SNPEFF DOWNLOAD¶
Download snpeff DB for a given species.
Software dependencies¶
- snpeff ==4.3.1t
- bcftools =1.10
Example¶
This wrapper can be used in the following way:
rule snpeff_download:
output:
# wildcard {reference} may be anything listed in `snpeff databases`
directory("resources/snpeff/{reference}")
log:
"logs/snpeff/download/{reference}.log"
params:
reference="{reference}"
wrapper:
"0.60.1/bio/snpeff/download"
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 snakemake.shell import shell
from pathlib import Path
reference = snakemake.params.reference
outdir = Path(snakemake.output[0]).parent.resolve()
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell("snpEff download -dataDir {outdir} {reference} {log}")