Removing single quotes from job argument (#5)

jannisspeer · Mar 23, 2024 · 7ff6028 · 7ff6028
1 parent 4fd57cc
commit 7ff6028
Showing 1 changed file with 8 additions and 0 deletions.
diff --git a/snakemake_executor_plugin_htcondor/__init__.py b/snakemake_executor_plugin_htcondor/__init__.py
@@ -83,6 +83,14 @@ def run_job(self, job: JobExecutorInterface):
         job_exec = self.get_python_executable()
         job_args = self.format_job_exec(job).removeprefix(job_exec + " ")
 
+        # HTCondor cannot handle single quotes
+        if "'" in job_args:
+            job_args = job_args.replace("'", "")
+            self.logger.warning(
+                "The job argument contains a single quote. "
+                "Removing it to avoid issues with HTCondor."
+            )
+
         # Creating submit dictionary which is passed to htcondor.Submit
         submit_dict = {
             "executable": job_exec,