Commit 0109059c authored by bow's avatar bow
Browse files

Add missing mock bam2wig executables in GentrapTest

parent e459cf6e
......@@ -147,20 +147,20 @@ class GentrapTest extends TestNGSuite with Matchers {
if (expMeasures.contains("cufflinks_guided")) {
gentrap.functions
.collect {
case x: Cufflinks => x.outputGenesFpkm.getParentFile.toString.endsWith("cufflinks_guided")
case x: Ln => x.output.toString.endsWith(".genes_fpkm_cufflinks_guided") ||
x.output.toString.endsWith(".isoforms_fpkm_cufflinks_guided")
}
case x: Cufflinks => x.outputGenesFpkm.getParentFile.toString.endsWith("cufflinks_guided")
case x: Ln => x.output.toString.endsWith(".genes_fpkm_cufflinks_guided") ||
x.output.toString.endsWith(".isoforms_fpkm_cufflinks_guided")
}
.count(identity) shouldBe numSamples * 3 // three types of jobs per sample
}
if (expMeasures.contains("cufflinks_blind")) {
gentrap.functions
.collect {
case x: Cufflinks => x.outputGenesFpkm.getParentFile.toString.endsWith("cufflinks_blind")
case x: Ln => x.output.toString.endsWith(".genes_fpkm_cufflinks_blind") ||
x.output.toString.endsWith(".isoforms_fpkm_cufflinks_blind")
}
case x: Cufflinks => x.outputGenesFpkm.getParentFile.toString.endsWith("cufflinks_blind")
case x: Ln => x.output.toString.endsWith(".genes_fpkm_cufflinks_blind") ||
x.output.toString.endsWith(".isoforms_fpkm_cufflinks_blind")
}
.count(identity) shouldBe numSamples * 3 // three types of jobs per sample
}
}
......@@ -186,6 +186,8 @@ object GentrapTest {
// mapping executables
"star", "bowtie", "samtools", "gsnap",
// gentrap executables
"cufflinks", "htseq-count", "grep", "pdflatex", "Rscript", "tabix", "bgzip"
"cufflinks", "htseq-count", "grep", "pdflatex", "Rscript", "tabix", "bgzip",
// bam2wig executables
"igvtools", "wigtobigwig"
).map { case exe => exe -> Map("exe" -> "test") }.toMap
}
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