Nextflow Registry | nf-core/ichorcna/createpon@0.0.0-0c7146d

nf-core/ichorcna/createpon @ 0.0.0-0c7146d

ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals

ichorcna cnv cna cfDNA wgs panel_of_normals

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @sppearce

Maintainers: @sppearce

Summary

ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals

Get started

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

include { ICHORCNA_CREATEPON } from 'nf-core/ichorcna/createpon'

License

MIT License

Process

`Name`	`ICHORCNA_CREATEPON`

Input 6 channels

`wigs` file	Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals. `*.{wig}`

`gc_wig` file	hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window `*.{wig}`

`map_wig` file	hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window `*.{wig}`

`centromere` file	Text file giving centromere locations of each genome, to exclude these windows `*.{txt}`

`rep_time_wig` file	Replication/timing .wig file. `*.{wig}`

`exons` file	BED file for exon regions to annotate CNA regions. `*.{bed}`

Output 3 channels

#1 rds

`${prefix}*.rds` file	R data file (.rds) containing panel of normals data, medians of each bin. `*.rds`

#2 txt

`${prefix}*.txt` file	Text file containing panel of normals data, medians of each bin. `*.txt`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
ichorcna	Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.	https://github.com/broadinstitute/ichorCNA

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:48:31 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fichorcna%2Fcreatepon/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/ichorcna/createpon/blobs/sha256:9fe4dadea88687a3ee4e3c53fc5e062604704f1d25df871a46e257dc3ec457d0
Size	3.0 KB
Checksum	sha256:9fe4dadea88687a3ee4e3c53fc5e062604704f1d25df871a46e257dc3ec457d0
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:48:31 (UTC)		1	3.0 KB	-