From 91a56630dc57bb634b83de364399b6709db51154 Mon Sep 17 00:00:00 2001
From: Chienchi Lo <chien-chi@pn2034281.lanl.gov>
Date: Wed, 13 Apr 2022 16:09:02 -0600
Subject: [PATCH] fix file extension

---
 jgi_assembly.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jgi_assembly.wdl b/jgi_assembly.wdl
index 4a2866c..cea7c4e 100755
--- a/jgi_assembly.wdl
+++ b/jgi_assembly.wdl
@@ -259,7 +259,7 @@ task read_mapping_pairs{
         reformat.sh -Xmx${default="105G" memory} in=${filename_unsorted} out=${filename_outsam} overwrite=true
         cat ${filename_errlog} | grep 'Percent mapped' | perl -ne 'print "#$_"' > mapping_stats.txt
         cat ${filename_cov} >> mapping_stats.txt
-        cp mapping_stats ${filename_cov}
+        cp mapping_stats.txt ${filename_cov}
         rm $mapping_input
     }
     output{