diff --git a/nextclade/Snakefile b/nextclade/Snakefile index a2aebcc..9eabd19 100644 --- 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 index c0d6c23..66daaf5 100644 --- 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