"""Snakemake wrapper for MultiQC.
This file is parth of Digestifly Demux.
"""
from snakemake import shell
__author__ = "Manuel Holtgrewe <*****@*****.**>"
shell.executable("/bin/bash")
shell(r"""
set -x
set -euo pipefail
rm -f {snakemake.output}
multiqc \
--zip-data-dir \
--outdir $(dirname {snakemake.output.html}) \
--interactive \
{snakemake.input}
""")
def reset_shell_exec_on_windows(prepend_usable_bash_to_path):
shell.executable(None)
from snakemake import shell
shell.executable("bash")
shell("echo {} > {}".format(snakemake.params["title"], snakemake.output[0]))