From af04710a62d6a11242c3f8c7418015a06ec428fa Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Feb 2015 21:33:45 +0100
Subject: [PATCH] Convert flexiprep testing to DataProvider
---
.../pipelines/flexiprep/FlexiprepTest.scala | 141 ++++--------------
1 file changed, 33 insertions(+), 108 deletions(-)
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
index 208f1c41a..7c17c6673 100644
--- a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
@@ -10,7 +10,7 @@ import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.Test
+import org.testng.annotations.{ DataProvider, Test }
/**
* Created by pjvan_thof on 2/11/15.
@@ -26,121 +26,46 @@ class FlexiprepTest extends TestNGSuite with Matchers {
}
}
- @Test def testDefault = {
- val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir), Map(FlexiprepTest.excutables.toSeq: _*))
- val flexiprep: Flexiprep = initPipeline(map)
-
- flexiprep.input_R1 = new File(flexiprep.outputDir, "bla.fq")
- flexiprep.sampleId = "1"
- flexiprep.libId = "1"
- flexiprep.script()
-
- flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 0
- flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 1
- flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 1
- flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 0
- flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
- flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 1
- }
-
- @Test def testDefaultPaired = {
- val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir), Map(FlexiprepTest.excutables.toSeq: _*))
- val flexiprep: Flexiprep = initPipeline(map)
-
- flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
- flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
- flexiprep.sampleId = "1"
- flexiprep.libId = "1"
- flexiprep.script()
-
- flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
- flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 1
- flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
- flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
- }
-
- @Test def testClipTrimPaired = {
- val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> false, "skip_clip" -> false),
- Map(FlexiprepTest.excutables.toSeq: _*))
- val flexiprep: Flexiprep = initPipeline(map)
-
- flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
- flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
- flexiprep.sampleId = "1"
- flexiprep.libId = "1"
- flexiprep.script()
-
- flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
- flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 1
- flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
- flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
- }
-
- @Test def testTrimPaired = {
- val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> false, "skip_clip" -> true),
- Map(FlexiprepTest.excutables.toSeq: _*))
- val flexiprep: Flexiprep = initPipeline(map)
-
- flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
- flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
- flexiprep.sampleId = "1"
- flexiprep.libId = "1"
- flexiprep.script()
-
- flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
- flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 0
- flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 0
- flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
- flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
- }
-
- @Test def testClipPaired = {
- val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> true, "skip_clip" -> false),
- Map(FlexiprepTest.excutables.toSeq: _*))
- val flexiprep: Flexiprep = initPipeline(map)
-
- flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
- flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
- flexiprep.sampleId = "1"
- flexiprep.libId = "1"
- flexiprep.script()
-
- flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
- flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 1
- flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 0
- flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+ @DataProvider(name = "flexiprepOptions", parallel = true)
+ def flexiprepOptions = {
+ val paired = Array(true, false)
+ val skipTrims = Array(true, false)
+ val skipClips = Array(true, false)
+ val zipped = Array(true, false)
+
+ for (
+ pair <- paired;
+ skipTrim <- skipTrims;
+ skipClip <- skipClips;
+ zip <- zipped
+ ) yield Array("", pair, skipTrim, skipClip, zip)
}
- @Test def testPaired = {
- val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> true, "skip_clip" -> true),
- Map(FlexiprepTest.excutables.toSeq: _*))
+ @Test(dataProvider = "flexiprepOptions")
+ def testFlexiprep(f: String, paired: Boolean, skipTrim: Boolean, skipClip: Boolean, zipped: Boolean) = {
+ val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir,
+ "skip_trim" -> skipTrim,
+ "skip_clip" -> skipClip
+ ), Map(FlexiprepTest.excutables.toSeq: _*))
val flexiprep: Flexiprep = initPipeline(map)
- flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
- flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+ flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq" + (if (zipped) ".gz" else ""))
+ if (paired) flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq" + (if (zipped) ".gz" else "")))
flexiprep.sampleId = "1"
flexiprep.libId = "1"
flexiprep.script()
- flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
- flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 0
- flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 0
- flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 0
- flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe (
+ if (paired && (skipClip && skipTrim)) 2
+ else if (!paired && (skipClip && skipTrim)) 1
+ else if (paired && !(skipClip && skipTrim)) 4
+ else if (!paired && !(skipClip && skipTrim)) 2)
+ flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe (if (zipped) (if (paired) 2 else 1) else 0)
+ flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe (if (paired) 2 else 1)
+ flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe (if (skipClip) 0 else (if (paired) 2 else 1))
+ flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe (if (skipClip) 0 else (if (paired) 1 else 0))
+ flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe (if (skipTrim) 0 else 1)
+ flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (paired) 2 else 1)
}
}
object FlexiprepTest {
--
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