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.
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. |
Basic Options
Name | Type & Properties | Description |
|---|---|---|
--cache_version | integer | Set data (cache, FASTA) version to install. |
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. |
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. |
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. |
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 Relationships
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Current component
ensembl_vep/vep_installbiobox v0.4.2
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