diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala index a629da59f..6603ddf8c 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala @@ -44,6 +44,9 @@ class ExamplePrintReads extends QScript { @Argument(doc="One or more genomic intervals over which to operate", shortName="L", required=false) var intervals: Seq[String] = Nil + @Argument(doc = "Don't output a program tag", shortName = "npt", required = false) + var noPGTag: Boolean = _ + def script() { val printReads = new PrintReads printReads.reference_sequence = referenceFile @@ -52,6 +55,7 @@ class ExamplePrintReads extends QScript { printReads.input_file :+= bamFile printReads.out = outFile printReads.intervalsString = intervals + printReads.no_pg_tag = noPGTag add(printReads) } } diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala index f44e458c3..f352a3966 100644 --- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala +++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala @@ -42,7 +42,8 @@ class QueueFeaturesQueueTest { " -S " + QueueTest.publicQScriptsPackageDir + "examples/ExamplePrintReads.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM_with_unmapped.bam", - " -out " + testOut).mkString + " -out " + testOut, + " -npt ").mkString spec.fileMD5s += testOut -> "3134a6c732d7f235373095586bc7d470" QueueTest.executeTest(spec) @@ -55,7 +56,8 @@ class QueueFeaturesQueueTest { " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM_with_unmapped.bam", " -L chr1", - " -out " + testOut2).mkString + " -out " + testOut2, + " -npt ").mkString spec2.fileMD5s += testOut2 -> "aa33e589879c4baf6a470d22da76d885" QueueTest.executeTest(spec2) }