From b4c7ded438c3d3cd3aa0156304ca70d1ee79a846 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 27 Sep 2016 20:13:23 +0200
Subject: [PATCH] Added more job testing
---
.../sasc/biopet/pipelines/basty/BastyTest.scala | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala b/basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
index b475af632..db7669604 100644
--- a/basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
+++ b/basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
@@ -3,9 +3,10 @@ package nl.lumc.sasc.biopet.pipelines.basty
import java.io.{File, FileOutputStream}
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.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.config.Config
import org.broadinstitute.gatk.queue.QSettings
@@ -41,10 +42,11 @@ class BastyTest extends TestNGSuite with Matchers {
def multisampleCalling: Boolean = true
def sampleCalling = false
def libraryCalling = false
- def dbsnp = true
+ def dbsnp = false
def svCalling = false
def cnvCalling = false
def annotation = false
+ def bootRuns: Option[Int] = None
@Test(dataProvider = "bastyOptions")
def testBasty(f: String, sample1: Boolean, sample2: Boolean): Unit = {
@@ -61,7 +63,8 @@ class BastyTest extends TestNGSuite with Matchers {
"use_base_recalibration" -> baseRecalibration,
"sv_calling" -> svCalling,
"cnv_calling" -> cnvCalling,
- "annotation" -> annotation), m)
+ "annotation" -> annotation,
+ "boot_runs" -> bootRuns), m)
}
@@ -105,6 +108,10 @@ class BastyTest extends TestNGSuite with Matchers {
(if (multisampleCalling) 2 else 0) +
(if (sampleCalling) numberSamples * 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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