fixing missing cutadapt mock values

public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

@@ -39,7 +39,7 @@ class CarpTest extends TestNGSuite with Matchers {
   def testCarp(f: String, sample1: Boolean, sample2: Boolean, sample3: Boolean, threatment: Boolean, control: Boolean): Unit = {
     val map = {
       var m = ConfigUtils.mergeMaps(Map("output_dir" -> CarpTest.outputDir
-      ), CarpTest.excutables)
+      ), CarpTest.executables)
 
       if (sample1) m = ConfigUtils.mergeMaps(CarpTest.sample1, m.toMap)
       if (sample2) m = ConfigUtils.mergeMaps(CarpTest.sample2, m.toMap)
@@ -82,12 +82,13 @@ class CarpTest extends TestNGSuite with Matchers {
 object CarpTest {
   val outputDir = Files.createTempDir()
 
-  val excutables = Map(
+  val executables = Map(
     "reference" -> "test",
     "seqstat" -> Map("exe" -> "test"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),
     "sickle" -> Map("exe" -> "test"),
+    "cutadapt" -> Map("exe" -> "test"),
     "bwa" -> Map("exe" -> "test"),
     "samtools" -> Map("exe" -> "test"),
     "macs2" -> Map("exe" -> "test"),

public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -48,7 +48,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
     val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir,
       "skip_trim" -> skipTrim,
       "skip_clip" -> skipClip
-    ), Map(FlexiprepTest.excutables.toSeq: _*))
+    ), Map(FlexiprepTest.executables.toSeq: _*))
     val flexiprep: Flexiprep = initPipeline(map)
 
     flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq" + (if (zipped) ".gz" else ""))
@@ -79,10 +79,11 @@ class FlexiprepTest extends TestNGSuite with Matchers {
 object FlexiprepTest {
   val outputDir = Files.createTempDir()
 
-  val excutables = Map(
+  val executables = Map(
     "seqstat" -> Map("exe" -> "test"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),
-    "sickle" -> Map("exe" -> "test")
+    "sickle" -> Map("exe" -> "test"),
+    "cutadapt" -> Map("exe" -> "test")
   )
 }
\ No newline at end of file

public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -57,7 +57,7 @@ class MappingTest extends TestNGSuite with Matchers {
       "number_chunks" -> chunks,
       "skip_markduplicates" -> skipMarkDuplicate,
       "skip_flexiprep" -> skipFlexiprep
-    ), Map(MappingTest.excutables.toSeq: _*))
+    ), Map(MappingTest.executables.toSeq: _*))
     val mapping: Mapping = initPipeline(map)
 
     mapping.input_R1 = new File(mapping.outputDir, "bla_R1.fq")
@@ -107,12 +107,13 @@ class MappingTest extends TestNGSuite with Matchers {
 object MappingTest {
   val outputDir = Files.createTempDir()
 
-  val excutables = Map(
+  val executables = Map(
     "reference" -> "test",
     "seqstat" -> Map("exe" -> "test"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),
     "sickle" -> Map("exe" -> "test"),
+    "cutadapt" -> Map("exe" -> "test"),
     "bwa" -> Map("exe" -> "test"),
     "star" -> Map("exe" -> "test"),
     "bowtie" -> Map("exe" -> "test"),