fix: logdir misconstruct when leading slash in wildcard

snakemake_executor_plugin_slurm/__init__.py

@@ -180,7 +180,9 @@ def run_job(self, job: JobExecutorInterface):
         group_or_rule = f"group_{job.name}" if job.is_group() else f"rule_{job.name}"
 
         try:
-            wildcard_str = "_".join(job.wildcards) if job.wildcards else ""
+            wildcard_str = (
+                "_".join(job.wildcards).replace("/", "_") if job.wildcards else ""
+            )
         except AttributeError:
             wildcard_str = ""
 
@@ -264,10 +266,10 @@ def run_job(self, job: JobExecutorInterface):
                     "specified. Assuming 'tasks_per_node=1'."
                     "Probably not what you want."
                 )
+
         # we need to set cpus-per-task OR cpus-per-gpu, the function
         # will return a string with the corresponding value
         call += f" {get_cpu_setting(job, gpu_job)}"
-
         if job.resources.get("slurm_extra"):
             self.check_slurm_extra(job)
             call += f" {job.resources.slurm_extra}"

tests/tests.py

@@ -110,3 +110,47 @@ def test_both_gres_and_gpu_set(self, mock_job):
             WorkflowError, match="GRES and GPU are set. Please only set one of them."
         ):
             set_gres_string(job)
+
+
+class TestWildcardsWithSlashes(snakemake.common.tests.TestWorkflowsLocalStorageBase):
+    """Test handling of wildcards with slashes to ensure log directories are correctly constructed."""
+
+    __test__ = True
+
+    def get_executor(self) -> str:
+        return "slurm"
+
+    def get_executor_settings(self) -> Optional[ExecutorSettingsBase]:
+        return ExecutorSettings(logdir="test_logdir")
+
+    def test_wildcard_slash_replacement(self):
+        """Test that slashes in wildcards are correctly replaced with underscores in log directory paths."""
+
+        # Create a mock job with wildcards containing slashes
+        class MockJob:
+            def __init__(self):
+                self.name = "test_job"
+                self.wildcards = ["/leading_slash", "middle/slash", "trailing/"]
+                self.is_group = lambda: False
+
+        # Create an executor instance
+        executor = Executor()
+        executor.workflow = snakemake.common.tests.DummyWorkflow()
+        executor.workflow.executor_settings = self.get_executor_settings()
+        executor.slurm_logdir = os.path.abspath("test_logdir")
+
+        # Manually call the wildcard sanitization logic from run_job method
+        try:
+            wildcard_str = (
+                "_".join(MockJob().wildcards).replace("/", "_")
+                if MockJob().wildcards
+                else ""
+            )
+        except AttributeError:
+            wildcard_str = ""
+
+        # Assert that slashes are correctly replaced with underscores
+        assert wildcard_str == "_leading_slash_middle_slash_trailing_"
+
+        # Verify no slashes remain in the wildcard string
+        assert "/" not in wildcard_str