Fixes for the comments made in the ticket #241

public/biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet
 
-import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
+import nl.lumc.sasc.biopet.utils.{BiopetExecutable, MainCommand}
 
 object BiopetToolsExecutable extends BiopetExecutable {
 
@@ -44,6 +44,5 @@ object BiopetToolsExecutable extends BiopetExecutable {
     nl.lumc.sasc.biopet.tools.SeqStat,
     nl.lumc.sasc.biopet.tools.VepNormalizer,
     nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
-    nl.lumc.sasc.biopet.tools.VcfWithVcf,
-    nl.lumc.sasc.biopet.tools.KrakenReportToJson)
+    nl.lumc.sasc.biopet.tools.VcfWithVcf)
 }

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala

@@ -19,7 +19,7 @@ package nl.lumc.sasc.biopet.tools
  * Created by wyleung on 25-9-15.
  */
 
-import java.io.{ File, PrintWriter }
+import java.io.{File, PrintWriter}
 
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
 import nl.lumc.sasc.biopet.utils.ToolCommand
@@ -28,30 +28,30 @@ import scala.collection.mutable
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
 
-case class KrakenHit(taxonomyID: Long,
-                     taxonomyName: String,
-                     cladeCount: Long,
-                     cladeSize: Long, // size of parent - including itself
-                     taxonRank: String,
-                     cladeLevel: Int,
-                     parentTaxonomyID: Long,
-                     children: ListBuffer[KrakenHit]) {
-  def toJSON(withChildren: Boolean = false): Map[String, Any] = {
-    val childJSON = if (withChildren) children.toList.map(entry => entry.toJSON(withChildren)) else List()
-    Map(
-      "name" -> taxonomyName,
-      "taxid" -> taxonomyID,
-      "taxonrank" -> taxonRank,
-      "cladelevel" -> cladeLevel,
-      "count" -> cladeCount,
-      "size" -> cladeSize,
-      "children" -> childJSON
-    )
-  }
+object KrakenReportToJson extends ToolCommand {
 
-}
+  case class KrakenHit(taxonomyID: Long,
+                       taxonomyName: String,
+                       cladeCount: Long,
+                       cladeSize: Long, // size of parent - including itself
+                       taxonRank: String,
+                       cladeLevel: Int,
+                       parentTaxonomyID: Long,
+                       children: ListBuffer[KrakenHit]) {
+    def toJSON(withChildren: Boolean = false): Map[String, Any] = {
+      val childJSON = if (withChildren) children.toList.map(entry => entry.toJSON(withChildren)) else List()
+      Map(
+        "name" -> taxonomyName,
+        "taxid" -> taxonomyID,
+        "taxonrank" -> taxonRank,
+        "cladelevel" -> cladeLevel,
+        "count" -> cladeCount,
+        "size" -> cladeSize,
+        "children" -> childJSON
+      )
+    }
 
-object KrakenReportToJson extends ToolCommand {
+  }
 
   var cladeIDs: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer.fill(32)(0)
   val spacePattern = "^( +)".r

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala

@@ -15,19 +15,19 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gears
 
-import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
+import nl.lumc.sasc.biopet.core.{PipelineCommand, SampleLibraryTag}
+import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
 import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
 import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
-import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, KrakenReportToJson }
+import nl.lumc.sasc.biopet.extensions.tools.{FastqSync, KrakenReportToJson}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
 /**
  * Created by wyleung
  */
-class Gears(val root: Configurable) extends QScript with SummaryQScript {
+class Gears(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
   def this() = this(null)
 
   @Input(doc = "R1 reads in FastQ format", shortName = "R1", required = false)
@@ -145,12 +145,10 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
   }
 
   /** Location of summary file */
-  def summaryFile = new File(outputDir, "gears.summary.json")
+  def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".gears.summary.json")
 
   /** Pipeline settings shown in the summary file */
-  def summarySettings: Map[String, Any] = Map.empty ++
-    (if (bamFile.isDefined) Map("input_bam" -> bamFile.get) else Map()) ++
-    (if (fastqR1.isDefined) Map("input_R1" -> fastqR1.get) else Map())
+  def summarySettings: Map[String, Any] = Map.empty
 
   /** Statistics shown in the summary file */
   def summaryFiles: Map[String, File] = Map.empty ++

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala

 package nl.lumc.sasc.biopet.pipelines.gears
 
-import java.io.{ PrintWriter, File }
-
-import nl.lumc.sasc.biopet.core.report.MultisampleReportBuilder
-import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
-import nl.lumc.sasc.biopet.core.report.ReportPage
-import nl.lumc.sasc.biopet.core.report.ReportSection
+import nl.lumc.sasc.biopet.core.report._
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class GearsReport(val root: Configurable) extends ReportBuilderExtension {
   val builder = GearsReport
-
-  override val defaultCoreMemory = 3.0
 }
 
-object GearsReport extends MultisampleReportBuilder {
+object GearsReport extends ReportBuilder {
 
   // FIXME: Not yet finished
-  // TODO: Summary all: Add summary (sunflare plot)
   // TODO: Sample specific: Add summary (sunflare plot)
-  // TODO: Add dusbin analysis (aggregated)
+  // TODO: Add dustbin analysis (aggregated)
   // TODO: Add alignment stats per sample for the dustbin analysis
 
   def indexPage = {
     ReportPage(
-      List("Samples" -> generateSamplesPage(pageArgs)) ++
+      List() ++
         Map(
           "Versions" -> ReportPage(List(), List((
             "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
@@ -38,16 +30,6 @@ object GearsReport extends MultisampleReportBuilder {
     )
   }
 
-  def samplePage(sampleId: String, args: Map[String, Any]) = {
-    ReportPage(List(), List(
-      "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp")
-    ), args)
-  }
-
-  def libraryPage(sampleId: String, libId: String, args: Map[String, Any]) = {
-    ReportPage(List(), List(), args)
-  }
-
   def reportName = "Gears :: Metagenomics Report"
 
 }