Merge pull request #1082 from nextstrain/check-for-empty-subsampling

Check for empty user-defined subsampling scheme

Snakefile

@@ -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"