Rename pipelines

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaGatk.scala → protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

@@ -9,17 +9,17 @@ import org.broadinstitute.gatk.queue.QScript
 /**
  * Created by pjvan_thof on 2/26/15.
  */
-class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
+class Shiva(val root: Configurable) extends QScript with ShivaTrait {
   qscript =>
   def this() = this(null)
 
   override def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
-    if (multisample) new ShivaVariantcallingGatk(qscript) {
+    if (multisample) new ShivaVariantcalling(qscript) {
       override def namePrefix = "multisample"
       override def configName = "shivavariantcalling"
       override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
     }
-    else new ShivaVariantcallingGatk(qscript) {
+    else new ShivaVariantcalling(qscript) {
       override def configName = "shivavariantcalling"
     }
   }
@@ -47,9 +47,9 @@ class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
       }
     }
 
-    override def doublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
-      if (input.size <= 1) super.doublePreProcess(input)
-      else super.doublePreProcess(input, true).collect {
+    override protected def addDoublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
+      if (input.size <= 1) super.addDoublePreProcess(input)
+      else super.addDoublePreProcess(input, true).collect {
         case file => {
           config("use_indel_realign", default = true).asBoolean match {
             case true  => addIndelRealign(file, sampleDir, false)
@@ -98,4 +98,4 @@ class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
   }
 }
 
-object ShivaGatk extends PipelineCommand
\ No newline at end of file
+object Shiva extends PipelineCommand
\ No newline at end of file

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingGatk.scala → protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala

@@ -9,7 +9,7 @@ import org.broadinstitute.gatk.queue.QScript
 /**
  * Created by pjvan_thof on 2/26/15.
  */
-class ShivaVariantcallingGatk(val root: Configurable) extends QScript with ShivaVariantcallingTrait {
+class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVariantcallingTrait {
   qscript =>
   def this() = this(null)
 
@@ -104,4 +104,4 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
   }
 }
 
-object ShivaVariantcallingGatk extends PipelineCommand
\ No newline at end of file
+object ShivaVariantcalling extends PipelineCommand
\ No newline at end of file

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaGatkTest.scala → protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

@@ -15,11 +15,11 @@ import org.testng.annotations.{ Test, DataProvider }
 /**
  * Created by pjvan_thof on 3/2/15.
  */
-class ShivaGatkTest extends TestNGSuite with Matchers {
-  def initPipeline(map: Map[String, Any]): ShivaGatk = {
-    new ShivaGatk() {
+class ShivaTest extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): Shiva = {
+    new Shiva() {
       override def configName = "shiva"
-      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaGatkTest.config))
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaTest.config))
       qSettings = new QSettings
       qSettings.runName = "test"
     }
@@ -40,10 +40,10 @@ class ShivaGatkTest extends TestNGSuite with Matchers {
                 multi: Boolean, single: Boolean, library: Boolean, dbsnp: Boolean,
                 covariates: Boolean, realign: Boolean, baseRecalibration: Boolean): Unit = {
     val map = {
-      var m: Map[String, Any] = ShivaGatkTest.config
-      if (sample1) m = ConfigUtils.mergeMaps(ShivaGatkTest.sample1, m.toMap)
-      if (sample2) m = ConfigUtils.mergeMaps(ShivaGatkTest.sample2, m.toMap)
-      if (sample3) m = ConfigUtils.mergeMaps(ShivaGatkTest.sample3, m.toMap)
+      var m: Map[String, Any] = ShivaTest.config
+      if (sample1) m = ConfigUtils.mergeMaps(ShivaTest.sample1, m.toMap)
+      if (sample2) m = ConfigUtils.mergeMaps(ShivaTest.sample2, m.toMap)
+      if (sample3) m = ConfigUtils.mergeMaps(ShivaTest.sample3, m.toMap)
       if (dbsnp) m = ConfigUtils.mergeMaps(Map("dbsnp" -> "test"), m.toMap)
       ConfigUtils.mergeMaps(Map("multisample_sample_variantcalling" -> multi,
         "single_sample_variantcalling" -> single,
@@ -80,7 +80,7 @@ class ShivaGatkTest extends TestNGSuite with Matchers {
   }
 }
 
-object ShivaGatkTest {
+object ShivaTest {
   val outputDir = Files.createTempDir()
 
   val config = Map(

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingGatkTest.scala → protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

@@ -19,11 +19,11 @@ import scala.collection.mutable.ListBuffer
 /**
  * Created by pjvan_thof on 3/2/15.
  */
-class ShivaVariantcallingGatkTest extends TestNGSuite with Matchers {
-  def initPipeline(map: Map[String, Any]): ShivaVariantcallingGatk = {
-    new ShivaVariantcallingGatk() {
+class ShivaVariantcallingTest extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): ShivaVariantcalling = {
+    new ShivaVariantcalling() {
       override def configName = "shivavariantcalling"
-      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingGatkTest.config))
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config))
       qSettings = new QSettings
       qSettings.runName = "test"
     }
@@ -94,11 +94,11 @@ class ShivaVariantcallingGatkTest extends TestNGSuite with Matchers {
   }
 
   @AfterClass def removeTempOutputDir() = {
-    FileUtils.deleteDirectory(ShivaVariantcallingGatkTest.outputDir)
+    FileUtils.deleteDirectory(ShivaVariantcallingTest.outputDir)
   }
 }
 
-object ShivaVariantcallingGatkTest {
+object ShivaVariantcallingTest {
   val outputDir = Files.createTempDir()
 
   val config = Map(