Added mapping tests for hisat2

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala

@@ -2,13 +2,13 @@ package nl.lumc.sasc.biopet.extensions.hisat
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Input
 
 /**
-  * Created by pjvan_thof on 7-6-16.
-  */
+ * Created by pjvan_thof on 7-6-16.
+ */
 class Hisat2Build(val root: Configurable) extends BiopetCommandLineFunction with Version {
 
   @Input(required = true)

generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala

@@ -14,13 +14,13 @@
  */
 package nl.lumc.sasc.biopet.pipelines.generateindexes
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 import java.util
 
 import nl.lumc.sasc.biopet.core.extensions.Md5sum
-import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.extensions._
-import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie2Build, BowtieBuild}
+import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie2Build, BowtieBuild }
 import nl.lumc.sasc.biopet.extensions.bwa.BwaIndex
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.gmap.GmapBuild

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala

@@ -11,8 +11,8 @@ import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
 /**
-  * Created by pjvan_thof on 31-5-16.
-  */
+ * Created by pjvan_thof on 31-5-16.
+ */
 class Impute2VcfTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): Impute2Vcf = {
     new Impute2Vcf {

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -98,6 +98,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
   val r2 = new File(outputDir, "input" + File.separator + "R2.fq")
   val r1Zipped = new File(outputDir, "input" + File.separator + "R1.fq.gz")
   val r2Zipped = new File(outputDir, "input" + File.separator + "R2.fq.gz")
+  val hisat2Index = new File(outputDir, "ref.1.ht2")
 
   @BeforeClass
   def createTempFiles: Unit = {
@@ -105,6 +106,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
     Files.touch(r2)
     Files.touch(r1Zipped)
     Files.touch(r2Zipped)
+    Files.touch(hisat2Index)
 
     copyFile("ref.fa")
     copyFile("ref.dict")
@@ -125,6 +127,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "db" -> "test",
     "bowtie_index" -> (outputDir + File.separator + "ref"),
+    "hisat2_index" -> (outputDir + File.separator + "ref"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),
     "gsnap" -> Map("exe" -> "test"),
@@ -135,6 +138,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
     "star" -> Map("exe" -> "test"),
     "bowtie" -> Map("exe" -> "test"),
     "bowtie2" -> Map("exe" -> "test"),
+    "hisat2" -> Map("exe" -> "test"),
     "stampy" -> Map("exe" -> "test", "genome" -> "test", "hash" -> "test"),
     "samtools" -> Map("exe" -> "test"),
     "kraken" -> Map("exe" -> "test", "db" -> "test"),
@@ -154,6 +158,7 @@ class MappingStarTest extends AbstractTestMapping("star")
 class MappingStar2PassTest extends AbstractTestMapping("star-2pass")
 class MappingBowtieTest extends AbstractTestMapping("bowtie")
 class MappingBowtie2Test extends AbstractTestMapping("bowtie2")
+class MappingHisat2Test extends AbstractTestMapping("hisat2")
 class MappingStampyTest extends AbstractTestMapping("stampy")
 class MappingGsnapTest extends AbstractTestMapping("gsnap")
 class MappingTophatTest extends AbstractTestMapping("tophat")