Nextflow Registry | nf-core/whatshap/haplotag@0.0.0-6c4ed3a

nf-core/whatshap/haplotag @ 0.0.0-6c4ed3a

Tag reads by haplotype

haplotypes tagging long-reads nanopore pacbio

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:52:58 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fwhatshap%2Fhaplotag/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/whatshap/haplotag/blobs/sha256:c7beab4d0840b5a19a9a9bb2f0f86ec7dc6fb36e03a73b0e01978e05e7a77d01
Size	3.6 KB
Checksum	sha256:c7beab4d0840b5a19a9a9bb2f0f86ec7dc6fb36e03a73b0e01978e05e7a77d01
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:52:58 (UTC)		4	3.6 KB