Update config key case for genbank features

Author: ahmig

config/config.yaml

@@ -64,7 +64,7 @@ WINDOW:
   WIDTH: 1000
   STEP: 50
 GB_FEATURES:
-  include:        # any
+  INCLUDE:        # any
     product:
       - "ORF1ab polyprotein"
       - "surface glycoprotein"
@@ -77,7 +77,7 @@ GB_FEATURES:
       - "ORF8 protein"
       - "nucleocapsid phosphoprotein"
       - "ORF10 protein"
-  # exclude: ...  # all
+  # EXCLUDE: ...  # all
 GISAID:
   CREDENTIALS: "config/gisaid.yaml"
   DATE_COLUMN: "CollectionDate"

workflow/scripts/N_S_sites_from_fasta.py

@@ -89,8 +89,8 @@ def main():
         logging.debug("Selecting all features")
         feature_iterator = iter(gb.features)
     else:
-        included = snakemake.params.features.get("include", {})
-        excluded = snakemake.params.features.get("exclude", {})
+        included = snakemake.params.features.get("INCLUDE", {})
+        excluded = snakemake.params.features.get("EXCLUDE", {})
         logging.debug(f"Selecting features including any of {included} and excluding all of {excluded}")
         feature_iterator = (
             feature for feature in gb.features

workflow/scripts/window.py

@@ -74,8 +74,8 @@ def main():
         logging.debug("Selecting all features")
         feature_iterator = iter(gb.features)
     else:
-        included = snakemake.params.features.get("include", {})
-        excluded = snakemake.params.features.get("exclude", {})
+        included = snakemake.params.features.get("INCLUDE", {})
+        excluded = snakemake.params.features.get("EXCLUDE", {})
         logging.debug(f"Selecting features including any of {included} and excluding all of {excluded}")
         feature_iterator = (
             feature for feature in gb.features