Fixed intermediate files

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

@@ -75,6 +75,8 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
       }
     }
 
+    override def keepMergedFiles: Boolean = config("keep_merged_files", default = false)
+
     override def summarySettings = super.summarySettings + ("use_indel_realigner" -> useIndelRealigner)
 
     lazy val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
@@ -87,7 +89,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
       super.addJobs()
 
       if (useIndelRealigner && libraries.values.flatMap(_.preProcessBam).size > 1) {
-        addIndelRealign(bamFile.get, sampleDir, libraries.size > 1)
+        addIndelRealign(bamFile.get, sampleDir, false)
       }
     }
   }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala

@@ -105,11 +105,12 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
 }
 object MarkDuplicates {
   /** Returns default MarkDuplicates */
-  def apply(root: Configurable, input: List[File], output: File): MarkDuplicates = {
+  def apply(root: Configurable, input: List[File], output: File, isIntermediate: Boolean = false): MarkDuplicates = {
     val markDuplicates = new MarkDuplicates(root)
     markDuplicates.input = input
     markDuplicates.output = output
     markDuplicates.outputMetrics = new File(output.getParent, output.getName.stripSuffix(".bam") + ".metrics")
+    markDuplicates.isIntermediate = isIntermediate
     markDuplicates
   }
 }
\ No newline at end of file

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala

@@ -65,12 +65,14 @@ class MergeSamFiles(val root: Configurable) extends Picard {
 
 object MergeSamFiles {
   /** Returns default MergeSamFiles */
-  def apply(root: Configurable, input: List[File], outputFile: File, sortOrder: String = null): MergeSamFiles = {
+  def apply(root: Configurable, input: List[File], outputFile: File,
+            sortOrder: String = null, isIntermediate: Boolean = false): MergeSamFiles = {
     val mergeSamFiles = new MergeSamFiles(root)
     mergeSamFiles.input = input
     mergeSamFiles.output = outputFile
     if (sortOrder == null) mergeSamFiles.sortOrder = "coordinate"
     else mergeSamFiles.sortOrder = sortOrder
+    mergeSamFiles.isIntermediate = isIntermediate
     mergeSamFiles
   }
 }
\ No newline at end of file

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

@@ -160,6 +160,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
 
     def preProcessBam = bamFile
 
+    def keepMergedFiles: Boolean = config("keep_merged_files", default = true)
+
     def addJobs(): Unit = {
       addPerLibJobs() // This add jobs for each library
 
@@ -170,13 +172,13 @@ trait MultisampleMappingTrait extends MultiSampleQScript
         case (MergeStrategy.PreProcessMergeSam | MergeStrategy.PreProcessMarkDuplicates) if libraries.flatMap(_._2.preProcessBam).size == 1 =>
           add(Ln.linkBamFile(qscript, libraries.flatMap(_._2.preProcessBam).head, bamFile.get): _*)
         case MergeStrategy.MergeSam =>
-          add(MergeSamFiles(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get))
+          add(MergeSamFiles(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get, isIntermediate = keepMergedFiles))
         case MergeStrategy.PreProcessMergeSam =>
-          add(MergeSamFiles(qscript, libraries.flatMap(_._2.preProcessBam).toList, bamFile.get))
+          add(MergeSamFiles(qscript, libraries.flatMap(_._2.preProcessBam).toList, bamFile.get, isIntermediate = keepMergedFiles))
         case MergeStrategy.MarkDuplicates =>
-          add(MarkDuplicates(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get))
+          add(MarkDuplicates(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get, isIntermediate = keepMergedFiles))
         case MergeStrategy.PreProcessMarkDuplicates =>
-          add(MarkDuplicates(qscript, libraries.flatMap(_._2.preProcessBam).toList, bamFile.get))
+          add(MarkDuplicates(qscript, libraries.flatMap(_._2.preProcessBam).toList, bamFile.get, isIntermediate = keepMergedFiles))
         case _ => throw new IllegalStateException("This should not be possible, unimplemented MergeStrategy?")
       }