diff --git a/samtools.wdl b/samtools.wdl index de7f2a3652e1940bb343ecf77abb528eec679d7c..cc106d30d44f9c57529f8cb1017bd4bb84af6627 100644 --- a/samtools.wdl +++ b/samtools.wdl @@ -336,7 +336,6 @@ task View { File? referenceFasta String outputFileName = "view.bam" Boolean includeHeader = false - Boolean outputBam = false Boolean uncompressedBamOutput = false Int? includeFilter Int? excludeFilter @@ -356,7 +355,6 @@ task View { samtools view -b \ ~{"-T " + referenceFasta} \ ~{"-o " + outputFileName} \ - ~{true="-b " false="" outputBam} \ ~{true="-u " false="" uncompressedBamOutput} \ ~{"-f " + includeFilter} \ ~{"-F " + excludeFilter} \ @@ -368,7 +366,7 @@ task View { } output { - File outputBAM = outputFileName + File outputBam = outputFileName File outputBamIndex = outputIndexPath }