From acb198eefe99ec21d164d31ec96e7b89731f74b0 Mon Sep 17 00:00:00 2001
From: Thomas Sibley <tsibley@fredhutch.org>
Date: Wed, 25 May 2022 14:00:17 -0700
Subject: [PATCH] Pass the tree rule's mem_mb through to IQ-TREE

While most of our mem_mb definitions are only heuristics for Snakemake's
scheduler and the commands themselves aren't limited or aware of the
mem_mb defined, IQ-TREE *does* support memory limits.

Resolves <https://github.com/nextstrain/ncov/issues/949>.
---
 workflow/snakemake_rules/main_workflow.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk
index fbcbabc76..13ef8e3f7 100644
--- a/workflow/snakemake_rules/main_workflow.smk
+++ b/workflow/snakemake_rules/main_workflow.smk
@@ -811,7 +811,7 @@ rule tree:
         """
         augur tree \
             --alignment {input.alignment} \
-            --tree-builder-args {params.args} \
+            --tree-builder-args {params.args}' --mem {resources.mem_mb}M' \
             {params.exclude_sites} \
             --output {output.tree} \
             --nthreads {threads} 2>&1 | tee {log}