Nextflow Registry | nf-core/cnaqc@0.0.0-3fc6d40

nf-core/cnaqc @ 0.0.0-3fc6d40

Quality control of copy number data from bulk WGS assays

WGS copy number quality control

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @vvvirgy

Maintainers: @vvvirgy

Quality control of copy number data from bulk WGS assays

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

include { CNAQC } from 'nf-core/cnaqc'

MIT License

Process

`Name`	`CNAQC`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`snv_rds` file	R object with mutation data `*.rds`
`cna_rds` file	R object with copy number data `*.rds`
`tumour_sample` string	string containing sample name

Output 6 channels

#1 qc_rds tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`
`*_qc.rds` file	R object containing quality control results for the sample `*{_qc.rds}`

#2 versions

`versions.yml` file	YAML file containing versions of tools used in the module

#3 plot_pdf_qc tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`
`*_qc.pdf` file	plots of the quality control results for the sample `*{_qc.pdf}`

#4 qc_plot_rds tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`
`*_qc_plot.rds` file	R object containing plots of the quality control results for the sample `*{_qc_plot.rds}`

#5 data_plot_rds tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`
`*_data_plot.rds` file	R object containing plots of the CNA statistics for the sample `*{_data_plot.rds}`
`*_qc_plot.rds` file	R object containing plots of the quality control results for the sample `*{_qc_plot.rds}`

#6 plot_pdf_data tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name' ]`
`*_data.pdf` file	plots of the CNA statistics for the sample `*{_data.pdf}`

Tool	Description	Homepage
cnaqc	Copy number quality control	https://caravagnalab.github.io/CNAqc/

Version	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:07:10 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fcnaqc/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/cnaqc/blobs/sha256:adc2d3562556778acd40a48c807f4680f72aab6848c34e832e2d7c197ce8b3c7
Size	4.8 KB
Checksum	sha256:adc2d3562556778acd40a48c807f4680f72aab6848c34e832e2d7c197ce8b3c7
Downloads	2

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:10:35 (UTC)		3	4.7 KB
0.0.0-3fc6d40	22 Apr 2026 15:07:10 (UTC)		2