[cattle-outbreak] add genome clock filter

This should help remove outliers unrelated to the cattle-outbreak,
especially as the clock signal is worse than it might otherwise be for
these outliers due to our enforcing of the root strain.

See related discussion on slack <https://bedfordlab.slack.com/archives/CD84ELG0N/p1733773815454369>

Snakefile

@@ -203,7 +203,9 @@ def refine_clock_rates(w):
     return f"--clock-rate {info[w.segment][0]} --clock-std-dev {info[w.segment][1]}"
 
 def refine_clock_filter(w):
-    filter = get_config('refine', 'clock_filter_iqd', w)
+    filter = get_config('refine', 'genome_clock_filter_iqd', w) \
+        if w.segment=='genome' \
+        else get_config('refine', 'clock_filter_iqd', w)
     return f"--clock-filter-iqd {filter}" if filter else ""
 
 

config/h5n1-cattle-outbreak.yaml

@@ -75,6 +75,8 @@ refine:
   coalescent: const
   date_inference: marginal
 
+  genome_clock_filter_iqd:
+    FALLBACK: 3
   clock_filter_iqd:
     FALLBACK: false