diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala index 116d16f35..b64c715d4 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala @@ -164,7 +164,7 @@ class DataProcessingPipeline extends QScript { for (rg <- readGroups) { val intermediateInBam: File = if (index == readGroups.length) { inBam } else { swapExt(outBam, ".bam", index+1 + "-rg.bam") } val intermediateOutBam: File = if (index > 1) {swapExt(outBam, ".bam", index + "-rg.bam") } else { outBam} - val readGroup = new ReadGroup(rg.getReadGroupId, rg.getPlatform, rg.getLibrary, rg.getPlatformUnit, rg.getSample, rg.getSequencingCenter, rg.getDescription) + val readGroup = new ReadGroup(rg.getReadGroupId, rg.getLibrary, rg.getPlatform, rg.getPlatformUnit, rg.getSample, rg.getSequencingCenter, rg.getDescription) add(addReadGroup(intermediateInBam, intermediateOutBam, readGroup)) index = index - 1 }