CHM-EVAL-KIT
Download CHM-eval kit for benchmarking variant calling.
URL: https://github.com/lh3/CHM-eval
Example
This wrapper can be used in the following way:
rule chm_eval_kit:
output:
directory("resources/chm-eval-kit"),
params:
# Tag and version must match, see https://github.com/lh3/CHM-eval/releases.
tag="v0.5",
version="20180222",
log:
"logs/chm-eval-kit.log",
cache: "omit-software"
wrapper:
"v5.8.0-3-g915ba34/bio/benchmark/chm-eval-kit"
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
curl
Params
tag
: Release tag, see git official repositoryversion
: Release version, see git official repository
Code
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2020, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"
import os
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
url = (
"https://github.com/lh3/CHM-eval/releases/"
"download/{tag}/CHM-evalkit-{version}.tar"
).format(version=snakemake.params.version, tag=snakemake.params.tag)
os.makedirs(snakemake.output[0])
shell(
"(curl -L {url} | tar --strip-components 1 -C {snakemake.output[0]} -xf - &&"
"(cd {snakemake.output[0]}; chmod +x htsbox run-eval k8)) {log}"
)