Update summary creation for Flexiprep FastQC

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

@@ -67,27 +67,30 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
       line <- block if !line.startsWith("#");
       values = line.split("\t") if values.size >= 4
     ) yield values(3)
+  /** Summary of the FastQC run, stored in a [[Json]] object */
+  def summary: Json = {
 
     seqs.filter(x => found.exists(_.startsWith(x.name)))
   }
+    val outputDir: String = output.getAbsolutePath.stripSuffix(".zip")
+    val outputMap =
+      Map("plot_duplication_levels" -> "Images/duplication_levels.png",
+        "plot_kmer_profiles" -> "Images/kmer_profiles.png",
+        "plot_per_base_gc_content" -> "Images/per_base_gc_content.png",
+        "plot_per_base_n_content" -> "Images/per_base_n_content.png",
+        "plot_per_base_quality" -> "Images/per_base_quality.png",
+        "plot_per_base_sequence_content" -> "Images/per_base_sequence_content.png",
+        "plot_per_sequence_gc_content" -> "Images/per_sequence_gc_content.png",
+        "plot_per_sequence_quality" -> "Images/per_sequence_quality.png",
+        "plot_sequence_length_distribution" -> "Images/sequence_length_distribution.png",
+        "fastqc_data" -> "fastqc_data.txt")
+        .map {
+          case (name, relPath) =>
+            name -> Map("path" -> (outputDir + relPath))
+        }
 
-  def getSummary: Json = {
-    val subfixs = Map("plot_duplication_levels" -> "Images/duplication_levels.png",
-      "plot_kmer_profiles" -> "Images/kmer_profiles.png",
-      "plot_per_base_gc_content" -> "Images/per_base_gc_content.png",
-      "plot_per_base_n_content" -> "Images/per_base_n_content.png",
-      "plot_per_base_quality" -> "Images/per_base_quality.png",
-      "plot_per_base_sequence_content" -> "Images/per_base_sequence_content.png",
-      "plot_per_sequence_gc_content" -> "Images/per_sequence_gc_content.png",
-      "plot_per_sequence_quality" -> "Images/per_sequence_quality.png",
-      "plot_sequence_length_distribution" -> "Images/sequence_length_distribution.png",
-      "fastqc_data" -> "fastqc_data.txt")
-    val dir = output.getAbsolutePath.stripSuffix(".zip") + "/"
-    var outputMap: Map[String, Map[String, String]] = Map()
-    for ((k, v) <- subfixs) outputMap += (k -> Map("path" -> (dir + v)))
-
-    val temp = ("" := outputMap) ->: jEmptyObject
-    return temp.fieldOrEmptyObject("")
+    (("" := outputMap) ->: jEmptyObject)
+      .fieldOrEmptyObject("")
   }
 }
 

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

@@ -201,7 +201,7 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
 
   def fastqcSummary(fastqc: Fastqc): Option[Json] = {
     if (fastqc == null) return None
-    else return Option(fastqc.getSummary)
+    else return Option(fastqc.summary)
   }
 
   def clipstatSummary(): Option[Json] = {