Added combine reads for GearsSingle

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala

@@ -2,7 +2,8 @@ package nl.lumc.sasc.biopet.pipelines.gears
 
 import nl.lumc.sasc.biopet.core.SampleLibraryTag
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.Flash
+import nl.lumc.sasc.biopet.extensions.{Cutadapt, Flash}
+import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -15,18 +16,59 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
 
   @Input(doc = "R2 reads in FastQ format", shortName = "R2", required = false)
   var fastqR2: File = _
-
+  
+  override def fixedValues = Map("flash" -> Map("compress" -> true))
+  
   /** Init for pipeline */
   def init(): Unit = {
   }
 
+  private lazy val flash = new Flash(this)
+
+  private lazy val forwardPrimers: List[String] = config("forward_primers")
+  private lazy val reversePrimers: List[String] = config("reverse_primers")
+  
+  def combinedFastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty)
+    swapExt(outputDir, flash.combinedFastq, ".fastq.gz", ".clip.fastq.gz")
+  else flash.combinedFastq
+
+  def notCombinedR1Fastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty)
+    swapExt(outputDir, flash.notCombinedR1, ".fastq.gz", ".clip.fastq.gz")
+  else flash.notCombinedR1
+
+  def notCombinedR2Fastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty)
+    swapExt(outputDir, flash.notCombinedR2, ".fastq.gz", ".clip.fastq.gz")
+  else flash.notCombinedR2
+
   /** Pipeline itself */
   def biopetScript(): Unit = {
-    val flash = new Flash(this)
     flash.outputDirectory = new File(outputDir, "flash")
     flash.fastqR1 = fastqR1
     flash.fastqR2 = fastqR2
+    flash.isIntermediate = (forwardPrimers ::: reversePrimers).nonEmpty
     add(flash)
+
+    if ((forwardPrimers ::: reversePrimers).nonEmpty) {
+      val cutadapt = new Cutadapt(this)
+      cutadapt.fastq_input = flash.combinedFastq
+      cutadapt.fastq_output = this.combinedFastq
+      cutadapt.stats_output = swapExt(outputDir, cutadapt.fastq_output, ".fastq.gz", ".stats")
+      cutadapt.opt_anywhere ++= (forwardPrimers ::: reversePrimers)
+      add(cutadapt)
+      addSummarizable(cutadapt, "cutadapt")
+    }
+    
+    val combinedFastqc = Fastqc(this, this.combinedFastq, new File(outputDir, "combined_fastqc"))
+    add(combinedFastqc)
+    addSummarizable(combinedFastqc, "fastqc_combined")
+
+    val notCombinedR1Fastqc = Fastqc(this, this.combinedFastq, new File(outputDir, "not_combined_R1_fastqc"))
+    add(notCombinedR1Fastqc)
+    addSummarizable(notCombinedR1Fastqc, "fastqc_not_combined_R1")
+
+    val notCombinedR2Fastqc = Fastqc(this, this.combinedFastq, new File(outputDir, "not_combined_R2_fastqc"))
+    add(notCombinedR2Fastqc)
+    addSummarizable(notCombinedR2Fastqc, "fastqc_not_combined_R2")
   }
 
   /** Must return a map with used settings for this pipeline */

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala

@@ -104,12 +104,12 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
     lazy val combinedFastq = {
       r2 match {
         case Some(r2) =>
-          val flash = new Flash(this)
-          flash.outputDirectory = new File(outputDir, "combine_reads_flash")
-          flash.fastqR1 = r1
-          flash.fastqR2 = r2
-          add(flash)
-          flash.combinedFastq
+          val combineReads = new CombineReads(this)
+          combineReads.outputDir = new File(outputDir, "combine_reads")
+          combineReads.fastqR1 = r1
+          combineReads.fastqR2 = r2
+          add(combineReads)
+          combineReads.combinedFastq
         case _ => r1
       }
     }