From fae01fb4b2ea1a0fbd7823750065b6f40dd8bc90 Mon Sep 17 00:00:00 2001
From: Ryan Routsong <routsongrm@nih.gov>
Date: Thu, 8 Feb 2024 13:33:53 -0500
Subject: [PATCH] fix: remove -r from snakemake

---
 scripts/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/utils.py b/scripts/utils.py
index 4c93748..e8a22a8 100644
--- a/scripts/utils.py
+++ b/scripts/utils.py
@@ -266,7 +266,7 @@ def exec_pipeline(configs, dry_run=False, local=False):
         top_env['SNK_CONFIG'] = str(config_file.absolute())
         top_env['SINGULARITY_CACHEDIR'] = str(Path(this_config['out_to'], '.singularity').absolute())
         this_cmd = [
-            "snakemake", "-p", "-r",
+            "snakemake", "-p",
             "--use-singularity",
             "--rerun-incomplete",
             "--keep-incomplete",