Fix flexiprep bug and remove import ugliness in gears report

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

@@ -14,7 +14,6 @@
 <%@ var multisample: Boolean = true %>
 <%@ var allSamples: Seq[Sample] %>
 <%@ var allLibraries: Seq[Library] %>
-<%-- variables to be added to remove dependency upon futures --%>
 <%@ var settings: Map[(Int, Int), Map[String, Option[Any]]] %>
 <%@ var paired: Boolean %>
 <%@ var samples: Seq[Sample] %>

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala

@@ -295,8 +295,8 @@ object FlexiprepReadSummary {
         FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId)
 
     val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
-    val clippingPaths = Map(
-      "num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"))
+    val clippingPaths = Map("num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"),
+      "num_reads_discarded_too_long" -> List("num_reads_discarded_too_long"))
     val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_total"))
 
     val seqstatStats: Map[(Int, Int), Map[String, Option[Any]]] =

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

@@ -16,36 +16,17 @@ package nl.lumc.sasc.biopet.pipelines.gears
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.report.{
-  MultisampleReportBuilder,
-  ReportBuilderExtension,
-  ReportPage,
-  ReportSection
-}
-import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
-import nl.lumc.sasc.biopet.pipelines.gears
-import nl.lumc.sasc.biopet.core.report.{
-  MultisampleReportBuilder,
-  ReportBuilderExtension,
-  ReportPage,
-  ReportSection
-}
-import nl.lumc.sasc.biopet.pipelines.flexiprep.{
-  FlexiprepBaseSummary,
-  FlexiprepReadSummary,
-  FlexiprepReport
-}
+import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
+import nl.lumc.sasc.biopet.pipelines.flexiprep.{FlexiprepBaseSummary, FlexiprepReadSummary, FlexiprepReport}
 import nl.lumc.sasc.biopet.pipelines.gears
 import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Sample}
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
-import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{NoLibrary, NoModule, SampleId}
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ModuleName, NoLibrary, NoModule, SampleId}
-import nl.lumc.sasc.biopet.utils.summary.db.Schema.Library
-import nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample
 
-import scala.concurrent.{Await, Future}
 import scala.concurrent.duration.Duration
+import scala.concurrent.{Await, Future}
 
 /**
   * Report for Gears