--- a/wrapper.sh	Thu Dec 15 09:44:17 2016 -0500
+++ b/wrapper.sh	Fri Dec 16 09:53:09 2016 -0500
@@ -6,7 +6,7 @@
 log=$3 #becomes the main html page at the end
 outdir=$4
 output="$outdir/index.html" #copied to $log location at the end
-title=$5
+title="$5"
 include_fr1=$6
 functionality=$7
 unique=$8
@@ -37,8 +37,8 @@
 elif [[ "$type" == *"XZ compressed data"* ]] ; then
 	echo "ZX archive"
 	echo "tar -xJf $input -C $PWD/files/"
-	mkdir -p $PWD/files/$title
-	tar -xJf $input -C $PWD/files/$title
+	mkdir -p "$PWD/files/$title"
+	tar -xJf $input -C "$PWD/files/$title"
 fi
 
 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
@@ -439,7 +439,7 @@
 	mkdir $outdir/baseline/IGG
 	if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
 		cd $outdir/baseline/IGG
-		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
+		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
 	else
 		echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
 	fi