--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build-and-run-job-scripts.sh	Fri Dec 14 00:40:15 2018 -0500
@@ -0,0 +1,45 @@
+# run job scripts within the tool outputs directory
+cd ${REPORT_FILES_PATH}
+
+#========== build and run job 1 script ============
+cat >temp.sh <<EOF
+skewer \\
+	${X_A} \\
+	${X_B} \\
+	-x ${X_x} \\
+	-y ${X_y} \\
+	-m ${X_m} \\
+	-r ${X_r} \\
+	-d ${X_D} \\
+	-q ${X_q} \\
+	-Q ${X_Q} \\
+	-l ${X_l} \\
+	-j ${X_j} \\
+	-M ${X_M} \\
+	-b ${X_b} \\
+	-c ${X_b} \\
+	-n ${X_n} \\
+	-u ${X_u} \\
+	-f ${X_f} \\
+	-z ${X_z} \\
+	-qiime ${X_E} \\
+	-quiet ${X_F} \\
+	-i ${X_i} \\
+	-o trim > skewer.log.txt 2>&1
+EOF
+
+# remove empty input lines
+grep -v '\-M  \\' temp.sh |\
+  grep -v 'None' |\
+  grep -v 'NO_ARGUMENT_NO' |\
+  sed 's/NO_ARGUMENT_YES//g' > job-1-script.sh
+
+rm temp.sh
+
+# run job 1 script
+sh job-1-script.sh
+
+# rename log file
+if [ -e trim-trimmed.log ]; then
+  cp trim-trimmed.log trim-trimmed.txt
+fi
\ No newline at end of file