if (mimeType != null && mimeType.equals(MimeType.FASTQ)) { Pattern patternR1 = Pattern.compile(String.format("^%s.*_L00%d_R1\\.fastq\\.gz$", sequencerRunName, laneIndex));
MimeType mimeType = MimeType.valueOf(commandLine.getOptionValue("mimeType")); app.setMimeType(mimeType); } catch (Exception e) {
sequencerRun.getName(), htsfSample.getBarcode(), laneIndex, 1)); copy1Job.addArgument(CopyCLI.DESTINATION, r1FastqFile.getAbsolutePath()); copy1Job.addArgument(CopyCLI.MIMETYPE, MimeType.FASTQ.toString()); graph.addVertex(copy1Job); graph.addEdge(makeJob, copy1Job); getWorkflowPlan().getSequencerRun().getName(), htsfSample.getBarcode(), laneIndex, 2)); copy2Job.addArgument(CopyCLI.DESTINATION, r2FastqFile.getAbsolutePath()); copy2Job.addArgument(CopyCLI.MIMETYPE, MimeType.FASTQ.toString()); graph.addVertex(copy2Job); graph.addEdge(makeJob, copy2Job);
if (fileData.getMimeType().equals(mimeType)) { List<Job> jobList = null; try {
MimeType mimeType = MimeType.valueOf(commandLine.getOptionValue("mimeType")); app.setMimeType(mimeType); } catch (Exception e) {
if (fileData.getMimeType().equals(MimeType.TEXT_VCF)) { possibleVCFFileList.add(new File(fileData.getPath(), fileData.getName()));
MimeType mimeType = MimeType.valueOf(commandLine.getOptionValue("mimeType")); app.setMimeType(mimeType); } catch (Exception e) {