Adding summary stats

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -183,12 +183,14 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     qcCmdR1.output = if (paired) new File("/dev/stdout")
     else fastqR1Qc
     qcCmdR1.isIntermediate = paired || !keepQcFastqFiles
+    addSummarizable(qcCmdR1, "qc_command_R1")
 
     if (paired) {
       val qcCmdR2 = new QcCommand(this, fastqc_R2)
       qcCmdR2.input = R2_in.get
       qcCmdR2.output = new File("/dev/stdout")
       qcCmdR2.read = "R2"
+      addSummarizable(qcCmdR2, "qc_command_R2")
 
       qcCmdR1.compress = false
       qcCmdR2.compress = false

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

@@ -2,6 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.summary.{SummaryQScript, Summarizable}
 import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetPipe }
 import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle, Cutadapt }
 import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
@@ -11,7 +12,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 /**
  * Created by pjvan_thof on 9/22/15.
  */
-class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetCommandLineFunction {
+class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetCommandLineFunction with Summarizable {
 
   val flexiprep = root match {
     case f: Flexiprep => f
@@ -35,6 +36,21 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
   var clip: Option[Cutadapt] = None
   var trim: Option[Sickle] = None
 
+  def summaryFiles = Map()
+
+  def summaryStats = Map()
+
+  override def addToQscriptSummary(qscript: SummaryQScript, name: String): Unit = {
+    clip match {
+      case Some(job) => qscript.addSummarizable(job, s"clipping_$read")
+      case _ =>
+    }
+    trim match {
+      case Some(job) => qscript.addSummarizable(job, s"trimming_$read")
+      case _ =>
+    }
+  }
+
   override def beforeGraph(): Unit = {
     super.beforeGraph()
     require(read != null)