diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
deleted file mode 100644
index 60c9d9a59..000000000
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
+++ /dev/null
@@ -1,67 +0,0 @@
-package org.broadinstitute.sting.queue.pipeline
-
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-import org.testng.annotations.Test
-import org.broadinstitute.sting.BaseTest
-
-class DataProcessingPipelineTest {
-  @Test(timeOut=36000000)
-  def testSimpleBAM {
-    val projectName = "test1"
-    val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
-    val spec = new PipelineTestSpec
-    spec.name = "DataProcessingPipeline"
-    spec.args = Array(
-      " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala",
-      " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
-      " -i " + BaseTest.publicTestDir + "exampleBAM.bam",
-      " -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf",
-      " -test ",
-      " -p " + projectName).mkString
-    spec.fileMD5s += testOut -> "45d97df6d291695b92668e8a55c54cd0"
-    PipelineTest.executeTest(spec)
-  }
-
-  @Test(timeOut=36000000)
-  def testBWAPEBAM {
-    val projectName = "test2"
-    val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
-    val spec = new PipelineTestSpec
-    spec.name = "DataProcessingPipeline"
-    spec.args = Array(
-      " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala",
-      " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
-      " -i " + BaseTest.publicTestDir + "exampleBAM.bam",
-      " -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf",
-      " -test ",
-      " -bwa /home/unix/carneiro/bin/bwa",
-      " -bwape ",
-      " -p " + projectName).mkString
-    spec.fileMD5s += testOut -> "9fca827ecc8436465b831bb6f879357a"
-    PipelineTest.executeTest(spec)
-  }
-
-}
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
deleted file mode 100644
index dd07cbfdc..000000000
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
+++ /dev/null
@@ -1,46 +0,0 @@
-package org.broadinstitute.sting.queue.pipeline
-
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-import org.testng.annotations.Test
-import org.broadinstitute.sting.BaseTest
-
-class PacbioProcessingPipelineTest {
-  @Test(timeOut=36000000)
-  def testPacbioProcessingPipeline {
-    val testOut = "exampleBAM.recal.bam"
-    val spec = new PipelineTestSpec
-    spec.name = "pacbioProcessingPipeline"
-    spec.args = Array(
-      " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala",
-      " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
-      " -i " + BaseTest.publicTestDir + "exampleBAM.bam",
-      " -blasr ",
-      " -test ",
-      " -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf").mkString
-    spec.fileMD5s += testOut -> "b84f9c45e045685067ded681d5e6224c"
-    PipelineTest.executeTest(spec)
-  }
-}