Commit 643418a2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

style changes

parent b8afbacb
......@@ -239,7 +239,7 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
p.commands.last._outputAsStdout = true
new BiopetPipe(p.commands ::: that :: Nil)
}
case _ => new BiopetPipe(List(this, that))
case _ => new BiopetPipe(List(this, that))
}
}
......
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Output, Input}
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* This class can pipe multiple BiopetCommandFunctions to 1 job
......@@ -33,7 +33,6 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
stdoutFile = stdoutFile.map(_.getAbsoluteFile)
stdinFile = stdinFile.map(_.getAbsoluteFile)
if (stdoutFile.isDefined) {
commands.last.stdoutFile = None
commands.last._outputAsStdout = true
......
......@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.tools.{SeqStat, FastqSync}
import nl.lumc.sasc.biopet.tools.{ SeqStat, FastqSync }
import org.broadinstitute.gatk.queue.QScript
class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.{Cat, Ln}
import nl.lumc.sasc.biopet.extensions.{ Cat, Ln }
class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq(root) {
var fastqc: Fastqc = _
......@@ -51,7 +51,7 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
analysisName = getClass.getSimpleName + "-skip"
(inputAsStdin, outputAsStsout) match {
case (true, true) => super.cmdLine
case _ => Ln(this, input, output).cmd
case _ => Ln(this, input, output).cmd
}
}
}
......
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