Adding Seqstat to the pipeline tests

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"),

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")

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"),