Commit caf77b81 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Style update by IDEA

parent d82b56a0
......@@ -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)
......
......@@ -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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