Use accession for node name but display strain

This is a companion commit to changes in Auspice <nextstrain/auspice#1668>
which allow any node-attr to be used as the tip label and which displays
this tip label in the node hover/click boxes as well as alongside nodes
(at suitable zoom levels). This allows us to drop the `set_final_strain_name`
script and ensures all node names are unique which improves the behaviour
of Auspice

This commit only changes the Nextstrain datasets, not the Nextclade ones

phylogenetic/defaults/clade-i/auspice_config.json

@@ -55,8 +55,12 @@
   "geo_resolutions": [
     "country"
   ],
+  "metadata_columns": [
+    "strain"
+  ],
   "display_defaults": {
     "color_by": "country",
+    "tip_label": "strain",
     "map_triplicate": true,
     "distance_measure": "num_date",
     "transmission_lines": false

phylogenetic/defaults/hmpxv1/auspice_config.json

@@ -60,8 +60,12 @@
   "geo_resolutions": [
     "country"
   ],
+  "metadata_columns": [
+    "strain"
+  ],
   "display_defaults": {
     "color_by": "lineage",
+    "tip_label": "strain",
     "map_triplicate": true,
     "distance_measure": "num_date",
     "transmission_lines": false

phylogenetic/defaults/hmpxv1_big/auspice_config.json

@@ -65,8 +65,12 @@
   "geo_resolutions": [
     "country"
   ],
+  "metadata_columns": [
+    "strain"
+  ],
   "display_defaults": {
     "color_by": "lineage",
+    "tip_label": "strain",
     "map_triplicate": true,
     "distance_measure": "num_date",
     "transmission_lines": false

phylogenetic/defaults/mpxv/auspice_config.json

@@ -70,8 +70,12 @@
   "geo_resolutions": [
     "country"
   ],
+  "metadata_columns": [
+    "strain"
+  ],
   "display_defaults": {
     "color_by": "clade_membership",
+    "tip_label": "strain",
     "map_triplicate": true,
     "distance_measure": "div",
     "transmission_lines": false

phylogenetic/rules/export.smk

@@ -89,8 +89,8 @@ rule export:
         description=config["description"],
         auspice_config=config["auspice_config"],
     output:
-        auspice_json=build_dir + "/{build_name}/raw_tree.json",
-        root_sequence=build_dir + "/{build_name}/raw_tree_root-sequence.json",
+        auspice_json=build_dir + "/{build_name}/tree.json",
+        root_sequence=build_dir + "/{build_name}/tree_root-sequence.json",
     params:
         strain_id=config["strain_id_field"],
     shell:
@@ -107,25 +107,3 @@ rule export:
             --include-root-sequence \
             --output {output.auspice_json}
         """
-
-
-rule final_strain_name:
-    input:
-        auspice_json=build_dir + "/{build_name}/raw_tree.json",
-        metadata=build_dir + "/{build_name}/metadata.tsv",
-        root_sequence=build_dir + "/{build_name}/raw_tree_root-sequence.json",
-    output:
-        auspice_json=build_dir + "/{build_name}/tree.json",
-        root_sequence=build_dir + "/{build_name}/tree_root-sequence.json",
-    params:
-        strain_id=config["strain_id_field"],
-        display_strain_field=config.get("display_strain_field", "strain"),
-    shell:
-        """
-        python3 scripts/set_final_strain_name.py --metadata {input.metadata} \
-                --metadata-id-columns {params.strain_id} \
-                --input-auspice-json {input.auspice_json} \
-                --display-strain-name {params.display_strain_field} \
-                --output {output.auspice_json}
-        cp {input.root_sequence} {output.root_sequence}
-        """