1. 05 Oct, 2020 1 commit
    • 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.