modules/cnvkit_genemetrics

Copy number variant detection from high-throughput sequencing data

cnvkitbamfastacopy number

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

Description

Copy number variant detection from high-throughput sequencing data

Input

name:type

description

pattern

`meta`
`:map`

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

`cnr`
`:file`

CNR file

*.cnr

`cns`
`:file`

CNS file [Optional]

*.cns

Output

name:type

description

pattern

`tsv`

`meta`
`:map`

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

`*.tsv`
`:file`

TSV file

*.tsv

`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_genemetrics

Description

Input

`meta`
`:map`

`cnr`
`:file`

`cns`
`:file`

Output

`tsv`

`meta`
`:map`

`*.tsv`
`: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_genemetrics

Description

Input

meta:map

cnr:file

cns:file

Output

tsv

meta:map

*.tsv: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`

`cnr`
`:file`

`cns`
`:file`

`tsv`

`meta`
`:map`

`*.tsv`
`: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