1__author__ = "Jan Forster"
2__copyright__ = "Copyright 2020, Jan Forster"
3__email__ = "j.forster@dkfz.de"
4__license__ = "MIT"
5
6from snakemake.shell import shell
7import os.path as path
8import sys
9
10extra = snakemake.params.get("extra", "")
11log = snakemake.log_fmt_shell(stdout=True, stderr=True)
12
13control = snakemake.input.get("control", "")
14if control == "":
15    control_command = ""
16else:
17    control_command = "-i " + control
18
19shell(
20    "(findPeaks"
21    " {snakemake.input.tag}"
22    " -style {snakemake.params.style}"
23    " {extra}"
24    " {control_command}"
25    " -o {snakemake.output})"
26    " {log}"
27)
28