Update run.sh

examples/pipelines/PirusBasic/run.sh

@@ -6,7 +6,7 @@ DB="/pipeline/db/"
 OUT="/pipeline/outputs/"
 IN="/pipeline/inputs/"
 LOG="/pipeline/logs/"
-RUN="/pipeline/job/"
+JOB="/pipeline/job/"
 
 # Dynamic parameters loaded from config.json
 FILE1=`cat ${IN}config.json | jq ".job.file1"`
@@ -21,7 +21,7 @@ NOTIFY_URL=`sed -e 's/^"//' -e 's/"$//' <<<"$NOTIFY_URL"`
 
 echo "START Plugin de test"
 echo "===================="
-cd ${RUN}
+cd ${JOB}
 pwd
 ls -l
 
@@ -47,12 +47,12 @@ echo "Loop"
 echo "===="
 for i in `seq 0 ${DURATION}`
 do
-        echo "$i %"
-        curl -X POST -d '{"progress" : {"min":"0", "max":"'${DURATION}'", "value":"'${i}'", "label" : "'${i}' / '${DURATION}'"}}' ${NOTIFY_URL}
-        if [ ${CRASH} = true ] && [ $i = 24]; then
-                return 500
-        fi
-        sleep 1
+    echo "$i %"
+    curl -X POST -d '{"progress" : {"min":"0", "max":"'${DURATION}'", "value":"'${i}'", "label" : "'${i}' / '${DURATION}'"}}' ${NOTIFY_URL}
+    if [ ${CRASH} = true ] && [ $i = 24]; then
+        return 500
+    fi
+    sleep 1
 done
 
 echo "Create output file"
@@ -62,4 +62,3 @@ zcat ${DB}/hg19/refGene.txt.zip | awk '$9 > 50{print $13}' >>  ${OUT}${OUTPUT}
 
 echo "Done"
 echo "===="
-