Changed custom adapters feeding

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

@@ -29,7 +29,15 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 class Cutadapt(root: Configurable, fastqc: Fastqc) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
 
   val ignoreFastqcAdapters: Boolean = config("ignore_fastqc_adapters", default = false)
-  val customAdaptersConfig: Map[String, Any] = config("custom_adapters", default = Map.empty)
+
+  val customAdaptersEnd: Map[String, Any] = config("custom_adapters_end", default = Map())
+  adapter ++= customAdaptersEnd.values.map(_.toString)
+
+  val customAdaptersFront: Map[String, Any] = config("custom_adapters_front", default = Map())
+  front ++= customAdaptersEnd.values.map(_.toString)
+
+  val customAdaptersAny: Map[String, Any] = config("custom_adapters_any", default = Map())
+  anywhere ++= customAdaptersEnd.values.map(_.toString)
 
   /** Clipped adapter names from FastQC */
   protected def seqToName: Map[String, String] = {
@@ -42,7 +50,7 @@ class Cutadapt(root: Configurable, fastqc: Fastqc) extends nl.lumc.sasc.biopet.e
   }
 
   def customAdapters: Set[AdapterSequence] = {
-    customAdaptersConfig.flatMap(adapter => {
+    (customAdaptersEnd ++ customAdaptersFront ++ customAdaptersAny).flatMap(adapter => {
       adapter match {
         case (adapterName: String, sequence: String) =>
           Some(AdapterSequence(adapterName, sequence))

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

@@ -103,13 +103,11 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
     clip = if (!flexiprep.skipClip) {
       val cutadapt = clip.getOrElse(new Cutadapt(root, fastqc))
 
-      val foundAdapters = if (!cutadapt.ignoreFastqcAdapters) {
-        fastqc.foundAdapters.map(_.seq) ++ cutadapt.customAdapters.map(_.seq)
-      } else {
-        cutadapt.customAdapters.map(_.seq)
-      }
+      val foundAdapters: Set[String] = if (!cutadapt.ignoreFastqcAdapters) {
+        fastqc.foundAdapters.map(_.seq)
+      } else Set()
 
-      if (foundAdapters.nonEmpty) {
+      if (foundAdapters.nonEmpty || cutadapt.adapter.nonEmpty || cutadapt.front.nonEmpty || cutadapt.anywhere.nonEmpty) {
         cutadapt.fastqInput = seqtk.output
         cutadapt.fastqOutput = new File(output.getParentFile, input.getName + ".cutadapt.fq")
         cutadapt.statsOutput = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")