Merge branch 'patch-shiva' into 'release-0.3.0'

Patch shiva

See merge request !131

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -88,8 +88,9 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
 
     for (bedFile <- bedFiles) {
       //TODO: Add target jobs to summary
-      val targetDir = new File(outputDir, bedFile.getName.stripSuffix(".bed"))
-      val targetInterval = BedToInterval(this, bedFile, inputBam, targetDir)
+      val targetDir = bedFile.getParentFile
+      val targetFile = new File(outputDir, bedFile.getName.stripSuffix(".bed") + ".interval")
+      val targetInterval = BedToInterval(this, bedFile, inputBam, targetFile)
       add(targetInterval, true)
       add(CalculateHsMetrics(this, inputBam, if (baitIntervalFile != null) baitIntervalFile
       else targetInterval.output, targetInterval.output, targetDir))

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

@@ -46,6 +46,8 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
     if (input.getName.endsWith(".bam")) inputTag = "-abam"
   }
 
+  override val defaultVmem = "6G"
+
   /** Returns command to execute */
   def cmdLine = required(executable) + required("coverage") +
     required(inputTag, input) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala

@@ -43,14 +43,6 @@ class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunctio
 }
 
 object BedToInterval extends ToolCommand {
-  def apply(root: Configurable, inputBed: File, inputBam: File, outputDir: String): BedToInterval = {
-    val bedToInterval = new BedToInterval(root)
-    bedToInterval.input = inputBed
-    bedToInterval.bamFile = inputBam
-    bedToInterval.output = new File(outputDir, inputBed.getName.stripSuffix(".bed") + ".interval")
-    return bedToInterval
-  }
-
   def apply(root: Configurable, inputBed: File, inputBam: File, output: File): BedToInterval = {
     val bedToInterval = new BedToInterval(root)
     bedToInterval.input = inputBed

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

@@ -219,7 +219,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
         val md = new MarkDuplicates(qscript)
         md.input = input
         md.output = new File(sampleDir, sampleId + ".dedup.bam")
-        md.outputMetrics = new File(sampleDir, sampleId + ".dedup.bam")
+        md.outputMetrics = new File(sampleDir, sampleId + ".dedup.metrics")
         md.isIntermediate = isIntermediate
         add(md)
         addSummarizable(md, "mark_duplicates")