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feat: allow to omit job cleanup with --kubernetes-omit-job-cleanup (for debugging) #55

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feat: allow to omit job cleanup with --kubernetes-omit-job-cleanup (for debugging) #55

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22 changes: 17 additions & 5 deletions snakemake_executor_plugin_kubernetes/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,14 @@ class ExecutorSettings(ExecutorSettingsBase):
"nargs": "+",
},
)
omit_job_cleanup: bool = field(
default=False,
metadata={
"help": "Do not delete jobs after they have finished or failed. "
"This is useful for debugging, or if your k8s cluster performs "
"automatic cleanups."
},
)


# Required:
Expand Down Expand Up @@ -502,7 +510,10 @@ def read_log(
self.logger.error(f"Job {j.external_jobid} failed.{msg}")
self.report_job_error(j, msg=msg, aux_logs=aux_logs)

if pod_name is not None:
if (
pod_name is not None
and not self.workflow.executor_settings.omit_job_cleanup
):
self._kubernetes_retry(
lambda j=j: self.safe_delete_job(
j.external_jobid, ignore_not_found=True
Expand All @@ -515,11 +526,12 @@ def read_log(
self.logger.info(f"Job {j.external_jobid} succeeded.")
self.report_job_success(j)

self._kubernetes_retry(
lambda j=j: self.safe_delete_job(
j.external_jobid, ignore_not_found=True
if not self.workflow.executor_settings.omit_job_cleanup:
self._kubernetes_retry(
lambda j=j: self.safe_delete_job(
j.external_jobid, ignore_not_found=True
)
)
)
else:
# still active
self.logger.debug(f"Job {j.external_jobid} is still active.")
Expand Down
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