Added igvtools_jar to mock config

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

@@ -125,7 +125,7 @@ object CarpTest {
     "bwa" -> Map("exe" -> "test"),
     "samtools" -> Map("exe" -> "test"),
     "macs2" -> Map("exe" -> "test"),
-    "igvtools" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "wigtobigwig" -> Map("exe" -> "test"),
     "md5sum" -> Map("exe" -> "test")
   )

gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -194,6 +194,7 @@ object GentrapTest {
     "ribosome_refflat" -> (outputDir + File.separator + "ref.fa"),
     "varscan_jar" -> "test",
     "rscript" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "gatk_jar" -> "test"
   ) ++ Seq(
       // fastqc executables
@@ -203,7 +204,7 @@ object GentrapTest {
       // gentrap executables
       "cufflinks", "htseqcount", "grep", "pdflatex", "rscript", "tabix", "bgzip", "bedtoolscoverage", "md5sum",
       // bam2wig executables
-      "igvtools", "wigtobigwig"
+      "wigtobigwig"
     ).map { case exe => exe -> Map("exe" -> "test") }.toMap
 
   val sample1: Map[String, Any] = Map(

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala

@@ -194,7 +194,7 @@ object MultisampleMappingTestTrait {
     "cutadapt" -> Map("exe" -> "test"),
     "bwa" -> Map("exe" -> "test"),
     "samtools" -> Map("exe" -> "test"),
-    "igvtools" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "wigtobigwig" -> Map("exe" -> "test"),
     "kraken" -> Map("exe" -> "test", "db" -> "test"),
     "krakenreport" -> Map("exe" -> "test", "db" -> "test"),

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

@@ -210,7 +210,7 @@ object ShivaTest {
     "bwa" -> Map("exe" -> "test"),
     "samtools" -> Map("exe" -> "test"),
     "macs2" -> Map("exe" -> "test"),
-    "igvtools" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "wigtobigwig" -> Map("exe" -> "test"),
     "md5sum" -> Map("exe" -> "test"),
     "bgzip" -> Map("exe" -> "test"),

tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala

@@ -134,7 +134,7 @@ object TinyCapTest {
     "cutadapt" -> Map("exe" -> "test"),
     "bowtie" -> Map("exe" -> "test"),
     "htseqcount" -> Map("exe" -> "test"),
-    "igvtools" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "wigtobigwig" -> Map("exe" -> "test")
   )