Nextflow Registry | nf-core/shapeit5/phasecommon@0.0.0-6c4ed3a

nf-core/shapeit5/phasecommon @ 0.0.0-6c4ed3a

Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data.

phasing haplotype shapeit

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @LouisLeNezet

Maintainers: @LouisLeNezet

Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data.

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

include { SHAPEIT5_PHASECOMMON } from 'nf-core/shapeit5/phasecommon'

MIT License

Process

`Name`	`SHAPEIT5_PHASECOMMON`

Input 1 channel

#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}`
`pedigree` file	Pedigree information in the following format: offspring father mother. `*.{txt, tsv}`
`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. `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}`
`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}`
`map` file	File containing the genetic map in Glimpse format. `*.gmap`

Output 2 channels

#1 phased_variant tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{bcf,graph,bh}` file	Phased variant dataset in BCF, GRAPH or XCF binary format. `*.{bcf,graph,bh}`

#2 versions_shapeit5 tuple

`${task.process}` string	The name of the process
`shapeit5` string	The name of the tool
`SHAPEIT5_phase_common \| sed "5!d;s/^.Version : //; s/ .*$//"` 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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:45:06 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fshapeit5%2Fphasecommon/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/shapeit5/phasecommon/blobs/sha256:aa4ea8db1428066a318293dc201caf29b96105f4bd901677b9ec631833744f50
Size	3.4 KB
Checksum	sha256:aa4ea8db1428066a318293dc201caf29b96105f4bd901677b9ec631833744f50
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:45:06 (UTC)	3	3.4 KB
0.0.0-3fc6d40	22 Apr 2026 15:30:58 (UTC)	3	3.5 KB
0.0.0-0c7146d	08 Apr 2026 19:37:32 (UTC)	3	3.4 KB