diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala index 75ba6c3ab2f74eec60d7854dcde064ad052f830b..9996dfed3befed4e8913ee1377d04953607dfbc9 100644 --- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala +++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala @@ -15,6 +15,7 @@ */ package nl.lumc.sasc.biopet.tools +import java.io.File import java.nio.file.Paths import org.scalatest.Matchers @@ -36,25 +37,25 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers { Paths.get(getClass.getResource(p).toURI).toString } - val vepped_path = resourcePath("/VEP_oneline.vcf.gz") - val unvepped_path = resourcePath("/unvepped.vcf.gz") + val veppedPath = resourcePath("/VEP_oneline.vcf.gz") + val unveppedPath = resourcePath("/unvepped.vcf.gz") val rand = new Random() @Test def testOutputTypeVcf() = { - val tmp_path = "/tmp/VcfWithVcf_" + rand.nextString(10) + ".vcf" - val arguments = Array("-I", unvepped_path, "-s", vepped_path, "-o", tmp_path, "-f", "CSQ") + val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath + val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ") main(arguments) } @Test def testOutputTypeVcfGz() = { - val tmp_path = "/tmp/VcfWithVcf_" + rand.nextString(10) + ".vcf.gz" - val arguments = Array("-I", unvepped_path, "-s", vepped_path, "-o", tmp_path, "-f", "CSQ") + val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath + val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ") main(arguments) } @Test def testOutputTypeBcf() = { - val tmp_path = "/tmp/VcfWithVcf_" + rand.nextString(10) + ".bcf" - val arguments = Array("-I", unvepped_path, "-s", vepped_path, "-o", tmp_path, "-f", "CSQ") + val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath + val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ") main(arguments) }