From 81737302e33d28c4312d4375956d7a37b49d1035 Mon Sep 17 00:00:00 2001
From: annahoge <36393555+annahoge@users.noreply.github.com>
Date: Thu, 21 Nov 2019 08:07:20 -0800
Subject: [PATCH] Made cp recursive.

---
 scripts/snakemake/TitanCNA.snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/snakemake/TitanCNA.snakefile b/scripts/snakemake/TitanCNA.snakefile
index 1d037d7..8537afb 100644
--- a/scripts/snakemake/TitanCNA.snakefile
+++ b/scripts/snakemake/TitanCNA.snakefile
@@ -113,7 +113,7 @@ rule copyOptSolution:
 		for i in `cut -f11 {input} | grep -v "path"`;
 		do
 			echo -e "Copying $curDir/${{i}} to {output}"
-			cp ${{curDir}}/${{i}}* {output}
+			cp -r ${{curDir}}/${{i}}* {output}
 		done		
 		"""