VEP DOWNLOAD CACHE

Download VEP cache for given species, build and release.

Software dependencies

  • ensembl-vep

Example

This wrapper can be used in the following way:

rule get_vep_cache:
    output:
        directory("resources/vep/cache")
    params:
        species="saccharomyces_cerevisiae",
        build="R64-1-1",
        release="98"
    log:
        "logs/vep/cache.log"
    cache: True  # save space and time with between workflow caching (see docs)
    wrapper:
        "0.56.0/bio/vep/cache"

Note that input, output and log file paths can be chosen freely. When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Authors

  • Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2020, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"

from pathlib import Path
from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

shell(
    "vep_install --AUTO cf "
    "--SPECIES {snakemake.params.species} "
    "--ASSEMBLY {snakemake.params.build} "
    "--CACHE_VERSION {snakemake.params.release} "
    "--CACHEDIR {snakemake.output} "
    "--CONVERT {log}"
)