project.yaml

version: '3.0'

expectations:
  population_size: 1000

actions:
    
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2022-04-30 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  process_data:
    run: r:latest analysis/create_age_standardised_outputs.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        figure: output/measures/standardised_*.csv