mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
48 lines
1.4 KiB
YAML
48 lines
1.4 KiB
YAML
|
name: cnvkit_reference
|
||
|
|
description:
|
||
|
|
keywords:
|
||
|
|
- cnvkit
|
||
|
|
- reference
|
||
|
|
tools:
|
||
|
|
- cnvkit:
|
||
|
|
description: |
|
||
|
|
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.
|
||
|
|
homepage: https://cnvkit.readthedocs.io/en/stable/index.html
|
||
|
|
documentation: https://cnvkit.readthedocs.io/en/stable/index.html
|
||
|
|
tool_dev_url: https://github.com/etal/cnvkit
|
||
|
|
doi: 10.1371/journal.pcbi.1004873
|
||
|
|
licence: ["Apache-2.0"]
|
||
|
|
|
||
|
|
input:
|
||
|
|
- fasta:
|
||
|
|
type: file
|
||
|
|
description: File containing reference genome
|
||
|
|
pattern: "*.{fasta}"
|
||
|
|
- targets:
|
||
|
|
type: file
|
||
|
|
description: File containing genomic regions
|
||
|
|
pattern: "*.{bed}"
|
||
|
|
- antitargets:
|
||
|
|
type: file
|
||
|
|
description: File containing off-target genomic regions
|
||
|
|
pattern: "*.{bed}"
|
||
|
|
|
||
|
|
output:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- reference:
|
||
|
|
type: file
|
||
|
|
description: File containing a copy-number reference (required for CNV calling in tumor_only mode)
|
||
|
|
pattern: "*.{cnn}"
|
||
|
|
- versions:
|
||
|
|
type: file
|
||
|
|
description: File containing software versions
|
||
|
|
pattern: "versions.yml"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@SusiJo"
|