phylogenetic: Use strain as default tip label

Testing <nextstrain/auspice#1668> Following changes made in mpox <nextstrain/mpox@4a268ba>
nextstrain · Aug 26, 2024 · 8fb92b5 · 8fb92b5
1 parent 418327a
commit 8fb92b5
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Showing 3 changed files with 6 additions and 72 deletions.
diff --git a/phylogenetic/defaults/auspice_config.json b/phylogenetic/defaults/auspice_config.json
@@ -46,8 +46,12 @@
     "region"
   ],
   "display_defaults": {
-    "map_triplicate": true
+    "map_triplicate": true,
+    "tip_label": "strain"
   },
+  "metadata_columns": [
+    "strain"
+  ],
   "filters": [
     "country",
     "region",

diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
@@ -38,7 +38,7 @@ rule export:
         auspice_config = "defaults/auspice_config.json",
         description = "defaults/description.md"
     output:
-        auspice_json = "results/raw_zika.json"
+        auspice_json = "auspice/zika.json"
     params:
         strain_id = config.get("strain_id_field", "strain"),
     shell:
@@ -54,22 +54,3 @@ rule export:
             --include-root-sequence-inline \
             --output {output.auspice_json}
         """
-
-rule final_strain_name:
-    input:
-        auspice_json="results/raw_zika.json",
-        metadata="data/metadata_all.tsv"
-    output:
-        auspice_json="auspice/zika.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}
-        """
diff --git a/phylogenetic/scripts/set_final_strain_name.py b/phylogenetic/scripts/set_final_strain_name.py