From caf77b81052720e02ff7af496af5e4862d677152 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 19 Oct 2015 16:00:56 +0200
Subject: [PATCH] Style update by IDEA
---
.../sasc/biopet/extensions/tools/KrakenReportToJson.scala | 6 +++---
.../scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala | 4 ++--
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
index c7f583940..44567a15a 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
@@ -32,9 +32,9 @@ class KrakenReportToJson(val root: Configurable) extends ToolCommandFuntion with
override def defaultCoreMemory = 1.0
override def cmdLine = super.cmdLine +
- required("-i", inputReport) +
- required("-o", output) +
- conditional(skipNames, "--skipnames")
+ required("-i", inputReport) +
+ required("-o", output) +
+ conditional(skipNames, "--skipnames")
def summaryStats: Map[String, Any] = {
val map = ConfigUtils.fileToConfigMap(output)
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 554ed5b29..4ae307a12 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
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
-import nl.lumc.sasc.biopet.extensions.picard.{SortSam, SamToFastq}
+import nl.lumc.sasc.biopet.extensions.picard.{ SortSam, SamToFastq }
import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
import nl.lumc.sasc.biopet.extensions.tools.{ KrakenReportToJson, FastqSync }
import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -76,7 +76,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
// start bam to fastq (only on unaligned reads) also extract the matesam
val samToFastq = new SamToFastq(qscript)
- samToFastq.input= samFilterUnmapped.output
+ samToFastq.input = samFilterUnmapped.output
samToFastq.stringency = Some("LENIENT")
samToFastq.fastqR1 = new File(outputDir, s"$outputName.unmapped.R1.fq.gz")
samToFastq.fastqR2 = new File(outputDir, s"$outputName.unmapped.R2.fq.gz")
--
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