feat: in job stability

snakemake_executor_plugin_slurm/__init__.py

@@ -26,6 +26,8 @@
 from snakemake_interface_common.exceptions import WorkflowError
 from snakemake_executor_plugin_slurm_jobstep import get_cpus_per_task
 
+from .utils import delete_slurm_environment
+
 
 @dataclass
 class ExecutorSettings(ExecutorSettingsBase):
@@ -85,10 +87,11 @@ def warn_on_jobcontext(self, done=None):
             if "SLURM_JOB_ID" in os.environ:
                 self.logger.warning(
                     "You are running snakemake in a SLURM job context. "
-                    "This is not recommended, as it may lead to unexpected behavior."
+                    "This is not recommended, as it may lead to unexpected behavior. "
                     "Please run Snakemake directly on the login node."
                 )
                 time.sleep(5)
+                delete_slurm_environment()
         done = True
 
     def additional_general_args(self):

snakemake_executor_plugin_slurm/utils.py

@@ -0,0 +1,16 @@
+# utility functions for the SLURM executor plugin
+
+import os
+
+
+def delete_slurm_environment():
+    """
+    Function to delete all environment variables
+    starting with 'SLURM_'. The parent shell will
+    still have this environment. This is needed to
+    submit within a SLURM job context to avoid
+    conflicting environments.
+    """
+    for var in os.environ:
+        if var.startswith("SLURM_"):
+            del os.environ[var]