List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex());
List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); logger.debug("readPairList.size(): {}", readPairList.size());
logger.info("outputDirectory.getAbsolutePath() = {}", outputDirectory.getAbsolutePath()); List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex());
htsfSample.getFileDatas(), this.mapseqDAOBean, SAMToolsFlagstat.class, MimeType.TEXT_STAT_SUMMARY, ncgenesWorkflow.getId());
Set<FileData> fileDataSet = htsfSample.getFileDatas();
List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex());
Set<FileData> fileDataSet = htsfSample.getFileDatas();
Set<FileData> fileDataSet = htsfSample.getFileDatas(); File bamFile = null;
Set<FileData> fileDataSet = htsfSample.getFileDatas();
Set<FileData> fileDataSet = htsfSample.getFileDatas(); File bamFile = null;
List<File> readPairList = PipelineUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); logger.info("fileList = {}", readPairList.size());
getName().replace("DOC", ""), getVersion()); Set<FileData> fileDataSet = htsfSample.getFileDatas();
Set<FileData> fileDataSet = htsfSample.getFileDatas();
Set<FileData> fileDataSet = htsfSample.getFileDatas();
getName().replace("IDCheck", ""), getVersion()); Set<FileData> fileDataSet = htsfSample.getFileDatas();
List<File> readPairList = PipelineUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); logger.info("fileList = {}", readPairList.size());
Set<FileData> fileDataSet = htsfSample.getFileDatas(); throw new WorkflowException("bam file to process was not found"); List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); logger.info("fileList = {}", readPairList.size());
List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); logger.debug("fileList = {}", readPairList.size());
List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); logger.debug("fileList = {}", readPairList.size());
Set<FileData> fileDataSet = htsfSample.getFileDatas();