Generate and export GenoFLU results for fauna

Includes both the per-segment results and the whole-genome genotype/ constellation
nextstrain · Feb 23, 2025 · 956dd12 · 956dd12
1 parent d2d08ad
commit 956dd12
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Showing 6 changed files with 30 additions and 1 deletion.
diff --git a/Snakefile b/Snakefile
@@ -652,6 +652,15 @@ rule auspice_config:
                 auspice_config['colorings'][division_idx]["title"] += " (inferred)"
             else:
                 auspice_config['display_defaults']['distance_measure'] = "div"
+
+        # If we have a coloring for 'genoflu' and we're not a genome build then export the genoflu call for the segment
+        genoflu_idx = next((i for i,c in enumerate(auspice_config['colorings']) if c['key']=='genoflu'), None)
+        if wildcards.segment!='genome' and genoflu_idx is not None:
+            auspice_config['colorings'].insert(genoflu_idx+1, {
+                    "key": f"genoflu_{wildcards.segment.upper()}",
+                    "title": f"GenoFLU ({wildcards.segment.upper()} segment)",
+                    "type": "categorical",
+                })
         with open(output.auspice_config, 'w') as fh:
             json.dump(auspice_config, fh, indent=2)
 

diff --git a/config/h5n1/auspice_config_h5n1.json b/config/h5n1/auspice_config_h5n1.json
@@ -60,6 +60,11 @@
       "title": "Provisional LABEL Clade",
       "type": "categorical"
     },
+    {
+      "key": "genoflu",
+      "title": "GenoFLU constellation",
+      "type": "categorical"
+    },
     {
       "key": "gisaid_clade",
       "title": "GISAID Clade",

diff --git a/config/h5nx/auspice_config_h5nx.json b/config/h5nx/auspice_config_h5nx.json
@@ -60,6 +60,11 @@
       "title": "Provisional LABEL Clade",
       "type": "categorical"
     },
+    {
+      "key": "genoflu",
+      "title": "GenoFLU constellation",
+      "type": "categorical"
+    },
     {
       "key": "gisaid_clade",
       "title": "GISAID Clade",

diff --git a/config/h7n9/auspice_config_h7n9.json b/config/h7n9/auspice_config_h7n9.json
@@ -35,6 +35,11 @@
       "title": "Host",
       "type": "categorical"
     },
+    {
+      "key": "genoflu",
+      "title": "GenoFLU constellation",
+      "type": "categorical"
+    },
     {
       "key": "furin_cleavage_motif",
       "title": "Furin Cleavage Motif",

diff --git a/config/h9n2/auspice_config_h9n2.json b/config/h9n2/auspice_config_h9n2.json
@@ -35,6 +35,11 @@
       "title": "Host",
       "type": "categorical"
     },
+    {
+      "key": "genoflu",
+      "title": "GenoFLU constellation",
+      "type": "categorical"
+    },
     {
       "key": "furin_cleavage_motif",
       "title": "Furin Cleavage Motif",

diff --git a/ingest/defaults/config.yaml b/ingest/defaults/config.yaml
@@ -14,4 +14,4 @@ s3_dst:
 path_to_fauna: ../../fauna
 
 genoflu:
-  fauna: false
+  fauna: true