ncgenesWorkflow.getId());
List<File> possibleVCFFileList = WorkflowUtil.lookupFileByJobAndMimeTypeAndWorkflowId(fileDataSet, getWorkflowBeanService().getMaPSeqDAOBean(), GATKUnifiedGenotyper.class, MimeType.TEXT_VCF, variantCallingWorkflow.getId()); if (possibleVCFFileList != null && possibleVCFFileList.size() > 0) { vcfFile = possibleVCFFileList.get(0);
MimeType.APPLICATION_BAM, ncgenesWorkflow.getId());
MimeType.APPLICATION_BAM, ncgenesWorkflow.getId());
MimeType.APPLICATION_BAM, ncgenesWorkflow.getId());
MimeType.APPLICATION_BAM, ncgenesWorkflow.getId());
List<File> possibleFileList = WorkflowUtil.lookupFileByJobAndMimeTypeAndWorkflowId(fileDataSet, getWorkflowBeanService().getMaPSeqDAOBean(), PicardMarkDuplicates.class, MimeType.APPLICATION_BAM, variantCallingWorkflow.getId());
MimeType.APPLICATION_BAM, ncgenesWorkflow.getId());
List<File> possibleVCFFileList = WorkflowUtil.lookupFileByJobAndMimeTypeAndWorkflowId(fileDataSet, getWorkflowBeanService().getMaPSeqDAOBean(), GATKUnifiedGenotyper.class, MimeType.TEXT_VCF, variantCallingWorkflow.getId());
MimeType.APPLICATION_BAM, ncgenesWorkflow.getId());
MimeType.APPLICATION_BAM, alignmentWorkflow.getId());
MimeType.APPLICATION_BAM, alignmentWorkflow.getId());
MimeType.APPLICATION_BAM, alignmentWorkflow.getId());
MimeType.APPLICATION_BAM, ncgenesWorkflow.getId());