Adding todo's

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

@@ -2,9 +2,9 @@ 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, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Created by pjvan_thof on 12/10/15.

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

@@ -2,9 +2,9 @@ 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.{Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
  * Created by pjvan_thof on 12/10/15.
@@ -21,7 +21,6 @@ class MergeOtuTables(val root: Configurable) extends BiopetCommandLineFunction w
   @Output(required = true)
   var outputFile: File = _
 
-
   override def beforeGraph(): Unit = {
     super.beforeGraph()
     require(input.nonEmpty)

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

@@ -137,6 +137,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
           add(Ln(qscript, qiimeClosed.head.otuMap, _closedOtuMap.get))
           add(Ln(qscript, qiimeClosed.head.otuTable, _closedOtuTable.get))
         }
+
+        //TODO: Plots
       } else {
         _closedOtuTable = None
         _closedOtuMap = None

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

@@ -113,6 +113,8 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
       qiimeClosed.fastqR1 = flexiprep.fastqR1Qc
       qiimeClosed.fastqR2 = flexiprep.fastqR2Qc
       add(qiimeClosed)
+
+      //TODO: Plots
     }
 
     addSummaryJobs()