diff --git a/phylogenetic/rules/construct_phylogeny.smk b/phylogenetic/rules/construct_phylogeny.smk index 60da9a2..1e6c489 100644 --- a/phylogenetic/rules/construct_phylogeny.smk +++ b/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} """