Use file names for logging errors in Flexiprep Cutadapt wrapper instead of read names

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

@@ -28,7 +28,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
  * @param root: Configurable object from which this wrapper is initialized.
  * @param fastqc: Fastqc wrapper that contains adapter information.
  */
-class Cutadapt(root: Configurable, fastqc: Fastqc, readName: String) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
+class Cutadapt(root: Configurable, fastqc: Fastqc) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
 
   /** Clipped adapter names from FastQC */
   protected def seqToName = fastqc.foundAdapters
@@ -49,16 +49,16 @@ class Cutadapt(root: Configurable, fastqc: Fastqc, readName: String) extends nl.
                 // adapter sequence is clipped but not found by FastQC ~ should not happen since all clipped adapter
                 // sequences come from FastQC
                 case _ =>
-                  throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in 'clipping_$readName'.")
+                  throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in '$fastq_input'.")
               }
           }.toMap
         // FastQC found no adapters
         case otherwise =>
-          logger.info(s"No adapters found for summarizing in 'clipping_$readName'.")
+          logger.info(s"No adapters found for summarizing in '$fastq_input'.")
           Map.empty[String, Map[String, Any]]
       }
       // "adapters" key not found ~ something went wrong in our part
-      case _ => throw new RuntimeException(s"Required key 'adapters' not found in stats entry 'clipping_$readName'.")
+      case _ => throw new RuntimeException(s"Required key 'adapters' not found in stats entry '$fastq_input'.")
     }
     initStats.updated("adapters", adapterCounts)
   }

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

@@ -93,7 +93,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
     clip = if (!flexiprep.skipClip) {
       val foundAdapters = fastqc.foundAdapters.map(_.seq)
       if (foundAdapters.nonEmpty) {
-        val cutadapt = new Cutadapt(root, fastqc, read)
+        val cutadapt = new Cutadapt(root, fastqc)
         cutadapt.fastq_input = seqtk.output
         cutadapt.fastq_output = new File(output.getParentFile, input.getName + ".cutadapt.fq")
         cutadapt.stats_output = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")