modules/rbt_vcfsplit

A tool for splitting VCF/BCF files into N equal chunks, including BND support

genomicssplittingVCFBCFvariants

https://github.com/nf-core/modules/[...]/modules/nf-core/rbt/vcfsplit

Description

A tool for splitting VCF/BCF files into N equal chunks, including BND support

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`vcf`
`:file`

VCF file with variants to be split

*.{vcf,bcf,vcf.gz}

`numchunks`
`:integer`

Number of chunks to split the VCF file into. The default is 15.

Output

name:type

description

pattern

`bcfchunks`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.bcf`
`:file`

Chunks of the input VCF file, split into numchunks equal parts.

*.bcf

`versions_rbt`

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

The process the versions were collected from

`rbt`
`:string`

The tool name

`rbt --version | grep -oE '[0-9]+(\.[0-9]+)+' | head -n 1`
`: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

`rbt`
`:string`

The tool name

`rbt --version | grep -oE '[0-9]+(\.[0-9]+)+' | head -n 1`
`:eval`

The expression to obtain the version of the tool

Tools

rust-bio-tools
MIT

A growing collection of fast and secure command line utilities for dealing with NGS data implemented on top of Rust-Bio.

github.com/rust-bio/rust-bio-tools no DOI available

modules/rbt_vcfsplit

Description

Input

`meta`
`:map`

`vcf`
`:file`

`numchunks`
`:integer`

Output

`bcfchunks`

`meta`
`:map`

`*.bcf`
`:file`

`versions_rbt`

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

`rbt`
`:string`

`rbt --version | grep -oE '[0-9]+(\.[0-9]+)+' | head -n 1`
`:eval`

Topics

`versions`

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

`rbt`
`:string`

`rbt --version | grep -oE '[0-9]+(\.[0-9]+)+' | head -n 1`
`:eval`

Tools

rust-bio-tools
MIT

included in

maintainer

get in touch

modules/rbt_vcfsplit

Description

Input

meta:map

vcf:file

numchunks:integer

Output

bcfchunks

meta:map

*.bcf:file

versions_rbt

${task.process}:string

rbt:string

rbt --version | grep -oE '[0-9]+(\.[0-9]+)+' | head -n 1:eval

Topics

versions

${task.process}:string

rbt:string

rbt --version | grep -oE '[0-9]+(\.[0-9]+)+' | head -n 1:eval

Tools

rust-bio-tools MIT

included in

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`numchunks`
`:integer`

`bcfchunks`

`meta`
`:map`

`*.bcf`
`:file`

`versions_rbt`

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

`rbt`
`:string`

`rbt --version | grep -oE '[0-9]+(\.[0-9]+)+' | head -n 1`
`:eval`

`versions`

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

`rbt`
`:string`

`rbt --version | grep -oE '[0-9]+(\.[0-9]+)+' | head -n 1`
`:eval`

rust-bio-tools
MIT