Merge branch 'patch-mutisample_summary' into 'develop'

Patch mutisample summary

See merge request !112

protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -31,10 +31,30 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
 
   var gatkPipeline: GatkPipeline = new GatkPipeline(qscript)
 
+  def summaryFile: File = new File(outputDir, "Sage.summary.json")
+
+  //TODO: Add summary
+  def summaryFiles: Map[String, File] = Map()
+
+  //TODO: Add summary
+  def summarySettings: Map[String, Any] = Map()
+
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
+    //TODO: Add summary
+    def summaryFiles: Map[String, File] = Map()
+
+    //TODO: Add summary
+    def summaryStats: Map[String, Any] = Map()
+
     def makeLibrary(id: String) = new Library(id)
     class Library(libId: String) extends AbstractLibrary(libId) {
+      //TODO: Add summary
+      def summaryFiles: Map[String, File] = Map()
+
+      //TODO: Add summary
+      def summaryStats: Map[String, Any] = Map()
+
       protected def addJobs(): Unit = {}
     }
 
@@ -56,6 +76,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
   def biopetScript() {
     gatkPipeline.biopetScript
     addAll(gatkPipeline.functions)
+    addSummaryQScript(gatkPipeline)
 
     addSamplesJobs()
   }

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -43,14 +43,28 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
 
   def summaryFile = new File(outputDir, "GatkPipeline.summary.json")
 
+  //TODO: Add summary
   def summaryFiles = Map()
 
+  //TODO: Add summary
   def summarySettings = Map()
 
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
+    //TODO: Add summary
+    def summaryFiles: Map[String, File] = Map()
+
+    //TODO: Add summary
+    def summaryStats: Map[String, Any] = Map()
+
     def makeLibrary(id: String) = new Library(id)
     class Library(libId: String) extends AbstractLibrary(libId) {
+      //TODO: Add summary
+      def summaryFiles: Map[String, File] = Map()
+
+      //TODO: Add summary
+      def summaryStats: Map[String, Any] = Map()
+
       val mapping = new Mapping(qscript)
       mapping.sampleId = Some(sampleId)
       mapping.libId = Some(libId)

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

@@ -18,39 +18,40 @@ package nl.lumc.sasc.biopet.core
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.{ Config }
+import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.utils.commandline.{ Argument }
 
-/**
- * This trait creates a structured way of use multisample pipelines
- */
-trait MultiSampleQScript extends BiopetQScript {
+/** This trait creates a structured way of use multisample pipelines */
+trait MultiSampleQScript extends SummaryQScript {
+  qscript =>
+
   @Argument(doc = "Only Sample", shortName = "sample", required = false)
   private val onlySamples: List[String] = Nil
 
   require(globalConfig.map.contains("samples"), "No Samples found in config")
 
-  /**
-   * Sample class with basic functions build in
-   * @param sampleId
-   */
-  abstract class AbstractSample(val sampleId: String) {
+  /** Sample class with basic functions build in */
+  abstract class AbstractSample(val sampleId: String) extends Summarizable {
     /** Overrules config of qscript with default sample */
     val config = new ConfigFunctions(defaultSample = sampleId)
 
-    /**
-     * Library class with basic functions build in
-     * @param libId
-     */
-    abstract class AbstractLibrary(val libId: String) {
+    /** Library class with basic functions build in */
+    abstract class AbstractLibrary(val libId: String) extends Summarizable {
       /** Overrules config of qscript with default sample and default library */
       val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
 
+      /** Name overules the one from qscript */
+      def addSummarizable(summarizable: Summarizable, name: String): Unit = {
+        qscript.addSummarizable(summarizable, name, Some(sampleId), Some(libId))
+      }
+
       /** Adds the library jobs */
       final def addAndTrackJobs(): Unit = {
         currentSample = Some(sampleId)
         currentLib = Some(libId)
         addJobs()
+        qscript.addSummarizable(this, "pipeline", Some(sampleId), Some(libId))
         currentLib = None
         currentSample = None
       }
@@ -83,10 +84,16 @@ trait MultiSampleQScript extends BiopetQScript {
       ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
     }
 
+    /** Name overules the one from qscript */
+    def addSummarizable(summarizable: Summarizable, name: String): Unit = {
+      qscript.addSummarizable(summarizable, name, Some(sampleId))
+    }
+
     /** Adds sample jobs */
     final def addAndTrackJobs(): Unit = {
       currentSample = Some(sampleId)
       addJobs()
+      qscript.addSummarizable(this, "pipeline", Some(sampleId))
       currentSample = None
     }
 
@@ -139,7 +146,7 @@ trait MultiSampleQScript extends BiopetQScript {
   }
 
   /**
-   * Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given
+   * Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given.
    */
   def addMultiSampleJobs()
 

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

@@ -9,18 +9,12 @@ import nl.lumc.sasc.biopet.core.config.Configurable
  *
  * Created by pjvan_thof on 2/14/15.
  */
-trait Summarizable extends Configurable {
+trait Summarizable {
 
-  /**
-   * Must return files to store into summary
-   * @return
-   */
+  /** Must return files to store into summary */
   def summaryFiles: Map[String, File]
 
-  /**
-   * Must returns stats to store into summary
-   * @return
-   */
+  /** Must returns stats to store into summary */
   def summaryStats: Map[String, Any]
 
   /**

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala

@@ -22,11 +22,25 @@ import org.broadinstitute.gatk.queue.QScript
 class MultisamplePipelineTemplate(val root: Configurable) extends QScript with MultiSampleQScript {
   def this() = this(null)
 
+  def summaryFile: File = new File(outputDir, "MultisamplePipelineTemplate.summary.json")
+
+  def summaryFiles: Map[String, File] = Map()
+
+  def summarySettings: Map[String, Any] = Map()
+
   def makeSample(id: String) = new Sample(id)
+
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
+    def summaryFiles: Map[String, File] = Map()
+
+    def summaryStats: Map[String, Any] = Map()
 
     def makeLibrary(id: String) = new Library(id)
     class Library(libId: String) extends AbstractLibrary(libId) {
+      def summaryFiles: Map[String, File] = Map()
+
+      def summaryStats: Map[String, Any] = Map()
+
       protected def addJobs(): Unit = {
         // Library jobs
       }

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

@@ -45,14 +45,28 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
 
   def summaryFile = new File(outputDir, "Carp.summary.json")
 
+  //TODO: Add summary
   def summaryFiles = Map()
 
+  //TODO: Add summary
   def summarySettings = Map()
 
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
+    //TODO: Add summary
+    def summaryFiles: Map[String, File] = Map()
+
+    //TODO: Add summary
+    def summaryStats: Map[String, Any] = Map()
+
     def makeLibrary(id: String) = new Library(id)
     class Library(libId: String) extends AbstractLibrary(libId) {
+      //TODO: Add summary
+      def summaryFiles: Map[String, File] = Map()
+
+      //TODO: Add summary
+      def summaryStats: Map[String, Any] = Map()
+
       val mapping = new Mapping(qscript)
       mapping.libId = Some(libId)
       mapping.sampleId = Some(sampleId)

public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala

@@ -33,10 +33,30 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
     addSamplesJobs()
   }
 
+  def summaryFile: File = new File(outputDir, "Kopisu.summary.json")
+
+  //TODO: Add summary
+  def summaryFiles: Map[String, File] = Map()
+
+  //TODO: Add summary
+  def summarySettings: Map[String, Any] = Map()
+
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
+    //TODO: Add summary
+    def summaryFiles: Map[String, File] = Map()
+
+    //TODO: Add summary
+    def summaryStats: Map[String, Any] = Map()
+
     def makeLibrary(id: String) = new Library(id)
     class Library(libId: String) extends AbstractLibrary(libId) {
+      //TODO: Add summary
+      def summaryFiles: Map[String, File] = Map()
+
+      //TODO: Add summary
+      def summaryStats: Map[String, Any] = Map()
+
       def addJobs(): Unit = {
 
       }

public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -58,10 +58,30 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
   )
   ), super.defaults)
 
+  def summaryFile: File = new File(outputDir, "Sage.summary.json")
+
+  //TODO: Add summary
+  def summaryFiles: Map[String, File] = Map()
+
+  //TODO: Add summary
+  def summarySettings: Map[String, Any] = Map()
+
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
+    //TODO: Add summary
+    def summaryFiles: Map[String, File] = Map()
+
+    //TODO: Add summary
+    def summaryStats: Map[String, Any] = Map()
+
     def makeLibrary(id: String) = new Library(id)
     class Library(libId: String) extends AbstractLibrary(libId) {
+      //TODO: Add summary
+      def summaryFiles: Map[String, File] = Map()
+
+      //TODO: Add summary
+      def summaryStats: Map[String, Any] = Map()
+
       val inputFastq: File = config("R1")
       val prefixFastq: File = createFile(".prefix.fastq")