Merge pull request #197 from nextstrain/add-nextclade-extension

Add Nextclade extension to public builds
nextstrain · Nov 19, 2024 · 20c935b · 20c935b
2 parents fc325b3 + afe2cd9
commit 20c935b
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Showing 10 changed files with 118 additions and 18 deletions.
diff --git a/config/h1n1pdm/auspice_config.json b/config/h1n1pdm/auspice_config.json
@@ -163,5 +163,16 @@
   "metadata_columns": [
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}
diff --git a/config/h1n1pdm/ha/auspice_config.json b/config/h1n1pdm/ha/auspice_config.json
@@ -267,5 +267,16 @@
     "gisaid_strain",
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}
diff --git a/config/h1n1pdm/na/auspice_config.json b/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."
+        }
+      ]
+    }
+  }
+}
diff --git a/config/h3n2/auspice_config.json b/config/h3n2/auspice_config.json
@@ -173,5 +173,16 @@
   "metadata_columns": [
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}
diff --git a/config/h3n2/ha/auspice_config.json b/config/h3n2/ha/auspice_config.json
@@ -261,5 +261,16 @@
     "gisaid_strain",
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}
diff --git a/config/h3n2/na/auspice_config.json b/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."
+        }
+      ]
+    }
+  }
+}
diff --git a/config/vic/auspice_config.json b/config/vic/auspice_config.json
@@ -148,5 +148,16 @@
   "metadata_columns": [
     "accession_ha",
     "accession_na"
-  ]
-}
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "subclade",
+          "displayName": "Subclade",
+          "description": "Experimental fine-grained subclade annotation."
+        }
+      ]
+    }
+  }
+}
diff --git a/config/vic/ha/auspice_config.json b/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."
+        }
+      ]
+    }
+  }
+}
diff --git a/config/vic/na/auspice_config.json b/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."
+        }
+      ]
+    }
+  }
+}
diff --git a/profiles/ci/builds.yaml b/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