snakemake-executor-plugin-sge 0.6.2__tar.gz → 0.6.4__tar.gz

{snakemake_executor_plugin_sge-0.6.2 → snakemake_executor_plugin_sge-0.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: snakemake-executor-plugin-sge
-Version: 0.6.2
+Version: 0.6.4
 Summary: A Snakemake executor plugin for submitting jobs to SGE/UGE/OGS clusters.
 License: MIT
 Keywords: snakemake,plugin,executor,cluster,sge,uge,gridengine

{snakemake_executor_plugin_sge-0.6.2 → snakemake_executor_plugin_sge-0.6.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-sge"
-version = "0.6.2"
+version = "0.6.4"
 description = "A Snakemake executor plugin for submitting jobs to SGE/UGE/OGS clusters."
 authors = ["Stylianos Charalampous <stylianosc@github.com>"]
 readme  = "README.md"

{snakemake_executor_plugin_sge-0.6.2 → snakemake_executor_plugin_sge-0.6.4}/snakemake_executor_plugin_sge/__init__.py

@@ -743,8 +743,10 @@ class Executor(RemoteExecutor):
             else f"rule_{jobs[0].name}"
         )
 
-        # Determine array-specific log directory from first job's workdir resource
-        first_job_logdir = self._get_job_logdir(jobs[0])
+        # Array jobs share one -o/-e path across all tasks, so per-task workdir
+        # paths are not usable.  Always use the main workflow log directory so
+        # logs from different subjects don't pile up in the first subject's folder.
+        first_job_logdir = self.sge_logdir_default
         first_job_logdir.mkdir(parents=True, exist_ok=True)
 
         # Helper files (manifests, scripts, task maps) are stored in .meta subdirectory
@@ -851,9 +853,10 @@ class Executor(RemoteExecutor):
             script_path.write_text(script_content)
             script_path.chmod(0o755)
 
-            # Use first job's workdir resource if available, else fall back to workflow workdir
-            workdir = jobs[0].resources.get("workdir") if hasattr(jobs[0], "resources") else None
-            workdir = workdir or self.workflow.workdir_init
+            # Use the main workflow workdir for the qsub -wd flag.  Individual
+            # task commands in the task map already carry full absolute paths, so
+            # the array-level working directory only needs to be a valid directory.
+            workdir = str(self.workflow.workdir_init)
 
             job_params = {
                 "run_uuid": self.run_uuid,

{snakemake_executor_plugin_sge-0.6.2 → snakemake_executor_plugin_sge-0.6.4}/snakemake_executor_plugin_sge/submit_string.py

@@ -300,13 +300,16 @@ def get_submit_command(
         f" -N {_safe(job_name)}"
     )
 
-    # Stdout/stderr: pass the log *directory*; SGE appends .oJOBID.TASKID
-    # Use -o dir/ -e dir/ (trailing slash = treat as directory on most SGE)
-    call += f" -o {_safe(str(log_dir) + '/')}"
+    # Stdout/stderr: specify exact log file paths using SGE variable expansion
+    # $JOB_ID expands to the job ID, $TASK_ID expands to the array task index
+    # This produces logs named like "1234567.1.log" (jobid.taskid.log)
+    log_stdout_path = log_dir / "$JOB_ID.$TASK_ID.log"
+    call += f" -o {_safe(str(log_stdout_path))}"
     if join_logs:
         call += " -j y"
     else:
-        call += f" -e {_safe(str(log_dir) + '/')}"
+        log_stderr_path = log_dir / "$JOB_ID.$TASK_ID.error"
+        call += f" -e {_safe(str(log_stderr_path))}"
 
     # ── working directory ──────────────────────────────────────────────
     if workdir: