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cmeestersfgvieiracoderabbitai[bot]
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fix: sbatch stderr parsing #2 (#165)
next attempt to fix the behaviour described in #161 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Bug Fixes** - Improved error handling for SLURM job submissions, providing clearer indications of submission failures. - Enhanced error reporting with detailed messages for job submission failures. - **Chores** - Minor adjustments to comments and formatting for better clarity. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: Filipe G. Vieira <[email protected]> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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snakemake_executor_plugin_slurm/__init__.py

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -231,9 +231,10 @@ def run_job(self, job: JobExecutorInterface):
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)
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except subprocess.CalledProcessError as e:
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raise WorkflowError(
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f"SLURM job submission failed. The error message was {e.output}"
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f"SLURM sbatch failed. The error message was {e.output}"
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)
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if err: # any other error message?
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# any other error message indicating failure?
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if "submission failed" in err:
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raise WorkflowError(
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f"SLURM job submission failed. The error message was {err}"
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)

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