ensembl_vep/vep_install

variant effect prediction

annotation

genomics

installation

cache

Description

Install Ensembl VEP cache data, FASTA files, and plugins for variant effect prediction.

The VEP installer script downloads and installs reference data required by VEP, including:

Cache files containing transcript and regulatory data
FASTA files for reference sequences
VEP plugins for extended functionality

See the VEP installation documentation for details.

Type

bash_script

License

Apache-2.0

Keywords

variant effect prediction

annotation

genomics

installation

cache

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
destdir: "$id.$key.destdir./opt/vep"  
cachedir: "$id.$key.cachedir./data/vep_cache"  
pluginsdir: "$id.$key.pluginsdir./data/vep_plugins"  
cache_version: [ 115 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/ensembl_vep/vep_install/main.nf \  
  -params-file params.yaml

Outputs

Name	Type & Properties	Description
--destdir	file output	Set destination directory for API install.
--cachedir	file output	Set destination directory for cache files.
--pluginsdir	file output	Set destination directory for VEP plugins files.

Name

Type & Properties

--destdir

file

output

--cachedir

file

output

--pluginsdir

file

output

Basic Options

Name	Type & Properties	Description
--cache_version	integer	Set data (cache, FASTA) version to install.

Name

Type & Properties

--cache_version

integer

Installation Options

Name	Type & Properties	Description
--auto	string	Run installer without user prompts. Use combinations of: - "a" (API + Faidx/htslib) - "l" (Faidx/htslib only) - "c" (cache) - "f" (FASTA) - "p" (plugins) Example: "ac" for API and cache.
--species	string multiple	Comma-separated list of species to install when using --auto.
--assembly	string	Assembly name to use if more than one during --auto.

Name

Type & Properties

--auto

string

--species

string

multiple

--assembly

string

Plugin Options

Name	Type & Properties	Description
--plugins	string multiple	Comma-separated list of plugins to install when using --auto. Use "list" to list all plugins or "all" to install all available plugins.

Name

Type & Properties

--plugins

string

multiple

Advanced Options

Name	Type & Properties	Description
--no_update	boolean_true	Do not check for updates to ensembl-vep or API.
--no_plugins	boolean_true	Skip plugin installation.
--no_htslib	boolean_true	Do not attempt to install Faidx/htslib.
--no_bioperl	boolean_true	Do not install BioPerl.
--prefer_bin	boolean_true	Use this if the installer fails with out of memory errors.
--convert	boolean_true	Convert downloaded caches to use tabix for retrieving co-located variants (requires tabix).
--quiet	boolean_true	Do not write any status output when using --auto.

Name

Type & Properties

--no_update

boolean_true

--no_plugins

boolean_true

--no_htslib

boolean_true

--no_bioperl

boolean_true

--prefer_bin

boolean_true

--convert

boolean_true

--quiet

boolean_true