feat: make status and cancel command configurable

snakemake_executor_plugin_slurm/__init__.py

@@ -148,6 +148,32 @@ class ExecutorSettings(ExecutorSettingsBase):
             "required": False,
         },
     )
+    status_command: Optional[str] = field(
+        default="sacct -X --parsable2 \
+                        --clusters all \
+                        --noheader --format=JobIdRaw,State \
+                        --starttime {sacct_starttime} \
+                        --endtime now --name {run_uuid}",
+        metadata={
+            "help": "The command to query the status of SLURM jobs. "
+            "This command should return one line for each job with "
+            "<raw/main_job_id>|<long_status_string>."
+            "If no accounting is enabled, an alternative is:",
+            # "squeue --states=all --format=%i|%T --noheader --name {run_uuid}",
+            "env_var": False,
+            "required": False,
+        },
+    )
+    cancel_command: Optional[str] = field(
+        default="scancel {jobids} --clusters=all",
+        metadata={
+            "help": "The command to cancel SLURM jobs. "
+            "This command should include the job IDs to cancel."
+            "In a federation the addiational argument --clusters=all might be used.",
+            "env_var": False,
+            "required": False,
+        },
+    )
 
 
 # Required:
@@ -458,12 +484,10 @@ async def check_active_jobs(
         # the more readable version ought to be re-adapted
 
         # -X: only show main job, no substeps
-        sacct_command = f"""sacct -X --parsable2 \
-                        --clusters all \
-                        --noheader --format=JobIdRaw,State \
-                        --starttime {sacct_starttime} \
-                        --endtime now --name {self.run_uuid}"""
-
+        sacct_command = self.workflow.executor_settings.status_command.format(
+            sacct_starttime=sacct_starttime, run_uuid=self.run_uuid
+        )
+
         # for better redability in verbose output
         sacct_command = " ".join(shlex.split(sacct_command))
 
@@ -590,7 +614,7 @@ def cancel_jobs(self, active_jobs: List[SubmittedJobInfo]):
                 # about 30 sec, but can be longer in extreme cases.
                 # Under 'normal' circumstances, 'scancel' is executed in
                 # virtually no time.
-                scancel_command = f"scancel {jobids} --clusters=all"
+                scancel_command = self.workflow.executor_settings.cancel_command.format(jobids=jobids)
 
                 subprocess.check_output(
                     scancel_command,