Adjust raxml to speed up tree building

Currently tree building for the global tree took ~4 hours (4:35:46). GitHub
Actions has a 6hour runtime limit. Changing some of the parameters with the
goal of speeding up tree building without losing quality of trees.

Testing:

1. `-f b` to `-f a` to use rapid bootstrapping
2. Use `-N 100` to set the number of bootstraps to 100
3. Use `-x 12345` to set the random seed for bootstrapping
4. Add `-i auto` to automatically determine the best starting tree

phylogenetic/rules/construct_phylogeny.smk

@@ -30,12 +30,15 @@ rule tree:
     benchmark:
         "benchmarks/tree.txt"
     threads: workflow.cores
+    params:
+        raxml_tree_builder_args="-f a -m GTRCAT -p 235813 -x 12345 -N 100 -i auto"
     shell:
         """
         augur tree \
             --alignment {input.alignment} \
             --output {output.tree} \
             --method raxml \
+            --tree-builder-args {params.raxml_tree_builder_args:q} \
             --nthreads {threads:q} 2>&1 | tee {log}
         """