Job request: 3184

version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  generate_study_population_with_codes:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_with_codes
    outputs:
      highly_sensitive:
        cohort: output/input_with_codes.csv


  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/prevalence_comparison.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        notebook: output/prevalence_comparison.html 
        table: safe-outputs/*
        
        
  generate_notebook_code_comparison:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/prevalence_deepdive.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
    needs: [generate_study_population_with_codes]
    outputs:
      moderately_sensitive:
        notebook: output/prevalence_deepdive.html 
        table: safe-outputs/by-codelist/*