From 306e857dc9c0b7ea3afaa0307e08bea75c0024ff Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 16 Feb 2015 15:13:49 +0100
Subject: [PATCH] Adding Seqstat to the pipeline tests
---
.../scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala | 1 -
.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala | 3 ++-
.../nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala | 4 ++--
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
index fd57a752a..d276e6b96 100644
--- a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+++ b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
@@ -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"),
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 7f6c81a34..c6754cd9e 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
@@ -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")
diff --git a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
index 19b773aba..3a83997d9 100644
--- a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+++ b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
@@ -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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