diff --git a/looper/conductor.py b/looper/conductor.py index fefb4b052..215fe3b46 100644 --- a/looper/conductor.py +++ b/looper/conductor.py @@ -522,11 +522,17 @@ def submit(self, force=False): _LOGGER.info("Dry run, not submitted") elif self._rendered_ok: sub_cmd = self.prj.dcc.compute.submission_command - submission_command = "{} {}".format(sub_cmd, script) + submission_command = f"{sub_cmd} {script}" # old way + if sub_cmd == ".": + sub_cmd_list = [script] + else: + sub_cmd_list = [sub_cmd, script] + # Capture submission command return value so that we can # intercept and report basic submission failures; #167 try: - subprocess.check_call(submission_command, shell=True) + # subprocess.check_call(submission_command, shell=True, executable="/bin/bash") # old way + subprocess.check_call(sub_cmd_list, shell=False) except subprocess.CalledProcessError: fails = ( "" if self.collate else [s.sample_name for s in self._samples]