nf-core/cnvkit/access @ 0.0.0-3fc6d40
Summary
Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file.
Get started
Add the following snippet to your workflow script to include this module.
include { CNVKIT_ACCESS } from 'nf-core/cnvkit/access'
License
MIT License
Process
Name
|
CNVKIT_ACCESS |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fasta
file
|
Genome FASTA. *.fasta
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
exclude_bed
file
|
Additional regions to exclude, in BED format. Can be used multiple times. |
Output
2 channels
#1
bed
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bed
file
|
File containing accessible regions. *.{bed}
|
#2
versions_cnvkit
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
cnvkit
string
|
The tool name |
cnvkit.py version | sed -e "s/cnvkit v//g"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| cnvkit | CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. | https://cnvkit.readthedocs.io/en/stable/index.html |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:07:12 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fcnvkit%2Faccess/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/cnvkit/access/blobs/sha256:3d614d1eabc0530a1bf976c35264fc879f2b8414dbb45289138a87e2a4b888ec |
| Size | 2.7 KB |
| Checksum | sha256:3d614d1eabc0530a1bf976c35264fc879f2b8414dbb45289138a87e2a4b888ec |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:10:36 (UTC) | 3 | 2.7 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:07:12 (UTC) | 3 | 2.7 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:52:59 (UTC) | 3 | 2.7 KB |