| sed -n '/Version/s/.*: //p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
glimpse	GLIMPSE 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 18:44:44 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fglimpse%2Fphase/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/glimpse/phase/blobs/sha256:b48a356a3c42ccc519d86d39dd7cc0e87b612780b10fdf2fe091d33aeb5a2af7
Size	3.5 KB
Checksum	sha256:b48a356a3c42ccc519d86d39dd7cc0e87b612780b10fdf2fe091d33aeb5a2af7
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:44:44 (UTC)		1	3.5 KB	-