feat!: added common setting for defining whether workflow sources shall be deployed.

Author: johanneskoester

snakemake_interface_executor_plugins/dag.py

@@ -17,3 +17,7 @@ def incomplete_external_jobid(self, job: JobExecutorInterface) -> Optional[str]:
     @abstractmethod
     def get_sources(self) -> Iterable[str]:
         ...
+
+    @abstractmethod
+    def get_unneeded_temp_files(self, job: JobExecutorInterface) -> Iterable[str]:
+        ...

snakemake_interface_executor_plugins/executors/real.py

@@ -97,6 +97,7 @@ def get_job_args(self, job: JobExecutorInterface, **kwargs):
                 format_cli_arg("--cores", kwargs.get("cores", self.cores)),
                 format_cli_arg("--attempt", job.attempt),
                 format_cli_arg("--force-use-threads", not job.is_group()),
+                format_cli_arg("--unneeded-temp-files", self.workflow.dag.unneeded_temp_files(job)),
                 self.get_resource_declarations(job),
             ]
         )

snakemake_interface_executor_plugins/settings.py

@@ -24,6 +24,10 @@ class CommonSettings:
         Whether to the executor implies to not have a shared file system.
     dryrun_exec : bool
         Whether to jobs will be executed in dry-run mode.
+    job_deploy_sources : bool
+        Whether to deploy workflow sources before job execution. This is e.g.
+        needed when remote jobs are guaranteed to be not executed on a shared
+        filesystem. For example, this is True in the kubernetes executor plugin.
     touch_exec : bool
         Whether job outputs will be touched only.
     use_threads : bool
@@ -46,6 +50,7 @@ class CommonSettings:
 
     non_local_exec: bool
     implies_no_shared_fs: bool
+    job_deploy_sources: bool
     dryrun_exec: bool = False
     touch_exec: bool = False
     use_threads: bool = False