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fix: provide proper error when using immediate submit in combination with checkpoint jobs. #1437

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merged 2 commits into from Feb 26, 2022
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fix: provide proper error when using immediate submit in combination with checkpoint jobs. #1437

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fix: provide proper error when using immediate submit in combination …
johanneskoester Feb 26, 2022
4a77067
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johanneskoester Feb 26, 2022
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3 changes: 2 additions & 1 deletion snakemake/__init__.py
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Expand Up @@ -2120,7 +2120,8 @@ def get_argument_parser(profile=None):
"$ snakemake --cluster 'sbatch --dependency {dependencies}.\n"
"Assuming that your submit script (here sbatch) outputs the "
"generated job id to the first stdout line, {dependencies} will "
"be filled with space separated job ids this job depends on.",
"be filled with space separated job ids this job depends on. "
"Does not work for workflows that contain checkpoint rules.",
)
group_cluster.add_argument(
"--jobscript",
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8 changes: 8 additions & 0 deletions snakemake/workflow.py
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Expand Up @@ -873,6 +873,14 @@ def files(items):
)
return False

if immediate_submit and any(dag.checkpoint_jobs):
logger.error(
"Immediate submit mode (--immediate-submit) may not be used for workflows "
"with checkpoint jobs, as the dependencies cannot be determined before "
"execution in such cases."
)
return False

updated_files.extend(f for job in dag.needrun_jobs for f in job.output)

if generate_unit_tests:
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