Added init version of summary

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

+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+
+/**
+ * Created by pjvan_thof on 2/14/15.
+ */
+trait Summarizable extends Configurable {
+
+  var summaryModule = configName
+
+  def summaryFiles: Map[String, File]
+
+  def summaryStats: Map[String, Any]
+
+  /**
+   * This function is used to merge
+   * @param v1
+   * @param v2
+   * @param key
+   * @return
+   */
+  def resolveSummaryConflict(v1: Any, v2: Any, key: String) = v1
+}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetQScript
+import nl.lumc.sasc.biopet.extensions.Md5sum
+
+/**
+ * Created by pjvan_thof on 2/14/15.
+ */
+trait SummaryQScript extends BiopetQScript {
+
+  /** Key is sample/library, None is sample or library is not applicable */
+  private[summary] var summarizables: Map[(Option[String], Option[String]), List[Summarizable]] = Map()
+  private[summary] var summaryQScripts: List[SummaryQScript] = Nil
+
+  def summaryFile: File
+
+  def addSummarizable(summarizable: Summarizable,
+                      sampleId: Option[String] = None,
+                      libraryId: Option[String] = None): Unit = {
+    require(libraryId.isDefined == sampleId.isDefined) // Library always require a sample
+    summarizables += (sampleId, libraryId) -> (summarizable :: summarizables.getOrElse((sampleId, libraryId), Nil))
+  }
+
+  def addSummaryQScript(summaryQScript: SummaryQScript): Unit = {
+    summaryQScripts :+= summaryQScript
+  }
+
+  def addSummaryJobs: Unit = {
+    val writeSummary = new WriteSummary(this)
+
+    //Automatic checksums
+    val keepChecksums: Boolean = config("keep_checksums_files", default = false)
+
+    for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles) {
+      if (writeSummary.md5sum) {
+        val md5sum = Md5sum(this, file)
+        md5sum.isIntermediate = !keepChecksums
+        writeSummary.deps :+= md5sum.output
+        add(md5sum)
+      }
+      //TODO: add more checksums types
+    }
+
+    add(writeSummary)
+  }
+}

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

+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.{PrintWriter, File}
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.queue.function.{ QFunction, InProcessFunction }
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 2/14/15.
+ */
+class WriteSummary(val root: Configurable) extends InProcessFunction with Configurable {
+  this.analysisName = getClass.getSimpleName
+
+  require(root.isInstanceOf[SummaryQScript], "root is not a SummaryQScript")
+
+  val summaryQScript = root.asInstanceOf[SummaryQScript]
+
+  @Input(doc = "deps", required = false)
+  var deps: List[File] = Nil
+
+  @Output(doc = "Summary output", required = true)
+  var out: File = summaryQScript.summaryFile
+
+  var md5sum: Boolean = config("summary_md5", default = true)
+  //TODO: add more checksums types
+
+  override def freezeFieldValues(): Unit = {
+    for (q <- summaryQScript.summaryQScripts) deps :+= q.summaryFile
+    for ((_, l) <- summaryQScript.summarizables; s <- l) s match {
+      case f: QFunction => deps :+= f.firstOutput
+      case _            =>
+    }
+    super.freezeFieldValues()
+  }
+
+  def run(): Unit = {
+    val writer = new PrintWriter(out)
+
+    writer.close()
+  }
+}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala

@@ -49,4 +49,11 @@ object Md5sum {
     md5sum.output = new File(outDir + fastqfile.getName + ".md5")
     return md5sum
   }
+
+  def apply(root: Configurable, file: File): Md5sum = {
+    val md5sum = new Md5sum(root)
+    md5sum.input = file
+    md5sum.output = new File(file.getParentFile, file.getName + ".md5")
+    return md5sum
+  }
 }

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

@@ -18,6 +18,8 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 
 import java.io.{ File, FileNotFoundException }
 
+import nl.lumc.sasc.biopet.core.summary.Summarizable
+
 import scala.io.Source
 
 import argonaut._, Argonaut._
@@ -32,7 +34,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
  * This wrapper implements additional methods for parsing FastQC output files and aggregating everything in a summary
  * object. The current implementation is based on FastQC v0.10.1.
  */
-class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(root) {
+class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(root) with Summarizable {
 
   /** Class for storing a single FastQC module result */
   protected case class FastQCModule(name: String, status: String, lines: Seq[String])
@@ -160,6 +162,10 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
 
     ConfigUtils.mapToJson(outputMap)
   }
+
+  def summaryFiles: Map[String, File] = Map("test" -> this.fastqfile)
+
+  def summaryStats: Map[String, Any] = Map()
 }
 
 object Fastqc {

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

@@ -15,6 +15,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
 
@@ -23,7 +24,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.{ Gzip, Pbzip2, Md5sum, Zcat, Seqstat }
 import nl.lumc.sasc.biopet.tools.FastqSync
 
-class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
+class Flexiprep(val root: Configurable) extends QScript with BiopetQScript with SummaryQScript {
   def this() = this(null)
 
   @Input(doc = "R1 fastq file (gzipped allowed)", shortName = "R1", required = true)
@@ -48,6 +49,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
   @Argument(doc = "Library ID", shortName = "library", required = true)
   var libId: String = _
 
+  def summaryFile = new File(outputDir, sampleId + "-" + libId + ".qc.summary.json")
+
   var paired: Boolean = input_R2.isDefined
   var R1_ext: String = _
   var R2_ext: String = _
@@ -264,6 +267,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
         summary.addMd5sum(md5sum_R2, R2 = true, after = true)
       }
       fastqc_R1_after = Fastqc(this, R1, outputDir + "/" + R1_name + ".qc.fastqc/")
+      addSummarizable(fastqc_R1_after)
       add(fastqc_R1_after)
       summary.addFastqc(fastqc_R1_after, after = true)
       if (paired) {
@@ -273,7 +277,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
       }
     }
 
-    add(summary)
+    //add(summary)
+    addSummaryJobs
   }
 
   def extractIfNeeded(file: File, runDir: String): File = {