Job request: 3183

version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population_descriptives:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_descriptives
    outputs:
      highly_sensitive:
        cohort: output/input_descriptives.csv
  
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
  
  generate_results:
    run: python:latest python analysis/generate_results.py
    needs: [generate_study_population, generate_study_population_descriptives]
    outputs:
      moderately_sensitive:
        num_patients: output/num_patients.json
        ae_attendance_count_dict: output/num_ae_attendances.json
        hosp_dict: output/emergency_hospitalisation.json
        ae_dict: output/ae.json
        any_ae_dict: output/ae_any.json
        all_ae_dict: output/ae_all.json
        discharge_csv: output/discharge_destination.csv
        performance_dict: output/model_performance.json
        sensitivity_dict: output/sensitivity.json
        model_csvs: output/model_*.csv
  
  generate_tree:
    run: python:latest python analysis/tree.py
    needs: [generate_study_population, generate_study_population_descriptives]
    outputs:
      moderately_sensitive:
        tree: output/tree.png
        results: output/results_df.csv
        fi: output/feature_importance.csv
        
  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/results.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_study_population, generate_study_population_descriptives]
    outputs:
      moderately_sensitive:
        notebook: output/results.html