diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala index 8938d264d7b4aa666ee0d5b0128f0c7d33c4df46..a538e97a1c281256b007ee37e115da48bfb0e393 100644 --- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala +++ b/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. diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala index 80e3e363f49ff4ecf87e2730c194c54e268df451..ae3d4edd29793327a5621339cf7463c288a8ae08 100644 --- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala +++ b/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) diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala index 3f10af4cc79374f5c3435632064f398da43df1d1..e9967eed55f34fd565078db86e13483c5904d40b 100644 --- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala +++ b/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 diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala index 4ae1e69ba75c24eb94115845ca73f8522c55cc2a..861f6f61f207d8066f1f8bffe4cc2abf9a831229 100644 --- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala +++ b/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()