fix: ensure proper handling of group jobs in combination with the slu…

…rm-jobstep executor
snakemake · Jan 16, 2024 · f5c3d4c · f5c3d4c
1 parent 18acfb6
commit f5c3d4c
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -16,8 +16,8 @@ keywords = ["snakemake", "plugin", "executor", "cluster", "slurm"]
 [tool.poetry.dependencies]
 python = "^3.11"
 snakemake-interface-common = "^1.13.0"
-snakemake-interface-executor-plugins = "^8.0.2"
-snakemake-executor-plugin-slurm-jobstep = "^0.1.5"
+snakemake-interface-executor-plugins = "^8.2.0"
+snakemake-executor-plugin-slurm-jobstep = "^0.1.10"
 throttler = "^1.2.2"
 
 [tool.poetry.group.dev.dependencies]

diff --git a/snakemake_executor_plugin_slurm/__init__.py b/snakemake_executor_plugin_slurm/__init__.py
@@ -39,6 +39,7 @@
     auto_deploy_default_storage_provider=False,
     # wait a bit until slurmdbd has job info available
     init_seconds_before_status_checks=40,
+    pass_group_args=True,
 )
 
 
@@ -51,7 +52,7 @@ def __post_init__(self):
         self._fallback_partition = None
 
     def additional_general_args(self):
-        return "--executor slurm-jobstep"
+        return "--executor slurm-jobstep --jobs 1"
 
     def run_job(self, job: JobExecutorInterface):
         # Implement here how to run a job.