diff --git a/protected/biopet-gatk-pipelines/pom.xml b/protected/biopet-gatk-pipelines/pom.xml
index f3a9ead7159eaaaccf28e80872cb20ebaea760a9..eec886f27f83120a2611f0b7330fa573587e61d1 100644
--- a/protected/biopet-gatk-pipelines/pom.xml
+++ b/protected/biopet-gatk-pipelines/pom.xml
@@ -44,5 +44,17 @@
<artifactId>Shiva</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.11</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
</dependencies>
</project>
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingGatk.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingGatk.scala
index 22551875c0a5175669fe4ecb5c3c036ec8c8859b..6dfeb9661f7d4006401ae8bb4da8018ccda320fd 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingGatk.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingGatk.scala
@@ -13,19 +13,18 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
qscript =>
def this() = this(null)
- override def callers = {
+ override def callersList = {
new HaplotypeCallerGvcf ::
new HaplotypeCallerAllele ::
new UnifiedGenotyperAllele ::
new UnifiedGenotyper ::
new HaplotypeCaller ::
- super.callers
+ super.callersList
}
class HaplotypeCaller extends Variantcaller {
val name = "haplotypecaller"
protected val defaultPrio = 1
- protected val defaultUse = true
def outputFile = new File(outputDir, namePrefix + ".haplotypecaller.vcf.gz")
@@ -40,7 +39,6 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
class UnifiedGenotyper extends Variantcaller {
val name = "unifiedgenotyper"
protected val defaultPrio = 20
- protected val defaultUse = false
def outputFile = new File(outputDir, namePrefix + ".unifiedgenotyper.vcf.gz")
@@ -55,7 +53,6 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
class HaplotypeCallerAllele extends Variantcaller {
val name = "haplotypecaller_allele"
protected val defaultPrio = 5
- protected val defaultUse = false
def outputFile = new File(outputDir, namePrefix + ".haplotypecaller_allele.vcf.gz")
@@ -72,7 +69,6 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
class UnifiedGenotyperAllele extends Variantcaller {
val name = "unifiedgenotyper_allele"
protected val defaultPrio = 9
- protected val defaultUse = false
def outputFile = new File(outputDir, namePrefix + ".unifiedgenotyper_allele.vcf.gz")
@@ -89,7 +85,6 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
class HaplotypeCallerGvcf extends Variantcaller {
val name = "haplotypecaller_gvcf"
protected val defaultPrio = 5
- protected val defaultUse = false
def outputFile = new File(outputDir, namePrefix + ".haplotypecaller_gvcf.vcf.gz")
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..f20e929586fb0ce500ba71da2db5929b09c8a981
--- /dev/null
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
@@ -0,0 +1,119 @@
+package nl.lumc.sasc.biopet.pipelines.gatk
+
+import java.io.File
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{UnifiedGenotyper, HaplotypeCaller}
+import nl.lumc.sasc.biopet.tools.{VcfStats, MpileupToVcf, VcfFilter}
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{DataProvider, Test, AfterClass}
+
+import scala.collection.mutable.ListBuffer
+
+/**
+ * Created by pjvan_thof on 3/2/15.
+ */
+class ShivaVariantcallingTest extends TestNGSuite with Matchers {
+ def initPipeline(map: Map[String, Any]): ShivaVariantcallingGatk = {
+ new ShivaVariantcallingGatk() {
+ override def configName = "shivavariantcalling"
+ override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config))
+ qSettings = new QSettings
+ qSettings.runName = "test"
+ }
+ }
+
+ @DataProvider(name = "shivaVariantcallingOptions")
+ def shivaVariantcallingOptions = {
+ val raw = Array(true, false)
+ val bcftools = Array(true, false)
+ val haplotypeCallerGvcf = Array(true, false)
+ val haplotypeCallerAllele = Array(true, false)
+ val unifiedGenotyperAllele = Array(true, false)
+ val unifiedGenotyper = Array(true, false)
+ val haplotypeCaller = Array(true, false)
+
+ (for (
+ bams <- 0 to 2;
+ raw <- raw;
+ bcftools <- bcftools;
+ haplotypeCallerGvcf <- haplotypeCallerGvcf;
+ haplotypeCallerAllele <- haplotypeCallerAllele;
+ unifiedGenotyperAllele <- unifiedGenotyperAllele;
+ unifiedGenotyper <- unifiedGenotyper;
+ haplotypeCaller <- haplotypeCaller
+ ) yield Array[Any](bams, raw, bcftools, unifiedGenotyper, haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele)
+ ).toArray
+ }
+
+ @Test(dataProvider = "shivaVariantcallingOptions")
+ def testShivaVariantcalling(bams: Int,
+ raw: Boolean,
+ bcftools: Boolean,
+ unifiedGenotyper: Boolean,
+ haplotypeCaller: Boolean,
+ haplotypeCallerGvcf: Boolean,
+ haplotypeCallerAllele: Boolean,
+ unifiedGenotyperAllele: Boolean) = {
+ val callers: ListBuffer[String] = ListBuffer()
+ if (raw) callers.append("raw")
+ if (bcftools) callers.append("bcftools")
+ if (unifiedGenotyper) callers.append("unifiedgenotyper")
+ if (haplotypeCallerGvcf) callers.append("haplotypecaller_gvcf")
+ if (haplotypeCallerAllele) callers.append("haplotypecaller_allele")
+ if (unifiedGenotyperAllele) callers.append("unifiedgenotyper_allele")
+ if (haplotypeCaller) callers.append("haplotypecaller")
+ val map = Map("variantcallers"-> callers.toList)
+ val pipeline = initPipeline(map)
+
+ pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
+
+ val illegalArgumentException = pipeline.inputBams.isEmpty ||
+ (!raw && !bcftools &&
+ !haplotypeCaller && !unifiedGenotyper &&
+ !haplotypeCallerGvcf && !haplotypeCallerAllele && !unifiedGenotyperAllele)
+
+ if (illegalArgumentException) intercept[IllegalArgumentException] {
+ pipeline.script()
+ }
+
+ if (!illegalArgumentException) {
+ pipeline.script()
+
+ pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe 1 + (if (raw) 1 else 0)
+ //pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
+ //FIXME: Can not check for bcftools because of piping
+ pipeline.functions.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
+ pipeline.functions.count(_.isInstanceOf[VcfFilter]) shouldBe (if (raw) bams else 0)
+ pipeline.functions.count(_.isInstanceOf[HaplotypeCaller]) shouldBe (if (haplotypeCaller) 1 else 0) +
+ (if (haplotypeCallerAllele) 1 else 0) + (if (haplotypeCallerGvcf) bams else 0)
+ pipeline.functions.count(_.isInstanceOf[UnifiedGenotyper]) shouldBe (if (unifiedGenotyper) 1 else 0) +
+ (if (unifiedGenotyperAllele) 1 else 0)
+ pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (1 + callers.size)
+ }
+ }
+
+ @AfterClass def removeTempOutputDir() = {
+ FileUtils.deleteDirectory(ShivaVariantcallingTest.outputDir)
+ }
+}
+
+object ShivaVariantcallingTest {
+ val outputDir = Files.createTempDir()
+
+ val config = Map(
+ "name_prefix" -> "test",
+ "output_dir" -> outputDir,
+ "reference" -> "test",
+ "gatk_jar" -> "test",
+ "samtools" -> Map("exe" -> "test"),
+ "bcftools" -> Map("exe" -> "test"),
+ "input_alleles" -> "test"
+ )
+}
\ No newline at end of file
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index d71379a9ff3d925f88991140bd831a2d6c7594e9..e8d530f00e63fe7587851130998d199e7dfdc409 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
@@ -38,10 +38,11 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
def finalFile = new File(outputDir, namePrefix + ".final.vcf.gz")
def biopetScript: Unit = {
- val callers = usedCallers.sortBy(_.prio)
+ val configCallers: Set[String] = config("variantcallers")
+ val callers = callersList.filter(x => configCallers.contains(x.name)).sortBy(_.prio)
require(!inputBams.isEmpty, "No input bams found")
- require(callers.exists(_.use), "must select atleast 1 variantcaller")
+ require(!callers.isEmpty, "must select atleast 1 variantcaller, possible to use: " + callersList.map(_.name).mkString(", "))
val cv = new CombineVariants(qscript)
cv.outputFile = finalFile
@@ -69,15 +70,11 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
addSummaryJobs
}
- def callers: List[Variantcaller] = List(new RawVcf, new Bcftools)
-
- def usedCallers: List[Variantcaller] = callers.filter(_.use)
+ protected def callersList: List[Variantcaller] = List(new RawVcf, new Bcftools)
trait Variantcaller {
val name: String
def outputDir = new File(qscript.outputDir, name)
- protected val defaultUse: Boolean
- lazy val use: Boolean = config("use_" + name, default = defaultUse)
protected val defaultPrio: Int
lazy val prio: Int = config("prio_" + name, default = defaultPrio)
def addJobs()
@@ -87,7 +84,6 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
class Bcftools extends Variantcaller {
val name = "bcftools"
protected val defaultPrio = 8
- protected val defaultUse = true
def outputFile = new File(outputDir, namePrefix + ".bcftools.vcf.gz")
@@ -117,7 +113,6 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
class RawVcf extends Variantcaller {
val name = "raw"
protected val defaultPrio = 999
- protected val defaultUse = true
def outputFile = new File(outputDir, namePrefix + ".raw.vcf.gz")
@@ -154,5 +149,8 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
def summarySettings = Map()
- def summaryFiles: Map[String, File] = usedCallers.map(x => (x.name -> x.outputFile)).toMap + ("final" -> finalFile)
+ def summaryFiles: Map[String, File] = {
+ val callers: Set[String] = config("variantcallers")
+ callersList.filter(x => callers.contains(x.name)).map(x => (x.name -> x.outputFile)).toMap + ("final" -> finalFile)
+ }
}
\ No newline at end of file
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index 8fa8d8badf6e88b3b1c309b37694a9a39425d67f..567bd022a99a7898db75b8b94866e0d1c9ff6f47 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -13,6 +13,8 @@ import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{ AfterClass, Test, DataProvider }
+import scala.collection.mutable.ListBuffer
+
/**
* Created by pjvan_thof on 3/2/15.
*/
@@ -36,17 +38,20 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
raw <- raw;
bcftools <- bcftools
) yield Array[Any](bams, raw, bcftools)
- ).toArray
+ ).toArray
}
@Test(dataProvider = "shivaVariantcallingOptions")
def testShivaVariantcalling(bams: Int, raw: Boolean, bcftools: Boolean) = {
- val map = Map("use_raw" -> raw, "use_bcftools" -> bcftools)
+ val callers: ListBuffer[String] = ListBuffer()
+ if (raw) callers.append("raw")
+ if (bcftools) callers.append("bcftools")
+ val map = Map("variantcallers"-> callers.toList)
val pipeline = initPipeline(map)
pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
- val illegalArgumentException = pipeline.inputBams.isEmpty || !raw && !bcftools
+ val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools)
if (illegalArgumentException) intercept[IllegalArgumentException] {
pipeline.script()
@@ -66,7 +71,6 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
@AfterClass def removeTempOutputDir() = {
FileUtils.deleteDirectory(ShivaVariantcallingTest.outputDir)
}
-
}
object ShivaVariantcallingTest {