Commit 306e857d authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Adding Seqstat to the pipeline tests

parent 8ce1b37a
......@@ -84,7 +84,6 @@ object CarpTest {
val excutables = Map(
"reference" -> "test",
"seqstat" -> Map("exe" -> "test"),
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
"sickle" -> Map("exe" -> "test"),
......
......@@ -11,6 +11,7 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
import nl.lumc.sasc.biopet.tools.Seqstat
import nl.lumc.sasc.biopet.tools.FastqSync
import nl.lumc.sasc.biopet.utils.ConfigUtils
......@@ -62,6 +63,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
else if (!paired && (skipClip && skipTrim)) 1
else if (paired && !(skipClip && skipTrim)) 4
else if (!paired && !(skipClip && skipTrim)) 2)
flexiprep.functions.count(_.isInstanceOf[Seqstat]) shouldBe (if (paired) 4 else 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))
......@@ -80,7 +82,6 @@ object FlexiprepTest {
val outputDir = Files.createTempDir()
val excutables = Map(
"seqstat" -> Map("exe" -> "test"),
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
"sickle" -> Map("exe" -> "test")
......
......@@ -17,7 +17,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.Cutadapt
import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
import nl.lumc.sasc.biopet.pipelines.flexiprep.Sickle
import nl.lumc.sasc.biopet.pipelines.flexiprep._
import nl.lumc.sasc.biopet.tools.FastqSync
import nl.lumc.sasc.biopet.tools.{ Seqstat, FastqSync }
import nl.lumc.sasc.biopet.utils.ConfigUtils
/**
......@@ -69,6 +69,7 @@ class MappingTest extends TestNGSuite with Matchers {
//Flexiprep
mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
mapping.functions.count(_.isInstanceOf[Zcat]) shouldBe 0
mapping.functions.count(_.isInstanceOf[Seqstat]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 4 else 2) * chunks)
mapping.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
mapping.functions.count(_.isInstanceOf[Cutadapt]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
mapping.functions.count(_.isInstanceOf[FastqSync]) shouldBe ((if (skipFlexiprep) 0 else if (paired && !skipFlexiprep) 1 else 0) * chunks)
......@@ -109,7 +110,6 @@ object MappingTest {
val excutables = Map(
"reference" -> "test",
"seqstat" -> Map("exe" -> "test"),
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
"sickle" -> Map("exe" -> "test"),
......
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