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

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

LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.

haplotag long-read genomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @fellen31

Maintainers: @fellen31

Summary

LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.

Get started

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

include { LONGPHASE_HAPLOTAG } from 'nf-core/longphase/haplotag'

License

MIT License

Process

`Name`	`LONGPHASE_HAPLOTAG`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`bam` file	Sorted BAM/CRAM file `*.{bam,cram}`
`bai` file	Index of sorted BAM/CRAM file `*.{bai,crai,csi}`
`snps` file	VCF file with SNPs (and INDELs) `*.{vcf,vcf.gz}`
`svs` file	VCF file with SVs `*.{vcf,vcf.gz}`
`mods` file	modcall-generated VCF with modifications `*.{vcf,vcf.gz}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. `[ id:'hg38' ]`
`fasta` file	Reference fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. `[ id:'hg38' ]`
`fai` file	Reference fai index `*.fai`

Output 3 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.{bam,cram}` file	BAM file with haplotagged reads `*.bam`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.log` file	Log file `*.log`

#3 versions_longphase tuple

`${task.process}` string	The name of the process
`longphase` string	The name of the tool
`longphase --version \| head -n 1 \| sed 's/Version: //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
longphase	LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.	https://github.com/twolinin/longphase

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:52:34 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Flongphase%2Fhaplotag/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/longphase/haplotag/blobs/sha256:c28079ee2de28b33a0080d5b982fb9a10dbdca9de4397768d7a894294eb9161f
Size	3.5 KB
Checksum	sha256:c28079ee2de28b33a0080d5b982fb9a10dbdca9de4397768d7a894294eb9161f
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:52:34 (UTC)		1	3.5 KB	-