Try building all gene trees

An example commit for building all gene trees. Uncertain if this is useful.
nextstrain · Jun 4, 2024 · ae45506 · ae45506
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commit ae45506
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Showing 2 changed files with 12 additions and 1 deletion.
diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
@@ -1,6 +1,6 @@
 configfile: "defaults/config_zika.yaml"
 
-genes = ['genome', 'ENV']
+genes = ['genome', 'ENV', 'CA', 'PRO', 'MP', 'NS1', 'NS2A', 'NS2B', 'NS3', 'NS4A', '2K', 'NS4B', 'NS5']
 
 wildcard_constraints:
     gene = "|".join(genes)

diff --git a/phylogenetic/defaults/config_zika.yaml b/phylogenetic/defaults/config_zika.yaml
@@ -13,6 +13,17 @@ filter:
   min_length:
     genome: 5385
     ENV: 1000
+    CA: 120
+    PRO: 90
+    MP: 70
+    NS1: 350
+    NS2A: 220
+    NS2B: 130
+    NS3: 610
+    NS4A: 120
+    2K: 23
+    NS4B: 250
+    NS5: 903
 
 refine:
   coalescent: "opt"