snakemake-executor-plugin-slurm 0.5.2__tar.gz → 0.6.0__tar.gz

{snakemake_executor_plugin_slurm-0.5.2 → snakemake_executor_plugin_slurm-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: snakemake-executor-plugin-slurm
-Version: 0.5.2
+Version: 0.6.0
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 Home-page: https://github.com/snakemake/snakemake-executor-plugin-slurm
 License: MIT

{snakemake_executor_plugin_slurm-0.5.2 → snakemake_executor_plugin_slurm-0.6.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "0.5.2"
+version = "0.6.0"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
 authors = [
     "Christian Meesters <meesters@uni-mainz.de>",

{snakemake_executor_plugin_slurm-0.5.2 → snakemake_executor_plugin_slurm-0.6.0}/snakemake_executor_plugin_slurm/__init__.py

@@ -6,6 +6,7 @@ __license__ = "MIT"
 import csv
 from io import StringIO
 import os
+import re
 import subprocess
 import time
 from datetime import datetime, timedelta
@@ -143,6 +144,7 @@ class Executor(RemoteExecutor):
         call += f" --cpus-per-task={get_cpus_per_task(job)}"
 
         if job.resources.get("slurm_extra"):
+            self.check_slurm_extra(job)
             call += f" {job.resources.slurm_extra}"
 
         exec_job = self.format_job_exec(job)
@@ -488,3 +490,15 @@ class Executor(RemoteExecutor):
             "'slurm_partition=<your default partition>'."
         )
         return ""
+
+    def check_slurm_extra(self, job):
+        jobname = re.compile(r"--job-name[=?|\s+]|-J\s?")
+        if re.search(jobname, job.resources.slurm_extra):
+            raise WorkflowError(
+                "The '--job-name' option is not allowed in the 'slurm_extra' "
+                "parameter. The job name is set by snakemake and must not be "
+                "overwritten. It is internally used to check the stati of all "
+                "submitted jobs by this workflow."
+                "Please consult the documentation if you are unsure how to "
+                "query the status of your jobs."
+            )