Fixed rna metrics

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

@@ -39,7 +39,6 @@ class BamMetrics(val root: Configurable) extends QScript
   var inputBam: File = _
 
   /** Settings for CollectRnaSeqMetrics */
-  var rnaMetricsSettings: Map[String, String] = Map()
   var transcriptRefFlatFile: Option[File] = config("transcript_refflat")
 
   /** return location of summary file */
@@ -107,8 +106,6 @@ class BamMetrics(val root: Configurable) extends QScript
       rnaMetrics.output = swapExt(outputDir, inputBam, ".bam", ".rna.metrics")
       rnaMetrics.chartOutput = Some(swapExt(outputDir, inputBam, ".bam", ".rna.metrics.pdf"))
       rnaMetrics.refFlat = transcriptRefFlatFile.get
-      rnaMetrics.ribosomalIntervals = rnaMetricsSettings.get("ribosomal_intervals").collect { case n => new File(n) }
-      rnaMetrics.strandSpecificity = rnaMetricsSettings.get("strand_specificity")
       add(rnaMetrics)
       addSummarizable(rnaMetrics, "rna")
     }

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/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -19,13 +19,13 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.FullVersion
 import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.extensions.picard.{MergeSamFiles, SortSam}
+import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
-import nl.lumc.sasc.biopet.extensions.tools.{MergeTables, WipeReads}
-import nl.lumc.sasc.biopet.extensions.{HtseqCount, Ln}
+import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
+import nl.lumc.sasc.biopet.extensions.{ HtseqCount, Ln }
 import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
-import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{CustomVarScan, Pdflatex, RawBaseCounter}
-import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{AggrBaseCount, PdfReportTemplateWriter, PlotHeatmap}
+import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{ CustomVarScan, Pdflatex, RawBaseCounter }
+import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{ AggrBaseCount, PdfReportTemplateWriter, PlotHeatmap }
 import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config._
@@ -98,17 +98,6 @@ class Gentrap(val root: Configurable) extends QScript
   /** Whether to do simple variant calling on RNA or not */
   var callVariants: Boolean = config("call_variants", default = false)
 
-  /** Settings for all Picard CollectRnaSeqMetrics runs */
-  private def collectRnaSeqMetricsSettings: Map[String, String] = Map(
-    "strand_specificity" -> (strandProtocol match {
-      case NonSpecific => StrandSpecificity.NONE.toString
-      case Dutp        => StrandSpecificity.SECOND_READ_TRANSCRIPTION_STRAND.toString
-      case otherwise   => throw new IllegalStateException(otherwise.toString)
-    })) ++ (ribosomalRefFlat match {
-      case Some(rbs) => Map("ribosomal_intervals" -> rbs.toString)
-      case None      => Map()
-    })
-
   /** Default pipeline config */
   override def defaults = Map(
     "merge_strategy" -> "preprocessmergesam",
@@ -117,6 +106,17 @@ class Gentrap(val root: Configurable) extends QScript
       "batch" -> 4,
       "format" -> "sam"
     ),
+    "bammetrics" -> Map(
+      "transcript_refflat" -> annotationRefFlat,
+      "collectrnaseqmetrics" -> ((if (strandProtocol != null) Map(
+        "strand_specificity" -> (strandProtocol match {
+          case NonSpecific => StrandSpecificity.NONE.toString
+          case Dutp        => StrandSpecificity.SECOND_READ_TRANSCRIPTION_STRAND.toString
+          case otherwise   => throw new IllegalStateException(otherwise.toString)
+        })
+      )
+      else Map()) ++ (if (ribosomalRefFlat != null) ribosomalRefFlat.map("ribosomal_intervals" -> _.getAbsolutePath).toList else Nil))
+    ),
     "cutadapt" -> Map("minimum_length" -> 20),
     // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
     "picard" -> Map(

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 }