VEP DOWNLOAD CACHE¶
Download VEP cache for given species, build and release.
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: "omit-software" # save space and time with between workflow caching (see docs)
wrapper:
"v1.19.1/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.
Software dependencies¶
ensembl-vep=108.1
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=True, stderr=True)
shell(
"vep_install --AUTO cf "
"--SPECIES {snakemake.params.species} "
"--ASSEMBLY {snakemake.params.build} "
"--VERSION {snakemake.params.release} "
"--CACHEDIR {snakemake.output} "
"--CONVERT "
"--NO_UPDATE "
"{extra} {log}"
)