Fixing fastqc plots

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

@@ -7,6 +7,7 @@
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(org.apache.commons.io.FileUtils)
 #import(java.io.File)
+#import(nl.lumc.sasc.biopet.core.report.ReportBuilder.ec)
 <%@ var summary: SummaryDb %>
 <%@ var runId: Int %>
 <%@ var sampleId: Option[Int] %>
@@ -16,6 +17,7 @@
 #{
     val settings = summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map(
     "skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
+    val run = Await.result(summary.getRuns(runId = Some(runId)).map(_.head), Duration.Inf)
 
     val paired: Boolean = settings("paired") == Some(true)
     val skipClip: Boolean = settings("skip_clip") == Some(true)
@@ -25,7 +27,7 @@
         val file = Await.result(summary.getFile(runId, "flexiprep", read, SampleId(sampleId.get), LibraryId(libId.get), plot), Duration.Inf)
         file.collect {
             case path => {
-                val file = new File(path.path.toString)
+                val file = new File(run.outputDir + File.separator + path.path.toString)
                 val newFile = new File(outputDir, read + "_" + file.getName)
                 if (file.exists()) FileUtils.copyFile(file, newFile)
                 newFile.getName
@@ -35,7 +37,7 @@
 
     def plotAvailable(read:String) = {
         val file = Await.result(summary.getFile(runId, "flexiprep", read, SampleId(sampleId.get), LibraryId(libId.get), plot), Duration.Inf)
-        file.map(x => new File(x.path).exists()).getOrElse(false)
+        file.map(x => new File(run.outputDir + File.separator + x.path).exists()).getOrElse(false)
     }
 
 }#