comparison build-and-run-job-scripts.sh @ 12:1a7af4f6b101 draft

planemo upload commit 61448862dc9016969191967aeefb7f7acce1e1f9-dirty

11:70de0b9c4c76

# run job scripts within the tool outputs directory
cd ${REPORT_FILES_PATH}

#========== build and run job 1 script ============
cat >job-1-script.sh <<EOF
skewer \\
	${X_A} \\
	${X_B} \\
	-x ${X_x} \\
	-y ${X_y} \\

	-f ${X_f} \\
	-z ${X_z} \\
	-qiime ${X_E} \\
	-quiet ${X_F} \\
	-i ${X_i} \\
	-o trim > /dev/null 2>&1
EOF

# remove empty input lines
grep -v '\-M  \\' temp.sh |\
  grep -v 'None' |\

12:1a7af4f6b101

# 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} \\

	-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' |\