diff --git a/tasks/src/main/scala/dagr/tasks/fgbio/GroupReadsByUmi.scala b/tasks/src/main/scala/dagr/tasks/fgbio/GroupReadsByUmi.scala index 0742dea2..1e8d6c62 100644 --- a/tasks/src/main/scala/dagr/tasks/fgbio/GroupReadsByUmi.scala +++ b/tasks/src/main/scala/dagr/tasks/fgbio/GroupReadsByUmi.scala @@ -46,6 +46,8 @@ class GroupReadsByUmi(val in: PathToBam, val minMapQ: Option[Int] = None, val strategy: AssignmentStrategy = AssignmentStrategy.Adjacency, val edits: Option[Int] = None, + val minUmiLength: Option[Int] = None, + val allowInterContig: Boolean = false, tmpDir: Option[DirPath] = None) extends FgBioTask(tmpDir=tmpDir) with Pipe[SamOrBam, SamOrBam] { /** Implement this to add the tool-specific arguments */ @@ -58,6 +60,8 @@ class GroupReadsByUmi(val in: PathToBam, minMapQ.foreach(m => buffer.append("-m", m)) buffer.append("-s", strategy.toString.toLowerCase) edits.foreach(e => buffer.append("-e", e)) + minUmiLength.foreach(m => buffer.append("-l", m)) + if (allowInterContig) buffer.append("-x") tmpDir.foreach(d => buffer.append(s"--tmp-dir=${d}")) } }