From 643418a2675cf51c59c668da67ba819f49ce3c55 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 14 Sep 2015 16:35:53 +0200
Subject: [PATCH] style changes
---
.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala | 2 +-
.../src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala | 3 +--
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 2 +-
.../nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala | 4 ++--
4 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index 0f9a4e6b0..2f098dfaa 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -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))
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
index c6e6ee131..8cd0737ac 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
@@ -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
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index b88c46451..fb585c678 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -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 {
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
index 60430ec32..b50adb4d7 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
@@ -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
}
}
}
--
GitLab