Commit 2d3a083a authored by Peter van 't Hof's avatar Peter van 't Hof

Added igvtools_jar to mock config

parent 0da332ac
......@@ -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")
)
......
......@@ -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(
......
......@@ -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"),
......
......@@ -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"),
......
......@@ -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")
)
......
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