No functional changes

biopet-framework/dependency-reduced-pom.xml

 <?xml version="1.0" encoding="UTF-8"?>
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <parent>
+    <artifactId>Biopet</artifactId>
+    <groupId>nl.lumc.sasc</groupId>
+    <version>0.1.0</version>
+  </parent>
   <modelVersion>4.0.0</modelVersion>
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>Biopet-Framework</artifactId>
@@ -28,16 +33,6 @@
           </execution>
         </executions>
       </plugin>
-      <plugin>
-        <artifactId>maven-surefire-plugin</artifactId>
-        <version>2.7.2</version>
-        <executions>
-          <execution>
-            <id>default-test</id>
-            <phase>none</phase>
-          </execution>
-        </executions>
-      </plugin>
       <plugin>
         <artifactId>maven-shade-plugin</artifactId>
         <version>2.3</version>

biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala

@@ -6,13 +6,13 @@ import org.broadinstitute.sting.commandline._
 import java.io.File
 
 class Zcat(val globalConfig: Config) extends CommandLineFunction {
-    def this() = this(new Config(Map()))
-    this.analysisName = "zcat"
-    val config: Config = globalConfig.getAsConfig("zcat")
-    logger.debug("Config for " + this.analysisName + ": " + config)
-	  
-    @Input(doc="Zipped file") var in: File = _
-    @Output(doc="Unzipped file") var out: File = _
-    
-    def commandLine = "zcat %s > %s".format(in, out)
+  def this() = this(new Config(Map()))
+  this.analysisName = "zcat"
+  val config: Config = globalConfig.getAsConfig("zcat")
+  logger.debug("Config for " + this.analysisName + ": " + config)
+  
+  @Input(doc="Zipped file") var in: File = _
+  @Output(doc="Unzipped file") var out: File = _
+  
+  def commandLine = "zcat %s > %s".format(in, out)
 }
\ No newline at end of file

flexiprep/dependency-reduced-pom.xml

@@ -73,6 +73,20 @@
       </plugin>
     </plugins>
   </build>
+  <dependencies>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>3.8.1</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.scalatest</groupId>
+      <artifactId>scalatest_2.9.2</artifactId>
+      <version>2.0.M4</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
   <properties>
     <app.main.class>nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep</app.main.class>
     <sting.shade.phase>package</sting.shade.phase>

flexiprep/examples/test.json

@@ -2,6 +2,7 @@
     "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
     
     "flexiprep": {
+        "native_link": true,
         "fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
         "cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
         "sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}