Build the tree with multiple threads
As with the augur align rule, this uses Snakemake's built-in threads keyword to
specify a default number of threads to use for tree building. This commit
specifically sets number of threads to 4 instead of using augur tree's default
of 1 thread.
@@ -165,11 +165,13 @@ rule tree:
alignment = rules.mask.output.alignment
output:
tree = "results/tree_raw.nwk"
+ threads: 4
shell:
"""
augur tree \
--alignment {input.alignment} \
- --output {output.tree}
+ --output {output.tree} \
+ --nthreads {threads}
"""
rule refine:
