Adding lost modules

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala

@@ -30,7 +30,7 @@ trait Summarizable {
   def summaryStats: Any
 
   /** Can be used to add additional Summarizable, this is executed at the start of WriteSummary*/
-  def addToQscriptSummary(qscript: SummaryQScript, name: String) {}
+  def addToQscriptSummary(qscript: SummaryQScript) {}
 
   /**
    * This function is used to merge value that are found at the same path in the map. Default there will throw a exception at conflicting values.

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -53,6 +53,8 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
   }
 
   def init(): Unit = {
+    qscript.summarizables.foreach(_._2.foreach(_.addToQscriptSummary(qscript)))
+
     val db = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
     if (qscript == root) { // This initialize the database
       qscript match {

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

@@ -86,31 +86,32 @@ class CollectMultipleMetrics(val parent: Configurable) extends Picard with Summa
     optional("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
     repeat("PROGRAM=", program, spaceSeparated = false)
 
-  override def addToQscriptSummary(qscript: SummaryQScript, name: String): Unit = {
+  override def addToQscriptSummary(qscript: SummaryQScript): Unit = {
+
+    def summarizable(stats: () => Any): Summarizable = new Summarizable {
+      def summaryStats = stats()
+      def summaryFiles: Map[String, File] = Map()
+    }
+
     program
       .filterNot(_ == Programs.CollectInsertSizeMetrics.toString && !new File(outputName + ".insert_size_metrics").exists())
       .foreach { p =>
-        val stats: Any = p match {
+        p match {
           case _ if p == Programs.CollectAlignmentSummaryMetrics.toString =>
-            Picard.getMetrics(new File(outputName + ".alignment_summary_metrics"), groupBy = Some("CATEGORY"))
+            qscript.addSummarizable(summarizable(() => Picard.getMetrics(new File(outputName + ".alignment_summary_metrics"), groupBy = Some("CATEGORY"))), p)
           case _ if p == Programs.CollectInsertSizeMetrics.toString =>
-            Map(
+            qscript.addSummarizable(summarizable(() => Map(
               "metrics" -> Picard.getMetrics(new File(outputName + ".insert_size_metrics")),
               "histogram" -> Picard.getHistogram(new File(outputName + ".insert_size_metrics"))
-            )
+            )), p)
           case _ if p == Programs.QualityScoreDistribution.toString =>
-            Picard.getHistogram(new File(outputName + ".quality_distribution_metrics"))
+            qscript.addSummarizable(summarizable(() => Picard.getHistogram(new File(outputName + ".quality_distribution_metrics"))), p)
           case _ if p == Programs.MeanQualityByCycle.toString =>
-            Picard.getHistogram(new File(outputName + ".quality_by_cycle_metrics"))
+            qscript.addSummarizable(summarizable(() => Picard.getHistogram(new File(outputName + ".quality_by_cycle_metrics"))), p)
           case _ if p == Programs.CollectBaseDistributionByCycle.toString =>
-            Picard.getHistogram(new File(outputName + ".base_distribution_by_cycle_metrics"), tag = "METRICS CLASS")
+            qscript.addSummarizable(summarizable(() => Picard.getHistogram(new File(outputName + ".base_distribution_by_cycle_metrics"), tag = "METRICS CLASS")), p)
           case _ => None
         }
-        val sum = new Summarizable {
-          override def summaryStats = stats
-          override def summaryFiles: Map[String, File] = Map()
-        }
-        qscript.addSummarizable(sum, p)
       }
   }
 

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala

@@ -70,7 +70,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
 
   override def summaryDeps = trim.map(_.summaryDeps).toList.flatten ::: super.summaryDeps
 
-  override def addToQscriptSummary(qscript: SummaryQScript, name: String): Unit = {
+  override def addToQscriptSummary(qscript: SummaryQScript): Unit = {
     clip match {
       case Some(job) => qscript.addSummarizable(job, s"clipping_$read")
       case _         =>