Simplify segmentation inference

ingest/Snakefile

@@ -10,13 +10,8 @@ for key, value in defaults.items():
     if not key in config:
         config[key] = value
 
-# Check if organism is segmented
-if "nucleotideSequences" not in config:
-    config["nucleotideSequences"] = ["main"]
-config["segmented"] = not (
-    len(config["nucleotideSequences"]) == 1
-    and config["nucleotideSequences"][0] == "main"
-)
+# Infer whether nucleotide sequences are segmented
+config["segmented"] = len(config["nucleotideSequences"]) > 1
 
 Path("results").mkdir(parents=True, exist_ok=True)
 with open("results/config.yaml", "w") as f:

ingest/config/defaults.yaml

@@ -1,5 +1,6 @@
 # Values here are defaults for the `config` variable in the Snakefile
 # Purpose is to keep the `values.yaml` config file clean
+nucleotideSequences: ["main"]
 post_start_sleep: 0
 log_level: DEBUG
 compound_country_field: ncbi_geo_location