Expose sort option in picard FastqToSam task (#397)

fulcrumgenomics · Jul 22, 2021 · f639abd · f639abd
1 parent 58065bf
commit f639abd
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/tasks/src/main/scala/dagr/tasks/picard/FastqToSam.scala b/tasks/src/main/scala/dagr/tasks/picard/FastqToSam.scala
@@ -28,6 +28,7 @@ import dagr.tasks.DataTypes.{Fastq, SamOrBam}
 import dagr.tasks.DagrDef
 import DagrDef.{PathToBam, PathToFastq}
 import dagr.core.execsystem.{Cores, Memory}
+import htsjdk.samtools.SAMFileHeader.SortOrder
 import htsjdk.samtools.util.FastqQualityFormat
 
 import scala.collection.mutable.ListBuffer
@@ -42,7 +43,8 @@ class FastqToSam(fastq1: PathToFastq,
  readGroupName: Option[String] = None,
  stripUnpairedMateNumber: Boolean = true,
  useSequentialFastqs: Boolean = false,
- qualityFormat: Option[FastqQualityFormat] = None)
+ qualityFormat: Option[FastqQualityFormat] = None,
+ sortOrder: Option[SortOrder] = Some(SortOrder.queryname))
  extends PicardTask with Pipe[Fastq,SamOrBam] {
  requires(Cores(1), Memory("2G"))
 
@@ -59,6 +61,6 @@ class FastqToSam(fastq1: PathToFastq,
  library.foreach(lb => buffer.append("LB=" + lb))
  if (useSequentialFastqs) buffer.append("USE_SEQUENTIAL_FASTQS=true")
  buffer.append("STRIP_UNPAIRED_MATE_NUMBER=" + stripUnpairedMateNumber)
- buffer.append("SO=queryname")
+ sortOrder.foreach(so => buffer.append("SO=" + so.name))
  }
 }