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{:bash}`
`:map`

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

`cnr{:bash}`
`:file`

CNR file

*.cnr

`cns{:bash}`
`:file`

CNS file [Optional]

*.cns

Output

name:type

description

pattern

`tsv{:bash}`

`meta{:bash}`
`:map`

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

`*.tsv{:bash}`
`:file`

TSV file

*.tsv

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

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{:bash}`
`:map`

`cnr{:bash}`
`:file`

`cns{:bash}`
`:file`

Output

`tsv{:bash}`

`meta{:bash}`
`:map`

`*.tsv{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

cnvkit
Apache-2.0

included in

maintainers

get in touch

modules/cnvkit_genemetrics

Description

Input

meta{:bash}:map

cnr{:bash}:file

cns{:bash}:file

Output

tsv{:bash}

meta{:bash}:map

*.tsv{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

cnvkit Apache-2.0

included in

maintainers

get in touch

`meta{:bash}`
`:map`

`cnr{:bash}`
`:file`

`cns{:bash}`
`:file`

`tsv{:bash}`

`meta{:bash}`
`:map`

`*.tsv{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

cnvkit
Apache-2.0