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fix: #348 no attempts to jobstep executor #371

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fix: #348 no attempts to jobstep executor #371

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5 changes: 5 additions & 0 deletions snakemake_executor_plugin_slurm/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -343,6 +343,11 @@ def run_job(self, job: JobExecutorInterface):

exec_job = self.format_job_exec(job)

# Prevent forwarding Snakemake retry attempts into the remote
# jobstep. Convert any "--attempt <n>" or "--attempt=<n>" to
# a single attempt in the remote context.
exec_job = re.sub(r"--attempt(?:[=\s]+)\d+", "--attempt 1", exec_job)

# and finally the job to execute with all the snakemake parameters
call += f' --wrap="{exec_job}"'

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