Commit fd8d9ae0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix imports

parent 5a9c2878
......@@ -368,7 +368,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def addBowtie(R1: File, R2: File, output: File, deps: List[File]): File = {
val bowtie = new Bowtie(this)
bowtie.R1 = R1
if (paired) bowtie.R2 = R2
if (paired) bowtie.R2 = Some(R2)
bowtie.deps = deps
bowtie.output = this.swapExt(output.getParent, output, ".bam", ".sam")
bowtie.isIntermediate = true
......
......@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import java.io.File
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions._
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
......@@ -12,10 +13,7 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, AddOrReplaceReadGroups, MarkDuplicates, SortSam }
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.pipelines.flexiprep.Cutadapt
import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
import nl.lumc.sasc.biopet.pipelines.flexiprep._
import nl.lumc.sasc.biopet.pipelines.flexiprep.{ SeqtkSeq, Cutadapt, Fastqc }
import nl.lumc.sasc.biopet.tools.{ Seqstat, FastqSync }
import nl.lumc.sasc.biopet.utils.ConfigUtils
......
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