Filter cattle-outbreak using GenoFLU B3.13

The previous approach relied on broad filtering -- minimum date of 2024,
region of North America -- a hardcoded exclude list and a clock filter.
As the diversity of sequences increased the clock-filter became less
effective and ultimately dropped all the desired strains. See
<#133> for more.

We now use GenoFLU constellations and can relax the date and region
filters accordingly. This relaxation didn't result in any
non-North-American samples included but did add one B3.13 genome from
2023: 'A/Goose/USA/23-038138-001-original/2023'.

These changes to filtering will also apply to the D1.1 builds, but
testing indicates no changes.

The segment-level approach is not addressed here, but could be similarly
adjusted to use the GenoFLU matching on the segment level. Specifically,
<https://github.com/nextstrain/avian-flu/pull/138/files> adds the
segment-level annotations and the expanded constellation is:
B3.13 = PA:ea1, HA:ea1, PB1:am4, MP:ea1, NA:ea1, PB2:am2.2, NP:am8, NS:am1.1

Closes #133

Snakefile

@@ -64,18 +64,21 @@ files = rules.files.params
 
 def subtypes_by_subtype_wildcard(wildcards):
 
+    # TODO - this function does more than strictly subtype filtering as certain builds filter to
+    # GenoFLU constellation, and in the future this may be expanded. We should rename the function!
     # TODO XXX - move to configs (started in https://github.com/nextstrain/avian-flu/pull/104 but
     # We should make the entire query config-definable)
     if wildcards.subtype == 'h5n1-d1.1':
         return "genoflu in 'D1.1'"
+    elif wildcards.subtype == 'h5n1-cattle-outbreak':
+        return "genoflu in 'B3.13'"
 
     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(f"subtype in [{', '.join([repr(s) for s in db[wildcards.subtype]])}]")

config/h5n1-cattle-outbreak/auspice_config_h5n1-cattle-outbreak.json

@@ -79,6 +79,11 @@
       "title": "Subtype",
       "type": "categorical"
     },
+    {
+      "key": "genoflu",
+      "title": "GenoFLU constellation",
+      "type": "categorical"
+    },
     {
       "key": "h5_label_clade",
       "title": "Provisional LABEL Clade",

config/h5n1-cattle-outbreak/dropped_strains_h5n1-cattle-outbreak.txt

@@ -9,6 +9,10 @@ A/Cattle/USA/24-009027-002-v/2024 # Duplicate of A/cattle/Michigan/24-009027-002
 A/PEFA/USA/24-005915-001-original/2024 # Duplicate of A/Peregrinefalcon/California/24-005915-001/2024
 A/Skunk/USA/24-006483-001-original/2024 # Duplicate of A/skunk/NewMexico/24-006483-001/2024
 
+# Many of the following exclude strains were added prior to filtering on GenoFLU
+# constellation B3.13 and thus may not be applicable any more. We can clean these up
+# in the future if desired.
+
 # Dropping these strains from include due to excess private mutations
 A/cattle/NorthCarolina/24-010327-002/2024
 A/cattle/Texas/24-009495-007/2024
@@ -246,30 +250,3 @@ A/westerngull/California/24-004708-001/2024
 A/WesternGull/USA/24-004708-001-original/2024
 A/WesternSandpiper/USA/24-004707-001-original/2024
 A/woodduck/NorthCarolina/W24-026/2024
-
-# D1.1 spillover 
-A/StripedSkunk/WA/W240530074-2-1/2024
-A/CATTLE/USA/25-002645-006/2025
-A/CATTLE/USA/25-002645-005/2025
-A/CATTLE/USA/25-002645-004/2025
-A/CATTLE/USA/25-002645-003/2025
-A/chicken/AR/24-037983-003-original/2024
-A/chicken/AR/24-037983-001-original/2024
-A/chicken/AR/24-037983-002-original/2024
-A/chicken/MN/24-038159-002-original/2024
-A/Duck/MN/24-038159-001-original/2024
-A/goose/MN/24-038159-004-original/2024
-A/Turkey/MN/24-035355-002-original/2024
-A/Turkey/MN/24-035355-001-original/2024
-A/Turkey/MN/24-035521-001-original/2024
-A/Turkey/MN/24-035524-003-original/2024
-A/Turkey/MN/24-035524-004-original/2024
-A/Turkey/MN/24-035524-001-original/2024
-A/Turkey/MN/24-035524-002-original/2024
-A/Turkey/MN/24-034932-001-original/2024
-A/Turkey/MN/24-034932-003-original/2024
-A/Turkey/MN/24-034932-002-original/2024
-A/Turkey/MN/24-035355-003-original/2024
-A/Turkey/MN/24-036792-002-original/2024
-A/Turkey/MN/24-036792-003-original/2024
-A/Turkey/MN/24-036792-001-original/2024

rules/cattle-flu.smk

@@ -14,9 +14,6 @@ rule filter_segments_for_genome:
         exclude = config['dropped_strains'],
     output:
         sequences = "results/{subtype}/{segment}/{time}/filtered_{genome_seg}.fasta"
-    params:
-        min_date = "2024-01-01",
-        query = 'region == "North America"'
     wildcard_constraints:
         subtype = 'h5n1-cattle-outbreak|h5n1-d1.1',
         segment = 'genome',
@@ -29,8 +26,6 @@ rule filter_segments_for_genome:
             --metadata {input.metadata} \
             --include {input.include} \
             --exclude {input.exclude} \
-            --min-date {params.min_date} \
-            --query {params.query:q} \
             --output-log {log} \
             --output-sequences {output.sequences}
         """