nextclade: switch IQ tree to pathogen mode, add H3 includes

nextstrain · Jan 4, 2025 · 37738f8 · 37738f8
1 parent 2146f87
commit 37738f8
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diff --git a/nextclade/Snakefile b/nextclade/Snakefile
@@ -236,7 +236,7 @@ rule tree:
             --alignment {input.alignment} \
             --output {output.tree} \
             --nthreads {threads} \
-            --tree-builder-args '-ninit 10 -n 4 -czb' \
+            --tree-builder-args '-ninit 10 -n 4 -czb --pathogen-force' \
             > /dev/null
         """
 

diff --git a/nextclade/dataset_config/h3n2/includes.txt b/nextclade/dataset_config/h3n2/includes.txt
@@ -46,3 +46,17 @@ A/Bangladesh/1079/2014
 A/Bangladesh/3039/2017
 A/SouthAfrica/R06488/2017
 A/Ehime/21/2017
+
+
+# J.2 proposals
+A/Croatia/10136RV/2023-egg
+A/DistrictOfColumbia/27/2023
+A/Colorado/142/2024
+A/Guyane/318/2024
+A/Ohio/253/2024
+A/India/Pune-NIV234429/2023
+A/Shanghai-Jingan/11698/2024
+A/VinaDelMar/44363/2024
+A/Bangladesh/4002/2024
+A/HongKong/2468/2024
+A/Ghana/FS-24-3952/2024