Add avg age and vaccination to nextflu-private builds

nextstrain · Dec 8, 2023 · 8519f65 · 8519f65
1 parent fc95b81
commit 8519f65
Show file tree

Hide file tree

Showing 4 changed files with 48 additions and 1 deletion.
diff --git a/profiles/nextflu-private/antigenic_distances.smk b/profiles/nextflu-private/antigenic_distances.smk
@@ -94,8 +94,25 @@ rule summarize_haplotype_titer_coverage:
             --output-node-data {output.node_data} 2>&1 | tee {log}
         """
 
+rule scores:
+    input:
+        metadata = "builds/{build_name}/metadata.tsv",
+        tree = "builds/{build_name}/{segment}/tree.nwk",
+    output:
+        node_data = "builds/{build_name}/{segment}/scores.json",
+    conda: "../../workflow/envs/nextstrain.yaml"
+    shell:
+        """
+        python3 scripts/scores.py \
+            --metadata {input.metadata} \
+            --tree {input.tree} \
+            --output {output}
+        """
+
 def get_private_node_data(wildcards):
-    node_data = []
+    node_data = [
+        "builds/{build_name}/{segment}/scores.json",
+    ]
 
     # Only try to annotate titer collections for HA.
     if wildcards.segment == "ha":

diff --git a/profiles/nextflu-private/h1n1pdm/ha/auspice_config.json b/profiles/nextflu-private/h1n1pdm/ha/auspice_config.json
@@ -127,6 +127,16 @@
       "title": "Epiweek (CDC)",
       "type": "ordinal"
     },
+    {
+      "key": "avg_age",
+      "title": "Avg age",
+      "type": "continuous"
+    },
+    {
+      "key": "vaccov",
+      "title": "Avg vaccination",
+      "type": "continuous"
+    },
     {
       "key": "egg_hi_cTiter",
       "title": "Antigenic advance (tree, ferret egg HI)",

diff --git a/profiles/nextflu-private/h3n2/ha/auspice_config.json b/profiles/nextflu-private/h3n2/ha/auspice_config.json
@@ -173,6 +173,16 @@
       "title": "Epiweek (CDC)",
       "type": "ordinal"
     },
+    {
+      "key": "avg_age",
+      "title": "Avg age",
+      "type": "continuous"
+    },
+    {
+      "key": "vaccov",
+      "title": "Avg vaccination",
+      "type": "continuous"
+    },
     {
       "key": "cell_fra_dTiter",
       "title": "Antigenic weight (tree, ferret cell FRA)",

diff --git a/profiles/nextflu-private/vic/ha/auspice_config.json b/profiles/nextflu-private/vic/ha/auspice_config.json
@@ -156,6 +156,16 @@
       "title": "Epiweek (CDC)",
       "type": "ordinal"
     },
+    {
+      "key": "avg_age",
+      "title": "Avg age",
+      "type": "continuous"
+    },
+    {
+      "key": "vaccov",
+      "title": "Avg vaccination",
+      "type": "continuous"
+    },
     {
       "key": "egg_hi_cTiter",
       "title": "Antigenic advance (tree, ferret egg HI)",