Commit 7e27eee9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding todo's

parent 83c0d1ee
......@@ -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.
......
......@@ -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)
......
......@@ -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
......
......@@ -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()
......
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