Description

Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through task.ext.args.

Input

name:type
description
pattern

meta{:bash}

:map

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

assembly{:bash}

:string

Genome assembly

species{:bash}

:string

Specie

cache_version{:bash}

:string

cache version

Output

name:type
description
pattern

cache{:bash}

meta{:bash}

:file

cache

*

prefix{:bash}

:file

cache

*

versions_ensemblvep{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

ensemblvep{:bash}

:string

The tool name

vep --help | sed -n '/ensembl-vep/s/.*: //p'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

ensemblvep{:bash}

:string

The tool name

vep --help | sed -n '/ensembl-vep/s/.*: //p'{:bash}

:string

The command used to generate the version of the tool

Tools

ensemblvep
Apache-2.0

VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

ensembl.org/info/docs/tools/vep ensembl.org/info/docs/tools/vep/script
included in
rnadnavarrnavarsarektumourevo
maintainer
Github user maxulysse
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