Nextflow Registry | nf-core/hificnv@0.0.0-6c4ed3a

nf-core/hificnv @ 0.0.0-6c4ed3a

Copy number variant calling from PacBio HiFi reads

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @chaochaowong

Maintainers: @chaochaowong

Copy number variant calling from PacBio HiFi reads

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

include { HIFICNV } from 'nf-core/hificnv'

MIT License

Process

`Name`	`HIFICNV`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`bam` file	Sorted BAM or CRAM file from PacBio HiFi reads `*.{bam,cram}`
`bai` file	BAM index file (CSI, CRAI, or BAI format) `*.{bai,csi,crai}`
`maf` file	Minor allele frequency file (VCF format) `*.{vcf,vcf.gz}`

#2 tuple

`meta2` map	Groovy Map containing reference genome information e.g. `[ id:'GATK.GRCh38' ]`
`ref` file	Reference genome FASTA file `*.{fa,fasta,fa.gz,fasta.gz}`

#3 tuple

`meta3` map	Groovy Map containing exclude regions information e.g. `[ id:'excluded_regions' ]`
`exclude` file	BED file containing regions to exclude from CNV calling `*.{bed,bed.gz}`

#4 tuple

`meta4` map	Groovy Map containing expected copy number information e.g. `[ id:'male_expected_cn' ]`
`expected_cn` file	BED file containing expected copy number regions `*.{bed,bed.gz}`

Output 5 channels

#1 maf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.maf.bw` file	Minor allele frequency bigWig file `*.maf.bw`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.vcf.gz` file	Copy number variants in VCF format `*.{vcf.gz}`

#3 depth tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.depth.bw` file	Depth coverage bigWig file `*.depth.bw`

#4 copynum tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.copynum.bedgraph` file	Copy number bedGraph file `*.copynum.bedgraph`

#5 versions_hificnv tuple

`${task.process}` string	Name of the process
`hificnv` string	Name of the tool
`hificnv --version \| sed 's/.* //g'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
hificnv	Copy number variant caller designed for PacBio HiFi reads	https://github.com/PacificBiosciences/HiFiCNV

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:23:53 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fhificnv/0.0.0-6c4ed3a/download