diff --git a/tasks/src/main/scala/dagr/tasks/fgbio/ClipBam.scala b/tasks/src/main/scala/dagr/tasks/fgbio/ClipBam.scala index 7dc18a09..85fa9b44 100755 --- a/tasks/src/main/scala/dagr/tasks/fgbio/ClipBam.scala +++ b/tasks/src/main/scala/dagr/tasks/fgbio/ClipBam.scala @@ -25,13 +25,14 @@ package dagr.tasks.fgbio import com.fulcrumgenomics.commons.CommonsDef.PathToFasta -import dagr.tasks.DagrDef.PathToBam +import dagr.tasks.DagrDef.{FilePath, PathToBam} import scala.collection.mutable.ListBuffer class ClipBam(val input: PathToBam, val output: PathToBam, val ref: PathToFasta, + val metrics: Option[FilePath] = None, @deprecated("Use clipping-mode instead.", since="0.2.1") val softClip: Option[Boolean] = None, val clippingMode: Option[String] = None, @@ -50,6 +51,7 @@ class ClipBam(val input: PathToBam, buffer.append("-i", input) buffer.append("-o", output) buffer.append("-r", ref) + metrics.foreach (m => buffer.append("-m", m)) softClip.foreach (s => buffer.append("-s", s)) clippingMode.foreach (c => buffer.append("-c", c)) autoClipAttributes.foreach(a => buffer.append("-a", a))