project.yaml

version: '3.0'

expectations:
  population_size: 1000

actions:

  # Generate ethnicity study population
  generate_study_population_ethnicity:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_ethnicity 
      --output-dir=output
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv

  # Stroke and transient ischaemic attack
  generate_study_population_stia_reg:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_stia_reg 
      --index-date-range "2021-04-01 to 2022-03-01 by month" 
      --output-dir=output
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_stia_reg*.csv
  
  join_ethnicity_stia:
    run: >
      cohort-joiner:v0.0.12 
        --lhs output/input_stia*.csv
        --rhs output/input_ethnicity.csv
        --output-dir output/joined
    needs: [generate_study_population_ethnicity, generate_study_population_stia_reg]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_stia*.csv

  generate_measures_stia_reg:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_stia_reg 
       --output-dir=output/joined
     needs: [join_ethnicity_stia]
     outputs:
       moderately_sensitive:
         measure_csv: output/joined/measure_stia_reg_*_rate.csv