modules/cnvkit_access

Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file.

cvnkitaccessfastacopy number

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

Description

Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file.

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta`
`:file`

Genome FASTA.

*.fasta

`meta2`
`:map`

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

`exclude_bed`
`:file`

Additional regions to exclude, in BED format. Can be used multiple times.

Output

name:type

description

pattern

`bed`

`meta`
`:map`

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

`*.bed`
`:file`

File containing accessible regions.

*.{bed}

`versions_cnvkit`

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

The process the versions were collected from

`cnvkit`
`:string`

The tool name

`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 process the versions were collected from

`cnvkit`
`:string`

The tool name

`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_access

Description

Input

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`exclude_bed`
`: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_access

Description

Input

meta :map

fasta :file

meta2 :map

exclude_bed :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

cnvkitApache-2.0

maintainers

get in touch

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`exclude_bed`
`: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