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

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

Tag reads by haplotype

haplotypes tagging long-reads nanopore pacbio

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @sofiademmou

Maintainers: @sofiademmou

Tag reads by haplotype

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

include { WHATSHAP_HAPLOTAG } from 'nf-core/whatshap/haplotag'

MIT License

Process

`Name`	`WHATSHAP_HAPLOTAG`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`vcf` file	VCF file with phased variants (must be gzip-compressed and indexed) `*.{vcf.gz}`
`tbi` file	VCF index file `*.{tbi,csi}`
`bam` file	BAM/CRAM file with alignments to be tagged by haplotype `*.{bam,cram}`
`bai` file	BAM index file `*.bai`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`fasta` file	Reference file. Must be accompanied by .fai index `*.{fasta,fa}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`fai` file	Index for reference file. `*.fai`

`include_tsv_output` boolean	Whether to include TSV output file

Output 3 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.bam` file	BAM/CRAM/SAM file with tagged reads `*.{bam,cram,sam}`

#2 tsv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.{tsv,tsv.gz}` file	Write assignments of read names to haplotypes (tab separated) to given output file. If filename ends in .gz, then output is gzipped. `*.{tsv,tsv.gz}`

#3 versions_whatshap tuple

`${task.process}` string	The name of the process
`whatshap` string	The name of the tool
`whatshap --version` eval	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 19:23:27 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fwhatshap%2Fhaplotag/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/whatshap/haplotag/blobs/sha256:aa80c5e7a8d175f214abb058a363dc81615835c47f080c340ec532f5094e2953
Size	3.6 KB
Checksum	sha256:aa80c5e7a8d175f214abb058a363dc81615835c47f080c340ec532f5094e2953
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:23:27 (UTC)		1	3.6 KB