SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName(), getVersion());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("Alignment", ""), getVersion());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("Clean", ""), getVersion());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("Symlink", ""), getVersion());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); logger.debug("sequencerRun: {}", sequencerRun.toString());
job.addArgument("--sequencerRunId", sequencerRun.getId().toString()); } else if (sequencerRun == null && htsfSample != null) { logger.debug("htsfSample.getSequencerRun().getId().toString(): {}", htsfSample.getSequencerRun() .getId().toString()); job.addArgument("--sequencerRunId", htsfSample.getSequencerRun().getId().toString());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File sequencerRunOutputDirectory = new File(baseDir, sequencerRun.getName()); File workflowDir = new File(sequencerRunOutputDirectory, "NCGenes");
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File sequencerRunOutputDirectory = new File(baseDir, sequencerRun.getName()); File workflowDir = new File(sequencerRunOutputDirectory, "NCGenes");
SequencerRun sequencerRun = htsfSample.getSequencerRun();
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName() .replace("DX", ""), getVersion());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("DOC", ""), getVersion());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName() .replace("DX", ""), getVersion());
SequencerRun sequencerRun = htsfSampleSet.iterator().next().getSequencerRun();
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("DOC", ""), getVersion());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("IDCheck", ""), getVersion());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("IncidentalVariantCalling", ""), getVersion());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("Alignment", ""), getVersion());
SequencerRun sequencerRun = htsfSample.getSequencerRun(); logger.debug("sequencerRun: {}", sequencerRun.toString());