chmevalbenchmark chmevalbenchmark chm-eval

chmevalbenchmark chm-eval

Version:
20180222
Identifier: TL_7c0536_5b.9f
Tool
1__author__ = "Johannes Köster"
2__copyright__ = "Copyright 2020, Johannes Köster"
3__email__ = "johannes.koester@uni-due.de"
4__license__ = "MIT"
5
6from snakemake.shell import shell
7
8log = snakemake.log_fmt_shell(stdout=False, stderr=True)
9
10kit = snakemake.input.kit
11vcf = snakemake.input.vcf
12build = snakemake.params.build
13extra = snakemake.params.get("extra", "")
14
15if not snakemake.output[0].endswith(".summary"):
16    raise ValueError("Output file must end with .summary")
17out = snakemake.output[0][:-8]
18
19shell("({kit}/run-eval -g {build} -o {out} {extra} {vcf} | sh) {log}")
20