Commit 38461999 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Sync with develop

parent 8c50da88
......@@ -18,8 +18,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class CatVariants(val root: Configurable) extends Gatk {
val analysisType = "CatVariants"
......@@ -32,7 +31,7 @@ class CatVariants(val root: Configurable) extends Gatk {
override def cmdLine = super.cmdLine +
(for (file <- inputFiles) yield {
required("-V", file)
required("-V", file)
}).mkString +
required("-o", outputFile)
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.File
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
......@@ -66,7 +66,6 @@ class Delly(val root: Configurable) extends QScript with Reference with SummaryQ
)
}
def biopetScript() {
// write the pipeline here
logger.info("Configuring Delly pipeline")
......
......@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference, SampleLibraryTag}
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.utils.Logging
......
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