Merge branch 'fix-flexiprep-fastqc_report_kmer' into 'develop'

Fix: Show a message for those plot, which were not created by FastQC. Some stati…

…stics cannot be collected by FastQC such as Kmer when the sequences are clean.

See merge request !355

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

@@ -14,14 +14,19 @@
 
     def getPlot(read:String) = {
         summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "files", read, plot, "path").collect {
-            case value => {
-                val file = new File(value.toString)
+            case path => {
+                val file = new File(path.toString)
                 val newFile = new File(outputDir, read + "_" + file.getName)
                 if (file.exists()) FileUtils.copyFile(file, newFile)
                 newFile.getName
             }
         }
     }
+
+    def plotAvailable(read:String) = {
+        new File(summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "files", read, plot, "path").get.toString).exists()
+    }
+
 }#
 
 <div class="row">
@@ -32,11 +37,19 @@
 <div class="row">
     <div class="col-md-1"><b>R1</b></div>
     <div class="col-md-5">
+    #if (plotAvailable( "fastqc_R1" ))
         <img class="img-responsive" src="${getPlot("fastqc_R1")}" />
+    #else
+        Image was not generated by FastQC
+    #end
     </div>
     #if (!skipTrim || !skipClip)
     <div class="col-md-5">
+    #if (plotAvailable( "fastqc_R1_qc" ))
         <img class="img-responsive" src="${getPlot("fastqc_R1_qc")}" />
+    #else
+        Image was not generated by FastQC
+    #end
     </div>
      #end
 </div>
@@ -44,11 +57,19 @@
     <div class="row">
         <div class="col-md-1"><b>R2</b></div>
         <div class="col-md-5">
+        #if (plotAvailable( "fastqc_R2" ))
             <img class="img-responsive" src="${getPlot("fastqc_R2")}" />
+        #else
+            Image was not generated by FastQC
+        #end
         </div>
         #if (!skipTrim || !skipClip)
         <div class="col-md-5">
+        #if (plotAvailable( "fastqc_R2_qc" ))
             <img class="img-responsive" src="${getPlot("fastqc_R2_qc")}" />
+        #else
+            Image was not generated by FastQC
+        #end
         </div>
          #end
     </div>

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

@@ -62,7 +62,7 @@ object FlexiprepReport extends ReportBuilder {
       fastqcPlotSection("Sequence quality", "plot_per_sequence_quality"),
       fastqcPlotSection("Base GC content", "plot_per_base_gc_content"),
       fastqcPlotSection("Sequence GC content", "plot_per_sequence_gc_content"),
-      fastqcPlotSection("Base seqeunce content", "plot_per_base_sequence_content"),
+      fastqcPlotSection("Base sequence content", "plot_per_base_sequence_content"),
       fastqcPlotSection("Duplication", "plot_duplication_levels"),
       fastqcPlotSection("Kmers", "plot_kmer_profiles"),
       fastqcPlotSection("Length distribution", "plot_sequence_length_distribution")
@@ -71,7 +71,7 @@ object FlexiprepReport extends ReportBuilder {
   )
 
   protected def fastqcPlotSection(name: String, tag: String) = {
-    name -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp", Map("plot" -> tag))
+    name -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp", Map("plot" -> tag))
   }
 
   /**