Ejemplo n.º 1
0
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)
Ejemplo n.º 2
0
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)
Ejemplo n.º 3
0
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)