File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName(), getVersion());
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("Alignment", ""), getVersion());
sequencerRun.getName(), htsfSample.getLaneIndex()); logger.debug("readPairList.size(): {}", readPairList.size()); File sequencerRunOutputDirectory = new File(getOutputDirectory(), sequencerRun.getName()); File casavaWorkflowDirectory = new File(sequencerRunOutputDirectory, "CASAVA/" + htsfSample.getName());
File flowcellDir = new File(sr.getBaseDirectory(), sr.getName()); File dataDir = new File(flowcellDir, "Data"); File reportsDir = new File(dataDir, "reports");
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("Symlink", ""), getVersion()); logger.info("outputDirectory.getAbsolutePath() = {}", outputDirectory.getAbsolutePath()); List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex());
if (workflowPlan.getSequencerRun() != null) { sb.append(String.format("SequencerRun Name: %s%n", workflowPlan .getSequencerRun().getName()));
File sequencerRunOutputDirectory = new File(baseDir, sequencerRun.getName()); File workflowDir = new File(sequencerRunOutputDirectory, "NCGenes"); File outputDirectory = new File(workflowDir, htsfSample.getName());
File sequencerRunOutputDirectory = new File(baseDir, sequencerRun.getName()); File workflowDir = new File(sequencerRunOutputDirectory, "NCGenes"); File outputDirectory = new File(workflowDir, htsfSample.getName());
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName() .replace("DX", ""), getVersion()); File tmpDir = new File(outputDirectory, "tmp");
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("DOC", ""), getVersion());
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName() .replace("DX", ""), getVersion());
SequencerRun sequencerRun = htsfSampleSet.iterator().next().getSequencerRun(); File sequencerRunOutputDirectory = new File(getOutputDirectory(), sequencerRun.getName()); File workflowDir = new File(sequencerRunOutputDirectory, getName().replace("RecalMergeBAM", ""));
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("DOC", ""), getVersion());
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("IDCheck", ""), getVersion());
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("IncidentalVariantCalling", ""), getVersion()); 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());
.toLowerCase()); 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());
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName());