diff --git a/samtools.wdl b/samtools.wdl index 587a53fb048a65f66f7adb482d91c87f3ba563cb..8503777ce7451d6a398f0485b45c178cc96162b6 100644 --- a/samtools.wdl +++ b/samtools.wdl @@ -571,6 +571,7 @@ task View { Int? excludeFilter Int? excludeSpecificFilter Int? MAPQthreshold + File? targetFile Int threads = 1 String memory = "1GiB" @@ -593,6 +594,7 @@ task View { ~{"-G " + excludeSpecificFilter} \ ~{"-q " + MAPQthreshold} \ ~{"--threads " + (threads - 1)} \ + ~{"--target-file " + targetFile} \ ~{inFile} samtools index ~{outputFileName} ~{outputIndexPath} }