modules/cnvkit_target

Transform bait intervals into targets more suitable for CNVkit.

cnvkittargetcnvcopy number

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

Description

Transform bait intervals into targets more suitable for CNVkit.

Input

name:type

description

pattern

`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}

`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

name:type

description

pattern

`bed`

`meta`
`:map`

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

`*.bed`
`:file`

File containing target regions

*.{bed}

`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 https://github.com/etal/cnvkit 10.1371/journal.pcbi.1004873

modules/cnvkit_target

Description

Input

`meta`
`:map`

`baits`
`:file`

`meta2`
`:map`

`annotation`
`:file`

Output

`bed`

`meta`
`:map`

`*.bed`
`: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

maintainers

get in touch

modules/cnvkit_target

Description

Input

meta:map

baits:file

meta2:map

annotation:file

Output

bed

meta:map

*.bed: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

maintainers

get in touch

`meta`
`:map`

`baits`
`:file`

`meta2`
`:map`

`annotation`
`:file`

`bed`

`meta`
`:map`

`*.bed`
`: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