Initial fix for #238

The issue is caused by the Cutadapt summary not being aware of the
clipped sequence names. This merge request extends the existing Cutadapt
wrapper in the Flexiprep module and makes it so that the wrapper is
aware of FastQC.

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

+/*
+ * Copyright (c) 2015 Leiden University Medical Center and contributors
+ *                    (see AUTHORS.md file for details).
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+ * Cutadapt wrapper specific for Flexiprep.
+ *
+ * This wrapper overrides the summary part so that instead of only displaying the clipped adapters, the sequence names
+ * are also displayed. In Flexiprep the sequence will always have names since they are detected by FastQC from a list
+ * of known adapters / contaminants.
+ *
+ * @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) {
+
+  /** Clipped adapter names from FastQC */
+  protected def seqToName = fastqc.foundAdapters
+    .map(adapter => adapter.seq -> adapter.name).toMap
+
+  override def summaryStats: Map[String, Any] = {
+    val initStats = super.summaryStats
+    // Map of adapter sequence and how many times it is found
+    val adapterCounts = initStats.get("adapters") match {
+      // "adapters" key found in statistics
+      case Some(v) => v match {
+        case m: Map[String, Int] => m.toSeq
+          .map {
+            case (seq, count) =>
+              seqToName.get(seq) match {
+                // adapter sequence is found by FastQC
+                case Some(n) => n -> (seq, count)
+                // adapter sequence is clipped but not found by FastQC ~ should not happen since all clipped adapter
+                // sequences come from FastQC
+                case None =>
+                  throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in 'clipping_$readName'.")
+              }
+          }.toMap
+        // FastQC found no adapters
+        case otherwise =>
+          logger.info(s"No adapters found for summarizing in 'clipping_$readName'.")
+          Map.empty[String, (String, Int)]
+      }
+      // "adapters" key not found ~ something went wrong in our part
+      case None => throw new RuntimeException(s"Required key 'adapters' not found in stats entry 'clipping_$readName'.")
+    }
+    initStats.updated("adapters", adapterCounts)
+  }
+}

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

@@ -19,7 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
 import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetCommandLineFunction }
-import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle, Cutadapt }
+import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle }
 import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
@@ -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)
+        val cutadapt = new Cutadapt(root, fastqc, read)
         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")