Nextflow Registry | nf-core/shapeit5/phaserare@0.0.0-0c7146d

nf-core/shapeit5/phaserare @ 0.0.0-0c7146d

Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate). Require feature AVX2.

phasing rare variants haplotype shapeit

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @LouisLeNezet

Maintainers: @LouisLeNezet

Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate). Require feature AVX2.

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

include { SHAPEIT5_PHASERARE } from 'nf-core/shapeit5/phaserare'

MIT License

Process

`Name`	`SHAPEIT5_PHASERARE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	Genotypes to be phased in plain VCF/BCF format. `*.{vcf,bcf,vcf.gz,bcf.gz}`
`input_index` file	Index file of the input_plain VCF/BCF file containing genotype likelihoods. `*.{vcf.gz.csi,bcf.gz.csi}`
`pedigree` file	Pedigree information in the following format: offspring father mother. `*.{txt, tsv}`
`input_region` string	Region to be considered in --input-plain (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. `chrXX:leftBufferPosition-rightBufferPosition`
`scaffold` file	Scaffold of haplotypes in VCF/BCF format. `*.{vcf.gz,bcf.gz}`
`scaffold_index` file	Index file of the scaffold file. `*.{vcf.gz.csi,bcf.gz.csi}`
`scaffold_region` string	Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20). `chrXX:leftBufferPosition-rightBufferPosition`
`map` file	File containing the genetic map in Glimpse format. `*.gmap`

`output_suffix` string	Module output format `*.{vcf,bcf,vcf.gz,bcf.gz}`

Output 2 channels

#1 phased_variant tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{vcf,bcf,vcf.gz,bcf.gz}` file	Phased variants in VCF/BCF format. `*.{vcf,bcf,vcf.gz,bcf.gz}`

#2 versions_shapeit5 tuple

`${task.process}` string	The name of the process
`shapeit5` string	The name of the tool
`SHAPEIT5_phase_rare \| sed "5!d;s/^.Version : //; s/ .*$//"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
shapeit5	Fast and accurate method for estimation of haplotypes (phasing)	https://odelaneau.github.io/shapeit5/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:13:42 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fshapeit5%2Fphaserare/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/shapeit5/phaserare/blobs/sha256:21423a6004e869ef5fa999b02fd67bf0ba69ea5a5b4c81bc9ce424cfc8b170be
Size	3.6 KB
Checksum	sha256:21423a6004e869ef5fa999b02fd67bf0ba69ea5a5b4c81bc9ce424cfc8b170be
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:13:42 (UTC)		1	3.6 KB	-