Nextflow Registry | nf-core/glimpse/phase@0.0.0-3fc6d40

nf-core/glimpse/phase @ 0.0.0-3fc6d40

main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods

phase imputation low-coverage glimpse

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

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	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:14:04 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fglimpse%2Fphase/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/glimpse/phase/blobs/sha256:e3bcf11be96e8bee6e1683ffc7ac5333e79294c775bf294e2dd78bd54166dc51
Size	3.5 KB
Checksum	sha256:e3bcf11be96e8bee6e1683ffc7ac5333e79294c775bf294e2dd78bd54166dc51
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:21:33 (UTC)	3	3.5 KB
0.0.0-3fc6d40	22 Apr 2026 15:14:04 (UTC)	3	3.5 KB
0.0.0-0c7146d	08 Apr 2026 19:06:19 (UTC)	4	3.5 KB