Commit ec99ed54 authored by Peter van 't Hof's avatar Peter van 't Hof

Added mapping tests for hisat2

parent 6f754064
......@@ -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)
......
......@@ -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
......
......@@ -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 {
......
......@@ -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")
......
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