def check_and_postprocess(args): """Check for newly dumped sequencer output, post-processing and transferring. """ with open(args.process_config) as in_handle: config = yaml.safe_load(in_handle) setup_local_logging() for dname in _find_unprocessed(config): runinfo = nglims.get_runinfo(config["galaxy_url"], config["galaxy_apikey"], dname) lane_details = nglims.flatten_lane_detail(runinfo) fcid_ss = samplesheet.from_flowcell(dname, lane_details) fastq_dir = demultiplex.run_bcl2fastq(dname, fcid_ss, config)
def check_and_postprocess(args): """Check for newly dumped sequencer output, post-processing and transferring. """ with open(args.process_config) as in_handle: config = yaml.safe_load(in_handle) setup_local_logging(config) for dname in _find_unprocessed(config): lane_details = nglims.get_runinfo(config["galaxy_url"], config["galaxy_apikey"], dname, utils.get_in(config, ("process", "storedir"))) fcid_ss = samplesheet.from_flowcell(dname, lane_details) _update_reported(config["msg_db"], dname) fastq_dir = demultiplex.run_bcl2fastq(dname, fcid_ss, config) bcbio_config, ready_fastq_dir = nglims.prep_samples_and_config(dname, lane_details, fastq_dir, config) transfer.copy_to_remote(dname, ready_fastq_dir, bcbio_config, config) _start_processing(dname, bcbio_config, config)
def check_and_postprocess(args): """Check for newly dumped sequencer output, post-processing and transferring. """ with open(args.process_config) as in_handle: config = yaml.safe_load(in_handle) setup_local_logging(config) for dname in _find_unprocessed(config): lane_details = nglims.get_runinfo(config["galaxy_url"], config["galaxy_apikey"], dname, utils.get_in(config, ("process", "storedir"))) fcid_ss = samplesheet.from_flowcell(dname, lane_details) _update_reported(config["msg_db"], dname) fastq_dir = demultiplex.run_bcl2fastq(dname, fcid_ss, config) bcbio_config, ready_fastq_dir = nglims.prep_samples_and_config(dname, lane_details, fastq_dir, config) transfer.copy_flowcell(dname, ready_fastq_dir, bcbio_config, config) _start_processing(dname, bcbio_config, config)