From 7bf2094430eda13199cd694a20b40c6493bf6aa1 Mon Sep 17 00:00:00 2001
From: Yueyao Gao <gaoyueya@broadinstitute.org>
Date: Tue, 2 Jul 2024 17:02:56 -0400
Subject: [PATCH] updated the padded command

---
 CNV-Profiler/CNV-Profiler.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CNV-Profiler/CNV-Profiler.wdl b/CNV-Profiler/CNV-Profiler.wdl
index 1678f8d..8dc0a22 100644
--- a/CNV-Profiler/CNV-Profiler.wdl
+++ b/CNV-Profiler/CNV-Profiler.wdl
@@ -121,7 +121,7 @@ task GetPaddedCnvBed {
         source activate env_viz
         python3 <<CODE
         padded_cnv_interval_list = []
-        with open(~{cnvBedFile}, 'r') as f:
+        with open("~{cnvBedFile}", 'r') as f:
             for line in f:
                 chr = line.strip().split('\t')[0]
                 start = line.strip().split('\t')[1]