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Check for empty user-defined subsampling scheme #1082

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Sep 19, 2023
Merged

Check for empty user-defined subsampling scheme #1082

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4 changes: 4 additions & 0 deletions Snakefile
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Expand Up @@ -34,6 +34,10 @@ import time
# [4] https://github.com/snakemake/snakemake/blob/a7ac40c96d6e2af47102563d0478a2220e2a2ab7/snakemake/workflow.py#L1088-L1094
# [5] https://github.com/snakemake/snakemake/blob/a7ac40c96d6e2af47102563d0478a2220e2a2ab7/snakemake/utils.py#L455-L476
user_subsampling = copy.deepcopy(config.get("subsampling", {}))
if user_subsampling is None:
logger.error("ERROR: The configuration file you have provided defines a `subsampling` section that appears to be empty.")
logger.error("Check that section of your configuration file to confirm that it isn't empty and that its contents are properly indented below the `subsampling` key.")
sys.exit(1)

configfile: "defaults/parameters.yaml"

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