Shift subtype lookups to config

Shifting hardcoded parameters into configs is generally simpler to
reason with and opens the door (ever so slightly) to adding novel
(wildcard) subtypes to the pipeline via config-only modifications.

Snakefile

@@ -233,19 +233,6 @@ rule files:
 files = rules.files.params
 
 
-def subtypes_by_subtype_wildcard(wildcards):
-    # TODO - shift this to config
-    db = {
-        'h5nx': ['h5n1', 'h5n2', 'h5n3', 'h5n4', 'h5n5', 'h5n6', 'h5n7', 'h5n8', 'h5n9'],
-        'h5n1': ['h5n1'],
-        'h7n9': ['h7n9'],
-        'h9n2': ['h9n2'],
-    }
-    db['h5n1-cattle-outbreak'] = [*db['h5nx']]
-    assert wildcards.subtype in db, (f"Subtype {wildcards.subtype!r} is not defined in the snakemake function "
-        "`subtypes_by_subtype_wildcard` -- is there a typo in the subtype you are targetting?")
-    return(db[wildcards.subtype])
-
 rule download_sequences:
     output:
         sequences = f"data/{S3_SRC.get('name', None)}/sequences_{{segment}}.fasta",
@@ -291,7 +278,7 @@ rule filter_sequences_by_subtype:
     output:
         sequences = "results/{subtype}/{segment}/sequences.fasta",
     params:
-        subtypes=subtypes_by_subtype_wildcard,
+        subtypes=lambda w: config['subtype_lookup'][w.subtype],
     shell:
         """
         augur filter \
@@ -307,7 +294,7 @@ rule filter_metadata_by_subtype:
     output:
         metadata = "results/{subtype}/metadata.tsv",
     params:
-        subtypes=subtypes_by_subtype_wildcard,
+        subtypes=lambda w: config['subtype_lookup'][w.subtype],
     shell:
         """
         augur filter \

gisaid/config.yaml

@@ -37,6 +37,13 @@ s3_src:
 local_ingest: false
 # P.S. To use local ingest files, comment out s3_src and change to local_ingest: fauna
 
+# For subtypes defined as build wildcards (e.g. "h5n1", "h5nx"), list out the subtype values
+# that we'll use to filter the starting metadata's 'subtype' column
+subtype_lookup:
+  h5nx: ['h5n1', 'h5n2', 'h5n3', 'h5n4', 'h5n5', 'h5n6', 'h5n7', 'h5n8', 'h5n9']
+  h5n1: ['h5n1']
+  h7n9: ['h7n9']
+  h9n2: ['h9n2']
 
 #### Parameters which control large overarching aspects of the build
 target_sequences_per_tree: 3000

h5n1-cattle-outbreak/config.yaml

@@ -32,6 +32,10 @@ s3_src:
 local_ingest: false
 # P.S. To use local ingest files, comment out s3_src and change to local_ingest: joined-ncbi (e.g.)
 
+# For subtypes defined as build wildcards (i.e. "h5n1-cattle-outbreak"), list out the subtype values
+# that we'll use to filter the starting metadata's 'subtype' column
+subtype_lookup:
+  h5n1-cattle-outbreak: ['h5n1', 'h5n2', 'h5n3', 'h5n4', 'h5n5', 'h5n6', 'h5n7', 'h5n8', 'h5n9']
 
 #### Parameters which control large overarching aspects of the build
 # Set a high target_sequences_per_tree to capture all circulating strains, as they will be pruned down