__author__ = "Taavi Päll"
__copyright__ = "Copyright 2019, Taavi Päll"
__email__ = "tapa741@gmail.com"
__license__ = "MIT"

from snakemake.shell import shell
import os

# Get extra arguments
extra = snakemake.params.get("extra", "")

# Setup log
log = snakemake.log_fmt_shell(stdout = False, stderr = True)

# Run commands
shell("(prokka"
      " {extra}"
      " --cpus {snakemake.threads}"
      " {snakemake.input}) {log}")
