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

Fix: Show a message for those plot, which were not created by FastQC. Some statistics cannot be collected by FastQC such as Kmer when the sequences are clean.

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 +14,22 @@
 
     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) = {
+        summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "files", read, plot, "md5").collect {
+            case md5 if md5 != "error_on_capture" => true
+            case otherwise => false
+        }.getOrElse(false)
+    }
+
 }#
 
 <div class="row">
@@ -32,11 +40,19 @@
 <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 +60,19 @@
     <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))
   }
 
   /**