nf-core/cnvkit/target @ 0.0.0-0c7146d
Summary
Transform bait intervals into targets more suitable for CNVkit.
Get started
Add the following snippet to your workflow script to include this module.
include { CNVKIT_TARGET } from 'nf-core/cnvkit/target'
License
MIT License
Process
Name
|
CNVKIT_TARGET |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
baits
file
|
BED or interval file listing the targeted regions. *.{bed}
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
annotation
file
|
Use gene models from this file to assign names to the target regions. *.{txt,bed,gff3,pil}
|
Output
2 channels
#1
bed
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bed
file
|
File containing target regions *.{bed}
|
#2
versions_cnvkit
tuple
${task.process}
string
|
The name of the process |
|---|---|
cnvkit
string
|
The name of the tool |
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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:31:52 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcnvkit%2Ftarget/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/cnvkit/target/blobs/sha256:29c37beaa94d985017df2c1019ed073fbe98faf1591a053a3ae23b2bd08332ce |
| Size | 2.5 KB |
| Checksum | sha256:29c37beaa94d985017df2c1019ed073fbe98faf1591a053a3ae23b2bd08332ce |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:31:52 (UTC) | 1 | 2.5 KB | - |