Commit b4c7ded4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added more job testing

parent 6f2d19e0
...@@ -3,9 +3,10 @@ package nl.lumc.sasc.biopet.pipelines.basty ...@@ -3,9 +3,10 @@ package nl.lumc.sasc.biopet.pipelines.basty
import java.io.{File, FileOutputStream} import java.io.{File, FileOutputStream}
import com.google.common.io.Files import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.{Raxml, RunGubbins}
import nl.lumc.sasc.biopet.extensions.gatk.{BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator} import nl.lumc.sasc.biopet.extensions.gatk.{BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator}
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import nl.lumc.sasc.biopet.extensions.tools.VcfStats import nl.lumc.sasc.biopet.extensions.tools.{BastyGenerateFasta, VcfStats}
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging} import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.utils.config.Config import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
...@@ -41,10 +42,11 @@ class BastyTest extends TestNGSuite with Matchers { ...@@ -41,10 +42,11 @@ class BastyTest extends TestNGSuite with Matchers {
def multisampleCalling: Boolean = true def multisampleCalling: Boolean = true
def sampleCalling = false def sampleCalling = false
def libraryCalling = false def libraryCalling = false
def dbsnp = true def dbsnp = false
def svCalling = false def svCalling = false
def cnvCalling = false def cnvCalling = false
def annotation = false def annotation = false
def bootRuns: Option[Int] = None
@Test(dataProvider = "bastyOptions") @Test(dataProvider = "bastyOptions")
def testBasty(f: String, sample1: Boolean, sample2: Boolean): Unit = { def testBasty(f: String, sample1: Boolean, sample2: Boolean): Unit = {
...@@ -61,7 +63,8 @@ class BastyTest extends TestNGSuite with Matchers { ...@@ -61,7 +63,8 @@ class BastyTest extends TestNGSuite with Matchers {
"use_base_recalibration" -> baseRecalibration, "use_base_recalibration" -> baseRecalibration,
"sv_calling" -> svCalling, "sv_calling" -> svCalling,
"cnv_calling" -> cnvCalling, "cnv_calling" -> cnvCalling,
"annotation" -> annotation), m) "annotation" -> annotation,
"boot_runs" -> bootRuns), m)
} }
...@@ -105,6 +108,10 @@ class BastyTest extends TestNGSuite with Matchers { ...@@ -105,6 +108,10 @@ class BastyTest extends TestNGSuite with Matchers {
(if (multisampleCalling) 2 else 0) + (if (multisampleCalling) 2 else 0) +
(if (sampleCalling) numberSamples * 2 else 0) + (if (sampleCalling) numberSamples * 2 else 0) +
(if (libraryCalling) numberLibs * 2 else 0)) (if (libraryCalling) numberLibs * 2 else 0))
pipeline.functions.count(_.isInstanceOf[BastyGenerateFasta]) shouldBe 2 + (2 * numberSamples)
pipeline.functions.count(_.isInstanceOf[Raxml]) shouldBe (2 * (2 + bootRuns.getOrElse(100)))
pipeline.functions.count(_.isInstanceOf[RunGubbins]) shouldBe 2
} }
} }
} }
......
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