No need for redo, it's now set by default

Change sampling now that we have more lineage A sequences
nextstrain · Nov 14, 2024 · be63389 · be63389
1 parent 442a5a5
commit be63389
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diff --git a/phylogenetic/defaults/hmpxv1/config.yaml b/phylogenetic/defaults/hmpxv1/config.yaml
@@ -67,7 +67,7 @@ subsample:
       - B.1.23
   b1:
     group_by: "--group-by country year"
-    sequences_per_group: "--subsample-max-sequences 100"
+    sequences_per_group: "--subsample-max-sequences 300"
     other_filters: "--exclude-where outbreak!=hMPXV-1 clade!=IIb"
 
 ## align

diff --git a/phylogenetic/rules/construct_phylogeny.smk b/phylogenetic/rules/construct_phylogeny.smk
@@ -30,7 +30,6 @@ rule tree:
         augur tree \
             --alignment {input.alignment} \
             --exclude-sites {input.tree_mask} \
-            --tree-builder-args="-redo" \
             --output {output.tree} \
             --nthreads {threads}
         """