diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala index 0fc8ea9ee3209e4bc73c2fd06d8f73d14aca6b04..a2f59eca1be3788c4c0361db10a2e32d3b000b74 100644 --- a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala +++ b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala @@ -119,12 +119,12 @@ class Mapping(private var globalConfig: Config) extends QScript { this.nCoresRequest = 2 this.jobResourceRequests :+= "h_vmem=4G" - this.RGLB = RGLB - this.RGPL = RGPL - this.RGPU = RGPU - this.RGSM = RGSM - if (RGCN != null) this.RGCN = RGCN - if (RGDS != null) this.RGDS = RGDS + this.RGLB = qscript.RGLB + this.RGPL = qscript.RGPL + this.RGPU = qscript.RGPU + this.RGSM = qscript.RGSM + if (RGCN != null) this.RGCN = qscript.RGCN + if (RGDS != null) this.RGDS = qscript.RGDS } add(addOrReplaceReadGroups)