--- a/wrapper.sh	Fri Nov 05 13:41:03 2021 +0000
+++ b/wrapper.sh	Tue Jan 25 11:28:29 2022 +0000
@@ -895,15 +895,26 @@
 echo "---------------- remove_files----------------"
 echo "---------------- remove_files----------------<br />" >> $log
 
-rm -r -v -f results/baseline
-rm -r -v -f files
-filename='remove_files.txt'
+rm -r -v -f $outdir/baseline
+rm -r -v -f $PWD/files
+rm -v $PWD/aa.txt
+rm -v $PWD/aa_change_stats.txt
+rm -v $PWD/gapped_aa.txt
+rm -v $PWD/gapped_nt.txt
+rm -v $PWD/hotspots.txt
+rm -v $PWD/junction.txt
+rm -v $PWD/mutationanalysis.txt
+rm -v $PWD/mutationstats.txt
+rm -v $PWD/sequences.txt
+rm -v $PWD/summary.txt
+rm -v $PWD/Rplots.pdf
+
+filename="$dir/remove_files.txt"
 
 while read file; do
-    rm -v -f $file
+    rm -v -f $outdir/$file
 done < "$filename"
 
-
 echo "---------------- Done! ----------------"
 echo "---------------- Done! ----------------<br />" >> $outdir/log.html