• Chris Jewell's avatar
    Major new pipelining structure · bfcaf904
    Chris Jewell authored
    enqueue_pipeline.sh --> covid_pipeline.sge --> prepare_config.py --> inference.py --> summary.py
    enqueue_pipeline.sh identifies the dataset and analysis period, launching 4 SGE jobs [P1, P1+2]\times[specimen_date, report_date]
    Each SGE job runs the inference and summary scripts, using information contained in a config.yaml file.
    The config.yaml file, together with results outputs, are stored in a results directory specified the config file
    and over-ridden in the top-level enqueue_pipeline.sh script.