modules/cnvkit_export

Convert copy number ratio tables (.cnr files) or segments (.cns) to another format.

cnvkitcopy numberexport

https://github.com/nf-core/modules/[...]/modules/nf-core/cnvkit/export

Description

Convert copy number ratio tables (.cnr files) or segments (.cns) to another format.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`cns`
`:file`

CNVKit CNS file.

*.cns

Output

name:type

description

pattern

`output`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.${suffix}`
`:file`

Output file

`versions_cnvkit`

`${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

Topics

name:type

description

pattern

`versions`

`${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

Tools

cnvkit
Apache-2.0

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.

cnvkit.readthedocs.io/en/stable

modules/cnvkit_export

Description

Input

`meta`
`:map`

`cns`
`:file`

Output

`output`

`meta`
`:map`

`${prefix}.${suffix}`
`:file`

`versions_cnvkit`

`${task.process}`
`:string`

`cnvkit`
`:string`

`cnvkit.py version | sed -e "s/cnvkit v//g"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`cnvkit`
`:string`

`cnvkit.py version | sed -e "s/cnvkit v//g"`
`:eval`

Tools

cnvkit
Apache-2.0

included in

maintainers

get in touch

modules/cnvkit_export

Description

Input

meta:map

cns:file

Output

output

meta:map

${prefix}.${suffix}:file

versions_cnvkit

${task.process}:string

cnvkit:string

cnvkit.py version | sed -e "s/cnvkit v//g":eval

Topics

versions

${task.process}:string

cnvkit:string

cnvkit.py version | sed -e "s/cnvkit v//g":eval

Tools

cnvkit Apache-2.0

included in

maintainers

get in touch

`meta`
`:map`

`cns`
`:file`

`output`

`meta`
`:map`

`${prefix}.${suffix}`
`:file`

`versions_cnvkit`

`${task.process}`
`:string`

`cnvkit`
`:string`

`cnvkit.py version | sed -e "s/cnvkit v//g"`
`:eval`

`versions`

`${task.process}`
`:string`

`cnvkit`
`:string`

`cnvkit.py version | sed -e "s/cnvkit v//g"`
`:eval`

cnvkit
Apache-2.0