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nf-core/longphase/phase @ 0.0.0-6c4ed3a

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

phase long-read genomics
Latest version: 0.0.0-6c4ed3a
Total downloads: 6
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_PHASE } from 'nf-core/longphase/phase'

License

MIT License

Process
Name LONGPHASE_PHASE
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(s)

 *.{bam,cram}
bai file

Index of sorted BAM/CRAM file(s)

 *.{bai,crai,csi}
snvs 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 4 channels
#1 sv_vcf tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}_SV.vcf.gz file

Compressed VCF file with phased SVs

 *_SV.vcf.gz
#2 mod_vcf tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}_mod.vcf.gz file

Compressed VCF file with phased modifications

 *.vcf.gz
#3 snv_vcf tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}.vcf.gz file

Compressed VCF file with phased SNVs and indels

 *.vcf.gz
#4 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 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:28:03 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Flongphase%2Fphase/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/longphase/phase/blobs/sha256:843dc77559c8bd79babf9ac02fa422e5f16e83f1fb9c0dde5148c55c18d607f8
Size 3.4 KB
Checksum sha256:843dc77559c8bd79babf9ac02fa422e5f16e83f1fb9c0dde5148c55c18d607f8