Nextflow Registry | nf-core/vcf2cytosure@0.0.0-0c7146d

nf-core/vcf2cytosure @ 0.0.0-0c7146d

Convert VCF with structural variations to CytoSure format

structural_variants array_cgh vcf cytosure

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @jemten

Convert VCF with structural variations to CytoSure format

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

include { VCF2CYTOSURE } from 'nf-core/vcf2cytosure'

MIT License

Process

`Name`	`VCF2CYTOSURE`

Input 5 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`coverage_bed` file	Bed file with coverage data `*.bed`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`cns` file	CN file from CNVkit, not compatible with coverage_bed file

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`snv_vcf` file	VCF file with SNVs to calculate probe coverage, not compatible with coverage_bed pattern: "*.{vcf,vcf.gz}"

`blacklist_bed` file	Bed file with regions to exclude `*.bed`

Output 2 channels

#1 cgh tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.cgh` file	SV:s in CytoSure format `*.cgh`

#2 versions_vcf2cytosure tuple

`${task.process}` string	The name of the process
`vcf2cytosure` string	The name of the tool
`vcf2cytosure --version 2>&1 \| sed -n 's/.*cytosure //p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
vcf2cytosure	Convert VCF with structural variations to CytoSure format	https://github.com/NBISweden/vcf2cytosure

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:21:50 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvcf2cytosure/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/vcf2cytosure/blobs/sha256:f0ba5caf0235fa8c63b1b585de5096360f8ded61c4a9756c4bbf37fc7e453b46
Size	2.6 KB
Checksum	sha256:f0ba5caf0235fa8c63b1b585de5096360f8ded61c4a9756c4bbf37fc7e453b46
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:21:50 (UTC)		1	2.6 KB	-