adding script to produce summary table after preproc

Author: fasnicar

preprocessing/make_sample_list.sh

@@ -0,0 +1,36 @@
+#! /bin/bash
+
+
+if [ $# -ne 2 ]; then
+    echo "No arguments";
+    echo "Usage:";
+    echo "./make_sample_list.sh <output_file> <input_folder>";
+    exit 1;
+fi;
+
+if [ "$1" == "" ]; then
+    echo "Output file parameter is empty";
+    exit 1;
+fi;
+
+if [ "$2" == "" ]; then
+    echo "Input folder parameter is empty";
+    exit 1;
+fi;
+
+if [ -f $1 ]; then
+    echo "Output file already exists";
+    exit 1;
+fi;
+
+if [ ! -d $2 ]; then
+    echo "Input folder does not exists";
+    exit 1;
+fi;
+
+echo -n "Writing output file: $1 ... ";
+
+echo -e "#sample\tn_cleaned_reads" > $1;
+tail -n1 $2/*/*_summary.stats | grep -v "^$" | grep -v "^==>" | cut -f1,3 >> $1;
+
+echo "Done!";