Small fixes in report

public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/gears.js

@@ -175,7 +175,7 @@ function loadTable(d, target) {
             .data(child)
             .on("click", outerclick);
         row.append("td").attr("class", "col-md-3").text( child.size );
-        row.append("td").attr("class", "col-md-3").text( child.value );
+        row.append("td").attr("class", "col-md-3").text( child.count );
 
     }
 
@@ -221,7 +221,7 @@ var y = d3.scale.sqrt()
 
 var color = d3.scale.category20c();
 
-var svg = d3.select("body").append("svg")
+var svg = d3.select("#svgholder").append("svg")
     .attr("width", width)
     .attr("height", height)
     .append("g")
@@ -248,7 +248,7 @@ var arc = d3.svg.arc()
 // Keep track of the node that is currently being displayed as the root.
 var node;
 
-d3.json("./tst.json", function(error, root) {
+function loadGears( root ) {
     console.log(root);
     node = root;
     var path = svg.datum(root).selectAll("path")
@@ -291,9 +291,7 @@ d3.json("./tst.json", function(error, root) {
 
     // Get total size of the tree = value of root node from partition.
     totalSize = path.node().__data__.value;
-
-});
-
+}
 d3.select(self.frameElement).style("height", height + "px");
 
 

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

@@ -148,18 +148,12 @@ object KrakenReportToJson extends ToolCommand {
       }
     })
 
-    val result = Map("unclasified" -> lines(0).toJSON(withChildren = false),
+    val result = Map("unclassified" -> lines(0).toJSON(withChildren = false),
       "classified" -> lines(1).toJSON(withChildren = true))
     mapToJson(result).spaces2
 
   }
 
-  def summary: String = {
-    val result = Map("unclasified" -> lines(0).toJSON(withChildren = false),
-      "classified" -> lines(1).toJSON(withChildren = true))
-    mapToJson(result).spaces2
-  }
-
   def main(args: Array[String]): Unit = {
     val commandArgs: Args = parseArgs(args)
 

public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp

@@ -33,9 +33,7 @@
 
 #if (showPlot)
 <div class="row">
-    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js" charset="utf-8"></script>
-    <script src="${rootPath}ext/js/gears.js"></script>
-
+    <div class="col-md-12">
     <h3 id='currentlevel'>Root</h3>
     <div>
         <span id="selection_name"></span> -
@@ -49,7 +47,15 @@
     </form>
     <div id="sequence"></div>
 
-    <div id="datatable">
+    <div id="datatable"></div>
+    <div id="svgholder"></div>
+
+    </div>
+
+
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js" charset="utf-8"></script>
+    <script src="${rootPath}ext/js/gears.js"></script>
+
     <script type="application/ecmascript">
 
     #{
@@ -58,9 +64,9 @@
     }#
 
         var krakenresult = JSON.parse('<%= unescape(bla) %>');
+        loadGears(krakenresult.kraken.classified);
+    </script>
 
 
-    </script>
-    </div>
 </div>
 #end

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

@@ -18,9 +18,9 @@ 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.extensions.picard.{ SortSam, SamToFastq }
+import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
 import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
-import nl.lumc.sasc.biopet.extensions.tools.{ KrakenReportToJson, FastqSync }
+import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, KrakenReportToJson }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -30,27 +30,25 @@ import org.broadinstitute.gatk.queue.QScript
 class Gears(val root: Configurable) extends QScript with SummaryQScript {
   def this() = this(null)
 
-  @Input(shortName = "R1", required = false)
-  var fastqFileR1: Option[File] = None
+  @Input(doc = "R1 reads in FastQ format", shortName = "R1", required = false)
+  var fastqR1: Option[File] = None
 
-  @Input(shortName = "R2", required = false)
-  var fastqFileR2: Option[File] = None
+  @Input(doc = "R2 reads in FastQ format", shortName = "R2", required = false)
+  var fastqR2: Option[File] = None
 
-  @Input(doc = "From the bam all the upmapped reads are used for kraken", shortName = "bam", required = false)
+  @Input(doc = "All unmapped reads will be extracted from this bam for analysis", shortName = "bam", required = false)
   var bamFile: Option[File] = None
 
   @Argument(required = false)
   var outputName: String = _
 
-  var GearsOutputFiles: scala.collection.mutable.Map[String, File] = scala.collection.mutable.Map.empty
-
   /** Executed before running the script */
   def init(): Unit = {
-    require(fastqFileR1.isDefined || bamFile.isDefined, "Must define fastq file(s) or a bam file")
-    require(fastqFileR1.isDefined != bamFile.isDefined, "Can't define a bam file and a R1 file")
+    require(fastqR1.isDefined || bamFile.isDefined, "Must define fastq file(s) or a bam file")
+    require(fastqR1.isDefined != bamFile.isDefined, "Can't define a bam file and a R1 file")
 
     if (outputName == null) {
-      if (fastqFileR1.isDefined) outputName = fastqFileR1.map(_.getName
+      if (fastqR1.isDefined) outputName = fastqR1.map(_.getName
         .stripSuffix(".gz")
         .stripSuffix(".fastq")
         .stripSuffix(".fq"))
@@ -97,41 +95,41 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
 
       // TODO: need some sanity check on whether R2 is really containing reads (e.g. Single End libraries)
       fastqSync.outputFastq2 = new File(outputDir, s"$outputName.unmapped.R2.sync.fq.gz")
-      fastqSync.outputStats = new File(outputDir, s"$outputName.sync.stats.json")
+      fastqSync.outputStats = new File(outputDir, s"$outputName.sync.stats")
       add(fastqSync)
+      addSummarizable(fastqSync, "fastqsync")
 
-      GearsOutputFiles += ("fastqsync_stats" -> fastqSync.outputStats)
-      GearsOutputFiles += ("fastqsync_R1" -> fastqSync.outputFastq1)
-      GearsOutputFiles += ("fastqsync_R2" -> fastqSync.outputFastq2)
+      outputFiles += ("fastqsync_stats" -> fastqSync.outputStats)
+      outputFiles += ("fastqsync_R1" -> fastqSync.outputFastq1)
+      outputFiles += ("fastqsync_R2" -> fastqSync.outputFastq2)
 
       List(fastqSync.outputFastq1, fastqSync.outputFastq2)
-    }.getOrElse(List(fastqFileR1, fastqFileR2).flatten)
+    }.getOrElse(List(fastqR1, fastqR2).flatten)
 
     // start kraken
     val krakenAnalysis = new Kraken(this)
     krakenAnalysis.input = fastqFiles
     krakenAnalysis.output = new File(outputDir, s"$outputName.krkn.raw")
 
-    krakenAnalysis.paired = (fastqFiles.length == 2)
+    krakenAnalysis.paired = fastqFiles.length == 2
 
-    krakenAnalysis.classified_out = Option(new File(outputDir, s"$outputName.krkn.classified.fastq"))
-    krakenAnalysis.unclassified_out = Option(new File(outputDir, s"$outputName.krkn.unclassified.fastq"))
+    krakenAnalysis.classified_out = Some(new File(outputDir, s"$outputName.krkn.classified.fastq"))
+    krakenAnalysis.unclassified_out = Some(new File(outputDir, s"$outputName.krkn.unclassified.fastq"))
     add(krakenAnalysis)
 
-    GearsOutputFiles += ("kraken_output_raw" -> krakenAnalysis.output)
-    GearsOutputFiles += ("kraken_classified_out" -> krakenAnalysis.classified_out.getOrElse(""))
-    GearsOutputFiles += ("kraken_unclassified_out" -> krakenAnalysis.unclassified_out.getOrElse(""))
+    outputFiles += ("kraken_output_raw" -> krakenAnalysis.output)
+    outputFiles += ("kraken_classified_out" -> krakenAnalysis.classified_out.getOrElse(""))
+    outputFiles += ("kraken_unclassified_out" -> krakenAnalysis.unclassified_out.getOrElse(""))
 
     // create kraken summary file
-
     val krakenReport = new KrakenReport(this)
     krakenReport.input = krakenAnalysis.output
     krakenReport.show_zeros = true
     krakenReport.output = new File(outputDir, s"$outputName.krkn.full")
     add(krakenReport)
 
-    GearsOutputFiles += ("kraken_report_input" -> krakenReport.input)
-    GearsOutputFiles += ("kraken_report_output" -> krakenReport.output)
+    outputFiles += ("kraken_report_input" -> krakenReport.input)
+    outputFiles += ("kraken_report_output" -> krakenReport.output)
 
     val krakenReportJSON = new KrakenReportToJson(this)
     krakenReportJSON.inputReport = krakenReport.output
@@ -140,8 +138,8 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
     add(krakenReportJSON)
     addSummarizable(krakenReportJSON, "krakenreport")
 
-    GearsOutputFiles += ("kraken_report_json_input" -> krakenReportJSON.inputReport)
-    GearsOutputFiles += ("kraken_report_json_output" -> krakenReportJSON.output)
+    outputFiles += ("kraken_report_json_input" -> krakenReportJSON.inputReport)
+    outputFiles += ("kraken_report_json_output" -> krakenReportJSON.output)
 
     addSummaryJobs()
   }
@@ -152,13 +150,13 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
   /** 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 (fastqFileR1.isDefined) Map("input_R1" -> fastqFileR1.get) else Map())
+    (if (fastqR1.isDefined) Map("input_R1" -> fastqR1.get) else Map())
 
   /** Statistics shown in the summary file */
   def summaryFiles: Map[String, File] = Map.empty ++
     (if (bamFile.isDefined) Map("input_bam" -> bamFile.get) else Map()) ++
-    (if (fastqFileR1.isDefined) Map("input_R1" -> fastqFileR1.get) else Map()) ++
-    GearsOutputFiles
+    (if (fastqR1.isDefined) Map("input_R1" -> fastqR1.get) else Map()) ++
+    outputFiles
 }
 
 /** This object give a default main method to the pipelines */