Wrappers are now split in general and specific flexiprep extensions

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

+package nl.lumc.sasc.biopet.extensions
+
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+
+class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
+  @Input(doc = "Input fastq file")
+  var fastq_input: File = _
+
+  @Output(doc = "Output fastq file")
+  var fastq_output: File = _
+
+  @Output(doc = "Output statistics file")
+  var stats_output: File = _
+
+  executable = config("exe", default = "cutadapt")
+  override def versionCommand = executable + " --version"
+  override val versionRegex = """(.*)""".r
+
+  var default_clip_mode: String = config("default_clip_mode", default = "3")
+  var opt_adapter: Set[String] = Set() + config("adapter")
+  var opt_anywhere: Set[String] = Set() + config("anywhere")
+  var opt_front: Set[String] = Set() + config("front")
+
+  var opt_discard: Boolean = config("discard")
+  var opt_minimum_length: String = config("minimum_length", 1)
+  var opt_maximum_length: String = config("maximum_length")
+
+  def cmdLine = required(executable) +
+    // options
+    repeat("-a", opt_adapter) +
+    repeat("-b", opt_anywhere) +
+    repeat("-g", opt_front) +
+    conditional(opt_discard, "--discard") +
+    optional("-m", opt_minimum_length) +
+    optional("-M", opt_maximum_length) +
+    // input / output
+    required(fastq_input) +
+    required("--output", fastq_output) +
+    " > " + required(stats_output)
+}
\ No newline at end of file

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.config._
+
+class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
+
+  @Input(doc = "Contaminants", required = false)
+  var contaminants: File = _
+
+  @Input(doc = "Fastq file", shortName = "FQ")
+  var fastqfile: File = _
+
+  @Output(doc = "Output", shortName = "out")
+  var output: File = _
+
+  executable = config("exe", default = "fastqc")
+  var java_exe: String = config("exe", default = "java", submodule = "java")
+  var kmers: Option[Int] = config("kmers")
+  var quiet: Boolean = config("quiet")
+  var noextract: Boolean = config("noextract")
+  var nogroup: Boolean = config("nogroup")
+  var extract: Boolean = config("extract", default = true)
+
+  override val versionRegex = """FastQC (.*)""".r
+  override def versionCommand = executable + " --version"
+  override val defaultThreads = 4
+
+  override def afterGraph {
+    this.checkExecutable
+    if (contaminants == null) {
+      val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
+      contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+    }
+  }
+
+  def cmdLine = required(executable) +
+    optional("--java", java_exe) +
+    optional("--threads", threads) +
+    optional("--contaminants", contaminants) +
+    optional("--kmers", kmers) +
+    conditional(nogroup, "--nogroup") +
+    conditional(noextract, "--noextract") +
+    conditional(extract, "--extract") +
+    conditional(quiet, "--quiet") +
+    required("-o", output.getParent()) +
+    required(fastqfile)
+}

flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Sickle.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

-package nl.lumc.sasc.biopet.extensions.fastq
+package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
-import scala.io.Source._
-import scala.sys.process._
 
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-
-import argonaut._, Argonaut._
-import scalaz._, Scalaz._
-
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "R1 input")
@@ -19,9 +13,6 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "R2 input", required = false)
   var input_R2: File = _
 
-  @Input(doc = "qualityType file", required = false)
-  var qualityTypeFile: File = _
-
   @Output(doc = "R1 output")
   var output_R1: File = _
 
@@ -41,17 +32,12 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
 
   var defaultQualityType: String = config("defaultqualitytype", default = "sanger")
   override val versionRegex = """sickle version (.*)""".r
+  override def versionCommand = executable + " --version"
 
   override def afterGraph {
     if (qualityType == null && defaultQualityType != null) qualityType = defaultQualityType
   }
 
-  override def versionCommand = executable + " --version"
-
-  override def beforeCmd {
-    qualityType = getQualityTypeFromFile
-  }
-
   def cmdLine = {
     var cmd: String = required(executable)
     if (input_R2 != null) {
@@ -67,26 +53,4 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
       required("-o", output_R1) +
       " > " + required(output_stats)
   }
-
-  def getQualityTypeFromFile: String = {
-    if (qualityType == null && qualityTypeFile != null) {
-      if (qualityTypeFile.exists()) {
-        for (line <- fromFile(qualityTypeFile).getLines) {
-          var s: String = line.substring(0, line.lastIndexOf("\t"))
-          return s
-        }
-      } else logger.warn("File : " + qualityTypeFile + " does not exist")
-    }
-    return null
-  }
-
-  def getSummary: Json = {
-    return jNull
-  }
 }
-
-object Sickle {
-  def mergeSummarys(jsons: List[Json]): Json = {
-    return jNull
-  }
-}
\ No newline at end of file

flexiprep/nbactions.xml

@@ -10,7 +10,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>
@@ -25,7 +25,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
+                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
@@ -41,7 +41,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>

flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Cutadapt.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala

-package nl.lumc.sasc.biopet.extensions.fastq
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
 
-import java.io.File
-import scala.io.Source._
-import scala.sys.process._
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import scala.io.Source
 
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.extensions.Ln
+import org.broadinstitute.gatk.utils.commandline.{ Input }
 
 import argonaut._, Argonaut._
 import scalaz._, Scalaz._
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.Ln
-
-class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
-  @Input(doc = "Input fastq file")
-  var fastq_input: File = _
 
+class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
   @Input(doc = "Fastq contams file", required = false)
   var contams_file: File = _
-
-  @Output(doc = "Output fastq file")
-  var fastq_output: File = _
-
-  @Output(doc = "Output statistics file")
-  var stats_output: File = _
-
-  executable = config("exe", default = "cutadapt")
-  override def versionCommand = executable + " --version"
-  override val versionRegex = """(.*)""".r
-
-  var default_clip_mode: String = config("default_clip_mode", default = "3")
-  var opt_adapter: Set[String] = Set() + config("adapter")
-  var opt_anywhere: Set[String] = Set() + config("anywhere")
-  var opt_front: Set[String] = Set() + config("front")
-
-  var opt_discard: Boolean = config("discard")
-  var opt_minimum_length: String = config("minimum_length", 1)
-  var opt_maximum_length: String = config("maximum_length")
-
+  
   override def beforeCmd() {
+    super.beforeCmd
     getContamsFromFile
   }
-
-  def cmdLine = {
+  
+  override def cmdLine = {
     if (!opt_adapter.isEmpty || !opt_anywhere.isEmpty || !opt_front.isEmpty) {
       analysisName = getClass.getName
-      required(executable) +
-        // options
-        repeat("-a", opt_adapter) +
-        repeat("-b", opt_anywhere) +
-        repeat("-g", opt_front) +
-        conditional(opt_discard, "--discard") +
-        optional("-m", opt_minimum_length) +
-        optional("-M", opt_maximum_length) +
-        // input / output
-        required(fastq_input) +
-        required("--output", fastq_output) +
-        " > " + required(stats_output)
+      super.cmdLine
     } else {
       analysisName = getClass.getSimpleName + "-ln"
       val lnOut = new Ln(this)
@@ -67,11 +39,11 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
       lnOut.cmd
     }
   }
-
+  
   def getContamsFromFile {
     if (contams_file != null) {
       if (contams_file.exists()) {
-        for (line <- fromFile(contams_file).getLines) {
+        for (line <- Source.fromFile(contams_file).getLines) {
           var s: String = line.substring(line.lastIndexOf("\t") + 1, line.size)
           if (default_clip_mode == "3") opt_adapter += s
           else if (default_clip_mode == "5") opt_front += s
@@ -85,7 +57,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
       } else logger.warn("File : " + contams_file + " does not exist")
     }
   }
-
+  
   def getSummary: Json = {
     return jNull
   }

flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Fastqc.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala

-package nl.lumc.sasc.biopet.extensions.fastq
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package nl.lumc.sasc.biopet.pipelines.flexiprep
 
 import java.io.File
+import nl.lumc.sasc.biopet.core.config.Configurable
 import scala.io.Source
-import scala.sys.process._
-
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import argonaut._, Argonaut._
 import scalaz._, Scalaz._
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-
-class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
-
-  @Input(doc = "Contaminants", required = false)
-  var contaminants: File = _
-
-  @Input(doc = "Fastq file", shortName = "FQ")
-  var fastqfile: File = _
-
-  @Output(doc = "Output", shortName = "out")
-  var output: File = _
-
-  executable = config("exe", default = "fastqc")
-  var java_exe: String = config("exe", default = "java", submodule = "java")
-  var kmers: Option[Int] = config("kmers")
-  var quiet: Boolean = config("quiet")
-  var noextract: Boolean = config("noextract")
-  var nogroup: Boolean = config("nogroup")
-  var extract: Boolean = config("extract", default = true)
-
-  override val versionRegex = """FastQC (.*)""".r
-  override val defaultThreads = 4
-
-  override def afterGraph {
-    this.checkExecutable
-    if (contaminants == null) {
-      val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
-      contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
-    }
-  }
-
-  override def versionCommand = executable + " --version"
-
-  def cmdLine = {
-    required(executable) +
-      optional("--java", java_exe) +
-      optional("--threads", threads) +
-      optional("--contaminants", contaminants) +
-      optional("--kmers", kmers) +
-      conditional(nogroup, "--nogroup") +
-      conditional(noextract, "--noextract") +
-      conditional(extract, "--extract") +
-      conditional(quiet, "--quiet") +
-      required("-o", output.getParent()) +
-      required(fastqfile)
-  }
-
+class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(root) {
   def getDataBlock(name: String): Array[String] = { // Based on Fastqc v0.10.1
     val outputDir = output.getName.stripSuffix(".zip")
     val dataFile = new File(outputDir + "/fastqc_data.txt")

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
-import scala.util.parsing.json._
-
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.queue.extensions.gatk._
-import org.broadinstitute.gatk.queue.extensions.picard._
-import org.broadinstitute.gatk.queue.function._
 import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-import nl.lumc.sasc.biopet.extensions._
-import nl.lumc.sasc.biopet.extensions.fastq._
+import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.{Cat, Ln, Pbzip2, Sha1sum, Zcat}
 import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
 
 class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala

@@ -2,10 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.Sha1sum
-import nl.lumc.sasc.biopet.extensions.fastq.Cutadapt
-import nl.lumc.sasc.biopet.extensions.fastq.Fastqc
-import nl.lumc.sasc.biopet.extensions.fastq.Sickle
-import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.FastqSync
+import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.{ FastqSync, Seqstat }
 import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.Seqstat
 import org.broadinstitute.gatk.queue.function.InProcessFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala

+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.config.Configurable
+import scala.io.Source
+
+import org.broadinstitute.gatk.utils.commandline.{ Input }
+
+
+import argonaut._, Argonaut._
+import scalaz._, Scalaz._
+
+class Sickle(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Sickle(root) {
+  @Input(doc = "qualityType file", required = false)
+  var qualityTypeFile: File = _
+
+  override def beforeCmd {
+    super.beforeCmd
+    qualityType = getQualityTypeFromFile
+  }
+  
+  def getQualityTypeFromFile: String = {
+    if (qualityType == null && qualityTypeFile != null) {
+      if (qualityTypeFile.exists()) {
+        for (line <- Source.fromFile(qualityTypeFile).getLines) {
+          var s: String = line.substring(0, line.lastIndexOf("\t"))
+          return s
+        }
+      } else logger.warn("File : " + qualityTypeFile + " does not exist")
+    }
+    return null
+  }
+
+  def getSummary: Json = {
+    return jNull
+  }
+}
+
+object Sickle {
+  def mergeSummarys(jsons: List[Json]): Json = {
+    return jNull
+  }
+}
\ No newline at end of file

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.extensions.fastq.Fastqc
+import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import argonaut._, Argonaut._
@@ -32,7 +32,6 @@ class Seqstat(val root: Configurable) extends PythonCommandLineFunction {
         case s if (s.contains("Illumina <1.3"))         => fmt = "solexa"
         case s if (s.contains("Illumina 1.3"))          => fmt = "illumina"
         case s if (s.contains("Illumina 1.5"))          => fmt = "illumina"
-        //case _ => null
       }
     }
   }

mapping/nbactions.xml

@@ -10,7 +10,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>
@@ -25,7 +25,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
+                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
@@ -41,7 +41,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>