Update Jenkinsfile

Jenkinsfile

@@ -12,10 +12,10 @@ pipeline{
 
 	// Set output folder name where files generated by step will be output.
     	environment {
-        	OUTPUT_FOLDER = "diagram"
-		ECR_URL = 'public.ecr.aws/reactome/diagram-converter'
-		CONT_NAME = 'diagram_converter_container'
-		CONT_ROOT = '/opt/diagram-converter'
+            OUTPUT_FOLDER = "diagram"
+            ECR_URL = 'public.ecr.aws/reactome/diagram-converter'
+            CONT_NAME = 'diagram_converter_container'
+            CONT_ROOT = '/opt/diagram-converter'
     	}
 
 	stages{
@@ -27,7 +27,7 @@ pipeline{
 				}
 			}
 		}
-		
+
 		stage('Setup: Pull and clean docker environment'){
 			steps{
 				sh "docker pull ${ECR_URL}:latest"
@@ -45,12 +45,13 @@ pipeline{
 				script{
 				    def releaseVersion = utils.getReleaseVersion()
 					sh "mkdir -p ${env.OUTPUT_FOLDER}"
+					sh "rm -rf ${env.OUTPUT_FOLDER}/*"
+					sh "mkdir -p reports"
+					sh "rm -rf reports/*"
 					withCredentials([usernamePassword(credentialsId: 'mySQLUsernamePassword', passwordVariable: 'mysqlPass', usernameVariable: 'mysqlUser')]){
 						withCredentials([usernamePassword(credentialsId: 'neo4jUsernamePassword', passwordVariable: 'neo4jPass', usernameVariable: 'neo4jUser')]){
 				 			sh """\
-							    docker run -v reports:${CONT_ROOT}/reports -v ${env.OUTPUT_FOLDER}:${CONT_ROOT}/${env.OUTPUT_FOLDER} --net=host --name ${CONT_NAME} \\
-						               ${ECR_URL}:latest \\
-						               /bin/bash -c 'java -Dlogback.configurationFile=src/main/resources/logback.xml -jar target/diagram-converter-exec.jar --graph_user $neo4jUser --graph_password $neo4jPass --rel_user $mysqlUser --rel_password $mysqlPass --rel_database ${env.REACTOME_DB} --output ./${env.OUTPUT_FOLDER}'
+							    docker run -v \$(pwd)/reports:${CONT_ROOT}/reports -v \$(pwd)/${env.OUTPUT_FOLDER}:${CONT_ROOT}/${env.OUTPUT_FOLDER} --net=host --name ${CONT_NAME} ${ECR_URL}:latest /bin/bash -c 'java -Dlogback.configurationFile=src/main/resources/logback.xml -jar target/diagram-converter-exec.jar --graph_user $neo4jUser --graph_password $neo4jPass --rel_user $mysqlUser --rel_password $mysqlPass --rel_database ${env.REACTOME_DB} --output ./${env.OUTPUT_FOLDER}'
 							"""
 					        	// Create archive that will be stored on S3.
 							sh "tar -zcf diagrams-v${releaseVersion}.tgz ${env.OUTPUT_FOLDER}/"