Merge branch 'fix-tophat' into 'develop'

Fix output file for tophat step

Still needs testing

See merge request !300

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

@@ -21,7 +21,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
   def this() = this(null)
 
   /** Make variantcalling submodule, this with the gatk modes in there */
-  override def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
+  override def makeVariantcalling(multisample: Boolean = false) = {
     if (multisample) new ShivaVariantcalling(qscript) {
       override def namePrefix = "multisample"
       override def configName = "shivavariantcalling"

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala

@@ -2,10 +2,10 @@ package nl.lumc.sasc.biopet.extensions.bowtie
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Extension for bowtie 2

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -20,7 +20,7 @@ import java.util.Date
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie2, Bowtie}
+import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie2, Bowtie }
 import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
 import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
 import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
@@ -380,7 +380,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
 
     // merge with mapped file
     val mergeSamFile = MergeSamFiles(this, List(tophat.outputAcceptedHits, sorter.output),
-      tophat.output_dir, "coordinate")
+      new File(tophat.output_dir, "fixed_merged.bam"), sortOrder = "coordinate")
     mergeSamFile.createIndex = true
     mergeSamFile.isIntermediate = true
     add(mergeSamFile)
@@ -395,6 +395,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     add(ar._1)
     ar._2
   }
+
   /** Adds stampy jobs */
   def addStampy(R1: File, R2: Option[File], output: File): File = {
 

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -36,10 +36,10 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
   }
 
   /** Method to make the variantcalling submodule of shiva */
-  def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
+  def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait with QScript = {
     if (multisample) new ShivaVariantcalling(qscript) {
       override def namePrefix = "multisample"
-      override def configName = "shivavariantcalling"
+      override def configName: String = "shivavariantcalling"
       override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
     }
     else new ShivaVariantcalling(qscript) {
@@ -69,7 +69,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
       } else None
 
       /** This will add jobs for this library */
-      override def addJobs = {
+      override def addJobs() = {
         super.addJobs()
 
         variantcalling.foreach(vc => {
@@ -78,10 +78,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
           vc.outputDir = new File(libDir, "variantcalling")
           if (preProcessBam.isDefined) vc.inputBams = Map(sampleId -> preProcessBam.get)
           else vc.inputBams = Map(sampleId -> bamFile.get)
-          vc.init()
-          vc.biopetScript()
-          addAll(vc.functions)
-          addSummaryQScript(vc)
+          add(vc)
         })
       }
     }
@@ -99,10 +96,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
           vc.sampleId = Some(sampleId)
           vc.outputDir = new File(sampleDir, "variantcalling")
           vc.inputBams = Map(sampleId -> bam)
-          vc.init()
-          vc.biopetScript()
-          addAll(vc.functions)
-          addSummaryQScript(vc)
+          add(vc)
         })
       }
     }
@@ -122,34 +116,25 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
   } else None
 
   /** This will add the mutisample variantcalling */
-  override def addMultiSampleJobs = {
+  override def addMultiSampleJobs() = {
     super.addMultiSampleJobs()
 
     multisampleVariantCalling.foreach(vc => {
       vc.outputDir = new File(outputDir, "variantcalling")
       vc.inputBams = samples.flatMap { case (sampleId, sample) => sample.preProcessBam.map(sampleId -> _) }
-      vc.init()
-      vc.biopetScript()
-      addAll(vc.functions)
-      addSummaryQScript(vc)
+      add(vc)
 
       annotation.foreach { toucan =>
         toucan.outputDir = new File(outputDir, "annotation")
         toucan.inputVCF = vc.finalFile
-        toucan.init()
-        toucan.biopetScript()
-        addAll(toucan.functions)
-        addSummaryQScript(toucan)
+        add(toucan)
       }
     })
 
     svCalling.foreach(sv => {
       sv.outputDir = new File(outputDir, "sv_calling")
       sv.inputBams = samples.flatMap { case (sampleId, sample) => sample.preProcessBam.map(sampleId -> _) }
-      sv.init()
-      sv.biopetScript()
-      addAll(sv.functions)
-      addSummaryQScript(sv)
+      add(sv)
     })
   }