Commit 30e7d8ce authored by Peter van 't Hof's avatar Peter van 't Hof

Added test for bam arg

parent 1cafa1af
......@@ -33,7 +33,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
def this() = this(null)
@Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
protected var inputBamsArg: List[File] = Nil
protected[shiva] var inputBamsArg: List[File] = Nil
var inputBams: Map[String, File] = Map()
......
......@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{ File, FileOutputStream }
import java.nio.file.Paths
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerVCF, BreakdancerConfig, BreakdancerCaller }
......@@ -149,6 +150,25 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
}
}
private def resourcePath(p: String): String = {
Paths.get(getClass.getResource(p).toURI).toString
}
@Test
def testInputBamsArg(): Unit = {
val pipeline = initPipeline(Map())
pipeline.inputBamsArg :+= new File(resourcePath("/paired01.bam"))
pipeline.init()
pipeline.script()
val summaryCallers = pipeline.summarySettings("sv_callers")
assert(summaryCallers.contains("delly"))
assert(summaryCallers.contains("clever"))
assert(summaryCallers.contains("breakdancer"))
}
@AfterClass def removeTempOutputDir() = {
FileUtils.deleteDirectory(ShivaSvCallingTest.outputDir)
}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment