Added closed reference method

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala

@@ -2,15 +2,15 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Input
 
 import scala.util.matching.Regex
 
 /**
-  * Created by pjvanthof on 16/12/15.
-  */
+ * Created by pjvanthof on 16/12/15.
+ */
 class Flash(val root: Configurable) extends BiopetCommandLineFunction with Version {
   executable = config("exe", default = "flash", freeVar = false)
 
@@ -47,7 +47,7 @@ class Flash(val root: Configurable) extends BiopetCommandLineFunction with Versi
   var compressProgArgs: Option[String] = config("compress_prog_args")
   var outputSuffix: Option[String] = config("output_suffix")
 
-  private def suffix = outputSuffix.getOrElse("fastq") + (if(compress) ".gz" else "")
+  private def suffix = outputSuffix.getOrElse("fastq") + (if (compress) ".gz" else "")
 
   def combinedFastq = new File(outputDirectory, s"$outputPrefix.extendedFrags.$suffix")
   def notCombinedR1 = new File(outputDirectory, s"$outputPrefix.notCombined_1.$suffix")

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions.qiime
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Input
 
@@ -36,6 +36,11 @@ class PickClosedReferenceOtus(val root: Configurable) extends BiopetCommandLineF
   var print_only: Boolean = config("print_only", default = false)
   var suppress_taxonomy_assignment: Boolean = config("suppress_taxonomy_assignment", default = false)
 
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    jobOutputFile = new File(outputDir, "std.log")
+  }
+
   def cmdLine = executable +
     required("-i", inputFasta) +
     required("-o", outputDir) +

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

+package nl.lumc.sasc.biopet.pipelines.gears
+
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, SampleLibraryTag }
+import nl.lumc.sasc.biopet.extensions.Flash
+import nl.lumc.sasc.biopet.extensions.qiime._
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 12/4/15.
+ */
+class GearsQiimeClosed(val root: Configurable) extends QScript with BiopetQScript with SampleLibraryTag {
+
+  var fastqR1: File = _
+
+  var fastqR2: Option[File] = None
+
+  override def defaults = Map(
+    "splitlibrariesfastq" -> Map(
+      "barcode_type" -> "not-barcoded"
+    )
+  )
+
+  def init() = {
+    require(fastqR1 != null)
+  }
+
+  def biopetScript() = {
+
+    val fastqFile = fastqR2 match {
+      case Some(r2) =>
+        val flash = new Flash(this)
+        flash.outputDirectory = new File(outputDir, "combine_reads_flash")
+        flash.fastqR1 = fastqR1
+        flash.fastqR2 = r2
+        add(flash)
+        flash.combinedFastq
+      case _ => fastqR1
+    }
+
+    val splitLib = new SplitLibrariesFastq(this)
+    splitLib.input :+= fastqFile
+    splitLib.outputDir = new File(outputDir, "split_libraries_fastq")
+    sampleId.foreach(splitLib.sample_ids :+= _)
+    add(splitLib)
+
+    val closedReference = new PickClosedReferenceOtus(this)
+    closedReference.inputFasta = splitLib.outputSeqs
+    closedReference.outputDir = new File(outputDir, "pick_closed_reference_otus")
+    add(closedReference)
+  }
+}

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

@@ -43,6 +43,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
 
   var gearsUseKraken: Boolean = config("gears_use_kraken", default = true)
   var gearsUserQiimeRtax: Boolean = config("gear_use_qiime_rtax", default = false)
+  var gearsUserQiimeClosed: Boolean = config("gear_use_qiime_closed", default = false)
 
   /** Executed before running the script */
   def init(): Unit = {
@@ -120,6 +121,16 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
       addAll(qiimeRatx.functions)
     }
 
+    if (gearsUserQiimeClosed) {
+      val qiimeClosed = new GearsQiimeClosed(this)
+      qiimeClosed.outputDir = new File(outputDir, "qiime_rtax")
+      qiimeClosed.fastqR1 = flexiprep.fastqR1Qc
+      qiimeClosed.fastqR2 = flexiprep.fastqR2Qc
+      qiimeClosed.init()
+      qiimeClosed.biopetScript()
+      addAll(qiimeClosed.functions)
+    }
+
     addSummaryJobs()
   }