Merge branch 'develop' into fix-BIOPET-513

.gitmodules

+[submodule "gatk"]
+	path = gatk
+	url = https://github.com/biopet/gatk.git

Jenkinsfile

+node('local') {
+    try {
+
+        stage('Init') {
+            tool 'JDK 8u102'
+            tool 'Apache Maven 3.3.9'
+        }
+
+        stage('Checkout') {
+            checkout scm
+            sh 'git submodule update --init --recursive'
+        }
+
+        stage('Build and Test') {
+            withMaven(maven: 'Apache Maven 3.3.9', jdk: 'JDK 8u102') {
+                sh 'mvn -B -T 2 -Dmaven.test.failure.ignore clean package'
+            }
+        }
+
+        stage('Report tests') {
+            junit '*/target/surefire-reports/*.xml'
+        }
+
+        if(currentBuild.result == null || "SUCCESS".equals(currentBuild.result)) {
+            currentBuild.result = "SUCCESS"
+            slackSend (color: '#00FF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
+        } else {
+            slackSend (color: '#FFFF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
+        }
+
+    } catch (e) {
+        if(currentBuild.result == null || "FAILED".equals(currentBuild.result)) {
+            currentBuild.result = "FAILED"
+        }
+        slackSend (color: '#FF0000', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
+
+        throw e
+    }
+}

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -345,8 +345,7 @@ object BammetricsReport extends ReportBuilder {
     val pathValues: Map[String, Array[Any]] = paths.map {
       case (key, path) =>
         val value = summary.getValueAsArray(sampleId, libId, path: _*)
-        require(value.isDefined, s"Sample: $sampleId, library: $libId on path: '${path.mkString(",")}' does not exist in summary")
-        key -> value.get
+        key -> value.getOrElse(Array())
     }
     require(pathValues.map(_._2.size).toList.distinct.size == 1, s"Arrays in summary does not have the same number of values, $paths")
     pathValues

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

@@ -47,6 +47,11 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
   private def changeScript(file: File): Unit = {
     val lines = Source.fromFile(file).getLines().toList
     val writer = new PrintWriter(file)
+    remoteCommand match {
+      case "bash" => writer.println("#!/bin/bash")
+      case "sh"   => writer.println("#!/bin/sh")
+      case _      => writer.println(s"#!$remoteCommand")
+    }
     writer.println("set -eubf")
     writer.println("set -o pipefail")
     lines.foreach(writer.println)
@@ -66,8 +71,9 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
       changeScript(new File(jt.getArgs.head.toString))
       jt.setRemoteCommand(remoteCommand)
     case ps: ProcessSettings =>
-      changeScript(new File(ps.getCommand.tail.head))
-      ps.setCommand(Array(remoteCommand) ++ ps.getCommand.tail)
+      changeScript(new File(ps.getCommand.last))
+      if (ps.getCommand.head != "srun")
+        ps.setCommand(Array(remoteCommand) ++ ps.getCommand.tail)
   }
 
   /**

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala

@@ -48,14 +48,19 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
   def coreMemory = _coreMemory
 
   /** This value is for SGE and is defined in seconds */
-  protected val maxWalltimeLimit: Option[Int] = config("max_walltime_limit")
+  wallTime = config("max_walltime")
+
+  /** This value is specific for slurm */
+  qualityOfSerice = config("quality_of_serice")
 
   var retry = 0
 
   override def freezeFieldValues(): Unit = {
     setResources()
-    if (useSge && vmem.isDefined) jobResourceRequests :+= s"h_vmem=${vmem.get}"
-    if (useSge && maxWalltimeLimit.isDefined) jobResourceRequests :+= s"h_rt=${maxWalltimeLimit.get}"
+    if (useSge) {
+      vmem.foreach(v => jobResourceRequests :+= s"h_vmem=$v")
+      wallTime.foreach(t => jobResourceRequests :+= s"h_rt=$t")
+    }
     super.freezeFieldValues()
   }
 
@@ -106,6 +111,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
     if (vmem.isDefined) jobResourceRequests = jobResourceRequests.filterNot(_.contains("h_vmem="))
     if (retry > 0) logger.info("Auto raise memory on retry")
     retry += 1
+    waitBeforeJob = waitBeforeJob.map(_ + (retry * 10))
     this.freezeFieldValues()
   }
 
@@ -117,8 +123,8 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
 
     _coreMemory = commands.map(cmd => cmd.coreMemory * (cmd.threads.toDouble / threads.toDouble)).sum
     memoryLimit = Some(_coreMemory * threads)
-    residentLimit = Some((_coreMemory + (0.5 * retry)) * residentFactor)
-    vmem = Some((_coreMemory * (vmemFactor + (0.5 * retry))) + "G")
+    residentLimit = Some((_coreMemory + (0.5 * retry)) * residentFactor * (if (multiplyRssThreads) threads else 1))
+    vmem = Some((_coreMemory * (vmemFactor + (0.5 * retry)) * (if (multiplyVmemThreads) threads else 1)) + "G")
   }
 
 }

gatk @ 7805065f

+Subproject commit 7805065f00df24c58948ea9961a4e9393ae64c70

pom.xml

@@ -24,6 +24,7 @@
     <version>0.8.0-SNAPSHOT</version>
     
     <modules>
+        <module>gatk</module>
         <module>biopet-package</module>
         <module>bam2wig</module>
         <module>bammetrics</module>