Add Nextclade extension to public builds

Adds Nextclade extension with "subclade" annotation to Auspice config
for all public builds, allowing users to get these subclade annotations
from Nextclade for any public tree.

To test this functionality, I added subclade annotations to the CI build
and confirmed that the extension worked as expected by uploading the CI
Auspice JSON to the staging server before and after I included the
extension in the JSON.

config/h1n1pdm/auspice_config.json

@@ -158,5 +158,16 @@
   "metadata_columns": [
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}

config/h1n1pdm/ha/auspice_config.json

@@ -263,5 +263,16 @@
     "gisaid_strain",
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}

config/h1n1pdm/na/auspice_config.json

@@ -196,5 +196,16 @@
     "gisaid_strain",
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}

config/h3n2/auspice_config.json

@@ -168,5 +168,16 @@
   "metadata_columns": [
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}

config/h3n2/ha/auspice_config.json

@@ -253,5 +253,16 @@
     "gisaid_strain",
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}

config/h3n2/na/auspice_config.json

@@ -209,5 +209,16 @@
     "gisaid_strain",
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}

config/vic/auspice_config.json

@@ -143,5 +143,16 @@
   "metadata_columns": [
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}

config/vic/ha/auspice_config.json

@@ -228,5 +228,16 @@
     "gisaid_strain",
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}

config/vic/na/auspice_config.json

@@ -221,5 +221,16 @@
     "gisaid_strain",
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}

profiles/ci/builds.yaml

@@ -50,6 +50,7 @@ builds:
       annotation: "config/h3n2/{segment}/genemap.gff"
       tree_exclude_sites: "config/h3n2/{segment}/exclude-sites.txt"
       clades: "config/h3n2/ha/clades.tsv"
+      subclades: "config/h3n2/{segment}/subclades.tsv"
       min_date: "12Y"
       auspice_config: "config/h3n2/auspice_config.json"
       enable_titer_models: true