Small tweaks to Nextclade builds (#291)

nextstrain · Nov 16, 2024 · af33cf2 · af33cf2
1 parent 0418e5d
commit af33cf2
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/nextclade/Snakefile b/nextclade/Snakefile
@@ -315,7 +315,7 @@ rule tree:
             --alignment {input.alignment} \
             --output {output.tree} \
             --nthreads 3 \
-            --tree-builder-args '--redo --pathogen-force --tree-search EXHAUSTIVE  --output-multifurcating-tree --make-consistent'
+            --tree-builder-args '--polytomy --pathogen-force --tree-search EXHAUSTIVE --output-multifurcating-tree --make-consistent'
         """
 
 

diff --git a/nextclade/config/config.yaml b/nextclade/config/config.yaml
@@ -8,8 +8,8 @@ clade-iib:
 clade-i:
   root: "reconstructed_ancestral_mpox"
   min_date: ""
-  exclude_where: "--exclude-where clade!=I"
-  subsampling: "--subsample-max-sequences 300 --group-by clade lineage year month country --probabilistic-sampling"
+  exclude_where: "--exclude-where clade=II clade=IIa clade=IIb clade=outgroup"
+  subsampling: "--subsample-max-sequences 1000 --group-by clade lineage year month country --probabilistic-sampling"
   annotation: "resources/clade-i/genome_annotation.gff3"
   genes: "resources/clade-i/genes.txt"
   general_include: "resources/clade-i/include_accessions.txt"
@@ -18,7 +18,7 @@ all-clades:
   root: "reconstructed_ancestral_mpox"
   min_date: ""
   exclude_where: ""
-  subsampling: "--subsample-max-sequences 1000 --group-by clade lineage year month country --probabilistic-sampling"
+  subsampling: "--subsample-max-sequences 2000 --group-by clade lineage year month country --probabilistic-sampling"
   general_include: "resources/include_accessions.txt"
 
 lineage-b.1: