job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, String.format("%s-%s_L%03d", sequencerRun.getName(), htsfSample.getBarcode(), htsfSample.getLaneIndex())); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, htsfSample.getBarcode()); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY,
htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName());
htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName());
htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName());
htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName());
sampleName); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument( PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform() .getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(
picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, sampleName); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun .getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob .addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, sampleName);
picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, sampleName); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun .getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob .addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, sampleName);
sampleName); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, sampleName);