Fix report, the logic to display SE or PE from flexiprep stats is deprecated...

Fix report, the logic to display SE or PE from flexiprep stats is deprecated since we always use flexiprep->cutadapt in SE mode. So only SE mode variables are generated and should be displayed in the report.

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

@@ -144,12 +144,7 @@
                             val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_qc", "reads", "num_total")
                             val clippingDiscardedToShort = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short").getOrElse(0).toString.toLong
                             val clippingDiscardedToLong = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long").getOrElse(0).toString.toLong
-                            var trimmingDiscarded: Long = 0
-                            if(paired == true) {
-                            trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming_" + read, "num_reads_discarded_" + read).getOrElse(0).toString.toLong
-                            } else {
-                            trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming_" + read, "num_reads_discarded_total").getOrElse(0).toString.toLong
-                            }
+                            var trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming_" + read, "num_reads_discarded_total").getOrElse(0).toString.toLong
                         }#
                         <td>${read}</td>
                         <td>${beforeTotal}</td>