--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build-and-run-job-scripts.sh	Sun Dec 30 12:52:51 2018 -0500
@@ -0,0 +1,23 @@
+# run job scripts within the tool outputs directory
+cd ${REPORT_FILES_PATH}
+
+#========== build and run job 1 script ============
+cat >htseq-count.sh <<EOF
+ htseq-count \\
+    $(echo ${X_A} | sed 's/,/ /g') \\
+    ${X_G} \\
+    -f ${X_f} \\
+    -r ${X_r} \\
+    -s ${X_S} \\
+    -a ${X_a} \\
+    -t ${X_T} \\
+    -i ${X_i} \\
+    -m ${X_m} > htseq-counts-raw.txt
+
+  grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' htseq-counts-raw.txt > counts.txt
+
+EOF
+
+# run job 1 script
+sh htseq-count.sh
+