private int addRandomSampleQCRoutineToDAX(Graph<CondorJob, CondorJobEdge> graph, int count, HTSFSample htsfSample, File fastqFile, CondorJob trimCountAdapterJob, File trimmedFastq, String outputPath) throws IOException { String sequenceDatabaseList = getPipelineBeanService().getAttributes().get("sequenceDatabaseList");
logger.info("sequencerRun: {}", getWorkflowPlan().getSequencerRun().toString()); try { htsfSampleSet.addAll(getPipelineBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); } catch (MaPSeqDAOException e) { String fastaDatabase = getPipelineBeanService().getAttributes().get("fastaDatabase"); String quantificationDatabaseKey = getPipelineBeanService().getAttributes().get("quantificationDatabaseKey"); String primerSequence1 = getPipelineBeanService().getAttributes().get("primerSequence1"); String primerSequence2 = getPipelineBeanService().getAttributes().get("primerSequence2");