Nextflow Registry | nf-core/gens/preparecovandbaf@0.0.0-0c7146d

nf-core/gens/preparecovandbaf @ 0.0.0-0c7146d

Tools for preparing inputs for visualization in Gens

gens preparecovandbaf preprocessing genomics CNV

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @jakob37

Maintainers: @jakob37

Tools for preparing inputs for visualization in Gens

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

include { PREPARECOVANDBAF } from 'nf-core/gens/preparecovandbaf'

MIT License

Process

`Name`	`PREPARECOVANDBAF`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`read_counts` file	Binned coverage calculations from GATK `*.{tsv}`
`gvcf` file	GVCF. It is used to calculate B-allele frequencies at the sites specified in baf_positions. It can be generated using any SNV-caller. `*.vcf.gz`
`gvcf_tbi` file	GVCF tabix index `*.vcf.gz.tbi`

`baf_positions` file	Sites to sample for BAF calculations `*.{tsv,tsv.gz}`

Output 5 channels

#1 baf_gz tuple

`meta` map	Groovy Map containing sample information
`*.baf.bed.gz` file	BAF bed (bgzipped)

#2 cov_gz tuple

`meta` map	Groovy Map containing sample information
`*.cov.bed.gz` file	Coverage bed (bgzipped)

#3 baf_tbi tuple

`meta` map	Groovy Map containing sample information
`*.baf.bed.gz.tbi` file	Tabix index for BAF bed

#4 cov_tbi tuple

`meta` map	Groovy Map containing sample information
`*.cov.bed.gz.tbi` file	Tabix index for coverage bed

#5 versions_preparecovandbaf tuple

`${task.process}` string	The process the versions were collected from
`preparecovandbaf` string	The tool name
`generate_cov_and_baf --version` string	The command used to generate the version of the tool

Tool	Description	Homepage
gens	Scripts for preparing input data to Gens	https://github.com/SMD-Bioinformatics-Lund/Prepare-Gens-input-data

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:44:16 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgens%2Fpreparecovandbaf/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gens/preparecovandbaf/blobs/sha256:f92e6c4227076a5dd7d485941bd84e806c7566bb83e4d89a8d2b5e2326488abc
Size	3.0 KB
Checksum	sha256:f92e6c4227076a5dd7d485941bd84e806c7566bb83e4d89a8d2b5e2326488abc
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:44:16 (UTC)		1	3.0 KB	-