Optionally pass a shell script to sbatch rather than wrapping the command directly to circumvent SLURM command-line character limit

Author: dmwnz

snakemake_executor_plugin_slurm/__init__.py

@@ -269,6 +269,20 @@ class ExecutorSettings(ExecutorSettingsBase):
         },
     )
 
+    pass_command_as_script: bool = field(
+        default=False,
+        metadata={
+            "help": (
+                "Pass to sbatch and srun the command to be executed as a shell script"
+                " (fed through stdin) instead of wrapping it in the command line "
+                "call. Useful when a limit exists on SLURM command line length (ie. "
+                "max_submit_line_size)."
+            ),
+            "env_var": False,
+            "required": False,
+        },
+    )
+
     def __post_init__(self):
         """Validate settings after initialization."""
         validate_executor_settings(self)
@@ -413,7 +427,10 @@ def warn_on_jobcontext(self, done=None):
         done = True
 
     def additional_general_args(self):
-        return "--executor slurm-jobstep --jobs 1"
+        general_args = "--executor slurm-jobstep --jobs 1"
+        if self.workflow.executor_settings.pass_command_as_script:
+            general_args += " --slurm-jobstep-pass-command-as-script"
+        return general_args
 
     def run_job(self, job: JobExecutorInterface):
         # Implement here how to run a job.
@@ -500,19 +517,31 @@ def run_job(self, job: JobExecutorInterface):
 
         exec_job = self.format_job_exec(job)
 
-        # and finally the job to execute with all the snakemake parameters
-        call += f' --wrap="{exec_job}"'
+        if not self.workflow.executor_settings.pass_command_as_script:
+            # and finally wrap the job to execute with all the snakemake parameters
+            call += f' --wrap="{exec_job}"'
+            subprocess_stdin = None
+        else:
+            # format the job to execute with all the snakemake parameters into a script
+            sbatch_script = "\n".join(["#!/bin/sh", exec_job])
+            self.logger.debug(f"sbatch script:\n{sbatch_script}")
+            # feed the shell script to sbatch via stdin
+            call += " /dev/stdin"
+            subprocess_stdin = sbatch_script
 
         self.logger.debug(f"sbatch call: {call}")
         try:
             process = subprocess.Popen(
                 call,
                 shell=True,
                 text=True,
+                stdin=subprocess.PIPE,
                 stdout=subprocess.PIPE,
                 stderr=subprocess.PIPE,
             )
-            out, err = process.communicate()
+            out, err = process.communicate(
+                input=subprocess_stdin  # feed the sbatch shell script through stdin
+            )
             if process.returncode != 0:
                 raise subprocess.CalledProcessError(
                     process.returncode, call, output=err
@@ -524,6 +553,11 @@ def run_job(self, job: JobExecutorInterface):
                     "SLURM sbatch failed. "
                     f"The error message was '{e.output.strip()}'.\n"
                     f"    sbatch call:\n        {call}\n"
+                    + (
+                        f"    sbatch script:\n{sbatch_script}\n"
+                        if subprocess_stdin is not None
+                        else ""
+                    )
                 ),
             )
             return