Fix report

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -104,19 +104,6 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
     }
     logger.info(s"Preprocessing done for $totalCount functions")
 
-    logger.info("Adding report")
-    this match {
-      case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
-        logger.info("Write report is skipped because sample flag is used")
-      case _ => reportClass.foreach { report =>
-        for (f <- functions) f match {
-          case w: WriteSummary => report.deps :+= w.jobOutputFile
-          case _               =>
-        }
-        add(report)
-      }
-    }
-
     val logDir = new File(outputDir, ".log" + File.separator + qSettings.runName.toLowerCase)
 
     if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
@@ -139,6 +126,20 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       }
     })
 
+    logger.info("Adding report")
+    this match {
+      case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
+        logger.info("Write report is skipped because sample flag is used")
+      case _ => reportClass.foreach { report =>
+        for (f <- functions) f match {
+          case w: WriteSummary => report.deps :+= w.jobOutputFile
+          case _               =>
+        }
+        report.jobOutputFile = new File(report.outputDir, ".report.out")
+        add(report)
+      }
+    }
+
     if (!skipWriteDependencies) WriteDependencies.writeDependencies(
       functions,
       new File(logDir, "graph"))

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala

@@ -38,8 +38,6 @@ object MappingReport extends ReportBuilder {
   override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
     .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
 
-  summary.getStatsSize(runId, Right("gears"), Some(Right("krakenreport")),
-    sample = sampleId.map(Left(_)), library = libId.map(Left(_)))
   def krakenExecuted: Boolean = Await.result(summary.getStatsSize(runId, Right("gears"), Some(Right("krakenreport")),
     sample = sampleId.map(Left(_)), library = libId.map(Left(_))), Duration.Inf) >= 1