Commit 7e542a61 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change back to get

parent a6d7e825
......@@ -24,6 +24,9 @@ import org.broadinstitute.gatk.utils.commandline.Argument
* @author Peter van 't Hof
*/
trait SampleLibraryTag extends Configurable {
//FIXME: not possible to have required sample / lib
@Argument(doc = "Sample ID", shortName = "sample", required = false)
var sampleId: Option[String] = root match {
case tag: SampleLibraryTag => tag.sampleId
......
......@@ -442,10 +442,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def addBowtie2(R1: File, R2: Option[File], output: File): File = {
val bowtie2 = new Bowtie2(this)
bowtie2.rg_id = Some(readgroupId)
bowtie2.rg +:= ("LB:" + libId.getOrElse("x"))
bowtie2.rg +:= ("LB:" + libId.get)
bowtie2.rg +:= ("PL:" + platform)
bowtie2.rg +:= ("PU:" + platformUnit)
bowtie2.rg +:= ("SM:" + sampleId.getOrElse("x"))
bowtie2.rg +:= ("SM:" + sampleId.get)
bowtie2.R1 = R1
bowtie2.R2 = R2
val sortSam = new SortSam(this)
......
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