Add summary framework to Carp

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.carp
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
 import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
@@ -34,7 +35,7 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
  * Chip-Seq analysis pipeline
  * This pipeline performs QC,mapping and peak calling
  */
-class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
+class Carp(val root: Configurable) extends QScript with MultiSampleQScript with SummaryQScript {
   qscript =>
   def this() = this(null)
 
@@ -42,25 +43,32 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
     "mapping" -> Map("skip_markduplicates" -> true, "aligner" -> "bwa")
   ), super.defaults)
 
+  def summaryFile = new File(outputDir, "Carp.summary.json")
+
+  def summaryFiles = Map()
+
+  def summaryData = Map()
+
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
     def makeLibrary(id: String) = new Library(id)
     class Library(libId: String) extends AbstractLibrary(libId) {
       val mapping = new Mapping(qscript)
+      mapping.libId = Some(libId)
+      mapping.sampleId = Some(sampleId)
+      mapping.outputDir = libDir
 
       def addJobs(): Unit = {
         if (config.contains("R1")) {
           mapping.input_R1 = config("R1")
           if (config.contains("R2")) mapping.input_R2 = config("R2")
-          mapping.libId = Some(libId)
-          mapping.sampleId = Some(sampleId)
-          mapping.outputDir = libDir
-
           mapping.init
           mapping.biopetScript
           addAll(mapping.functions)
 
         } else logger.error("Sample: " + sampleId + ": No R1 found for library: " + libId)
+
+        addSummaryQScript(mapping)
       }
     }