Make small tweaks to Nextclade datasets to align with hot-fixes (#355)

* Don't strip node attrs for clade-i build

* Add placement prior

* rec2025 -> recombinant

Author: corneliusroemer

nextclade/resources/clade-i/auspice_config_patch.json

@@ -4,10 +4,6 @@
     "path": "/title",
     "value": "Nextclade reference tree for Mpox virus (Clade I)"
   },
-  {
-    "op": "remove",
-    "path": "/extensions/nextclade/clade_node_attrs"
-  },
   {
     "op": "replace",
     "path": "/extensions/nextclade/placement_mask_ranges",

nextclade/scripts/clades_renaming.py

@@ -33,7 +33,7 @@
                 case "Ib":
                     outbreak_name = "sh2023"
                 case "Ib/IIb":
-                    outbreak_name = "rec2025"
+                    outbreak_name = "recombinant"
         elif old_clade_name == "sh2024":
             clade_name = "Ia"
             outbreak_name = old_clade_name
@@ -52,12 +52,19 @@
             outbreak_name = "sh2017"
             lineage_name = old_clade_name
 
-        new_node_data[name] = {
+        node_data = {
             "clade_membership": clade_name,
             "outbreak": outbreak_name,
             "lineage": lineage_name,
         }
 
+        # Add placement prior for Ib/IIb recombinants
+        # To discourage attachment of short sequences to this clade
+        if clade_name == "Ib/IIb":
+            node_data["placement_prior"] = -11.0
+
+        new_node_data[name] = node_data
+
     new_branch_labels = {}
 
     for name, node in data["branches"].items():