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

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

Phase variants in a VCF file using long-read sequencing data

phasing haplotypes vcf long-reads nanopore pacbio

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @haidyi

Maintainers: @haidyi

Phase variants in a VCF file using long-read sequencing data

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

include { WHATSHAP_PHASE } from 'nf-core/whatshap/phase'

MIT License

Process

`Name`	`WHATSHAP_PHASE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcf` file	VCF file with unphased variants (can be gzipped) `*.{vcf,vcf.gz}`
`tbi` file	VCF index file (optional but recommended) `*.{tbi,csi}`
`bam` file	BAM file with aligned reads `*.bam`
`bai` file	BAM index file (optional but recommended) `*.bai`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Reference genome in FASTA format `*.{fa,fasta}`
`fai` file	Reference genome index `*.fai`

Output 3 channels

#1 tbi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.vcf.gz.tbi` file	Phased VCF index file `*.vcf.gz.tbi`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.vcf.gz` file	Bgzipped phased VCF file `*.vcf.gz`

#3 versions_whatshap tuple

`${task.process}` string	The name of the process
`whatshap` string	The name of the tool
`whatshap --version` string	The expression to obtain the version of the tool

Tool	Description	Homepage
whatshap	WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.	https://whatshap.readthedocs.io/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:23:29 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fwhatshap%2Fphase/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/whatshap/phase/blobs/sha256:80c4f533ce029241481a2df2d0e0bd3fd1faefc9a7debfd0aab8645d2cf639cf
Size	3.0 KB
Checksum	sha256:80c4f533ce029241481a2df2d0e0bd3fd1faefc9a7debfd0aab8645d2cf639cf
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:23:29 (UTC)		1	3.0 KB	-