project.yaml

version: "3.0"

expectations:
  population_size: 50000

actions:

  2017:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2017
    outputs:
      highly_sensitive:
        cohort: output/input_2017.csv

  2017_ckd:
    run: stata-mp:latest analysis/ckd.do 2017
    needs: [2017]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2017_ckd.csv
      moderately_sensitive:
        log: logs/2017_ckd.log
  
  2017_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2017_ckd_complete
    needs: [2017, 2017_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2017_ckd_complete.csv

  2017_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2017
    needs: [2017, 2017_ckd, 2017_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2017_ckd_complete.dta
      moderately_sensitive:
        log: logs/2017_ckd_complete.log

  2017_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2017
    needs: [2017, 2017_ckd, 2017_ckd_complete, 2017_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2017_healthcare_use.log
        output: output/2017_healthcare_use.csv

  2017_healthcare_use_region:
    run: stata-mp:latest analysis/healthcare_use_region.do 2017
    needs: [2017, 2017_ckd, 2017_ckd_complete, 2017_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2017_ckd_complete_region.dta
      moderately_sensitive:
        log: logs/2017_healthcare_use_region.log
        output: output/2017_healthcare_use_region.csv

  2017_healthcare_use_imd:
    run: stata-mp:latest analysis/healthcare_use_imd.do 2017
    needs: [2017, 2017_ckd, 2017_ckd_complete, 2017_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2017_ckd_complete_imd.dta
      moderately_sensitive:
        log: logs/2017_healthcare_use_imd.log
        output: output/2017_healthcare_use_imd.csv

  2017_healthcare_use_ethnicity:
    run: stata-mp:latest analysis/healthcare_use_ethnicity.do 2017
    needs: [2017, 2017_ckd, 2017_ckd_complete, 2017_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2017_ckd_complete_ethnicity.dta
      moderately_sensitive:
        log: logs/2017_healthcare_use_ethnicity.log
        output: output/2017_healthcare_use_ethnicity.csv

  2018:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2018
    outputs:
      highly_sensitive:
        cohort: output/input_2018.csv

  2018_ckd:
    run: stata-mp:latest analysis/ckd.do 2018
    needs: [2018]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2018_ckd.csv
      moderately_sensitive:
        log: logs/2018_ckd.log
  
  2018_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2018_ckd_complete
    needs: [2018, 2018_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2018_ckd_complete.csv

  2018_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2018
    needs: [2018, 2018_ckd, 2018_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2018_ckd_complete.dta
      moderately_sensitive:
        log: logs/2018_ckd_complete.log

  2018_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2018
    needs: [2018, 2018_ckd, 2018_ckd_complete, 2018_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2018_healthcare_use.log
        output: output/2018_healthcare_use.csv

  2018_healthcare_use_region:
    run: stata-mp:latest analysis/healthcare_use_region.do 2018
    needs: [2018, 2018_ckd, 2018_ckd_complete, 2018_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2018_ckd_complete_region.dta
      moderately_sensitive:
        log: logs/2018_healthcare_use_region.log
        output: output/2018_healthcare_use_region.csv

  2018_healthcare_use_imd:
    run: stata-mp:latest analysis/healthcare_use_imd.do 2018
    needs: [2018, 2018_ckd, 2018_ckd_complete, 2018_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2018_ckd_complete_imd.dta
      moderately_sensitive:
        log: logs/2018_healthcare_use_imd.log
        output: output/2018_healthcare_use_imd.csv

  2018_healthcare_use_ethnicity:
    run: stata-mp:latest analysis/healthcare_use_ethnicity.do 2018
    needs: [2018, 2018_ckd, 2018_ckd_complete, 2018_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2018_ckd_complete_ethnicity.dta
      moderately_sensitive:
        log: logs/2018_healthcare_use_ethnicity.log
        output: output/2018_healthcare_use_ethnicity.csv

  2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019
    outputs:
      highly_sensitive:
        cohort: output/input_2019.csv

  2019_ckd:
    run: stata-mp:latest analysis/ckd.do 2019
    needs: [2019]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2019_ckd.csv
      moderately_sensitive:
        log: logs/2019_ckd.log
  
  2019_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019_ckd_complete
    needs: [2019, 2019_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2019_ckd_complete.csv

  2019_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2019
    needs: [2019, 2019_ckd, 2019_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2019_ckd_complete.dta
      moderately_sensitive:
        log: logs/2019_ckd_complete.log

  2019_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2019
    needs: [2019, 2019_ckd, 2019_ckd_complete, 2019_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2019_healthcare_use.log
        output: output/2019_healthcare_use.csv

  2019_healthcare_use_region:
    run: stata-mp:latest analysis/healthcare_use_region.do 2019
    needs: [2019, 2019_ckd, 2019_ckd_complete, 2019_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2019_ckd_complete_region.dta
      moderately_sensitive:
        log: logs/2019_healthcare_use_region.log
        output: output/2019_healthcare_use_region.csv

  2019_healthcare_use_imd:
    run: stata-mp:latest analysis/healthcare_use_imd.do 2019
    needs: [2019, 2019_ckd, 2019_ckd_complete, 2019_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2019_ckd_complete_imd.dta
      moderately_sensitive:
        log: logs/2019_healthcare_use_imd.log
        output: output/2019_healthcare_use_imd.csv

  2019_healthcare_use_ethnicity:
    run: stata-mp:latest analysis/healthcare_use_ethnicity.do 2019
    needs: [2019, 2019_ckd, 2019_ckd_complete, 2019_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2019_ckd_complete_ethnicity.dta
      moderately_sensitive:
        log: logs/2019_healthcare_use_ethnicity.log
        output: output/2019_healthcare_use_ethnicity.csv

  2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2020
    outputs:
      highly_sensitive:
        cohort: output/input_2020.csv

  2020_ckd:
    run: stata-mp:latest analysis/ckd.do 2020
    needs: [2020]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2020_ckd.csv
      moderately_sensitive:
        log: logs/2020_ckd.log
  
  2020_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2020_ckd_complete
    needs: [2020, 2020_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2020_ckd_complete.csv

  2020_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2020
    needs: [2020, 2020_ckd, 2020_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2020_ckd_complete.dta
      moderately_sensitive:
        log: logs/2020_ckd_complete.log

  2020_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2020
    needs: [2020, 2020_ckd, 2020_ckd_complete, 2020_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2020_healthcare_use.log
        output: output/2020_healthcare_use.csv

  2020_healthcare_use_region:
    run: stata-mp:latest analysis/healthcare_use_region.do 2020
    needs: [2020, 2020_ckd, 2020_ckd_complete, 2020_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2020_ckd_complete_region.dta
      moderately_sensitive:
        log: logs/2020_healthcare_use_region.log
        output: output/2020_healthcare_use_region.csv

  2020_healthcare_use_imd:
    run: stata-mp:latest analysis/healthcare_use_imd.do 2020
    needs: [2020, 2020_ckd, 2020_ckd_complete, 2020_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2020_ckd_complete_imd.dta
      moderately_sensitive:
        log: logs/2020_healthcare_use_imd.log
        output: output/2020_healthcare_use_imd.csv

  2020_healthcare_use_ethnicity:
    run: stata-mp:latest analysis/healthcare_use_ethnicity.do 2020
    needs: [2020, 2020_ckd, 2020_ckd_complete, 2020_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2020_ckd_complete_ethnicity.dta
      moderately_sensitive:
        log: logs/2020_healthcare_use_ethnicity.log
        output: output/2020_healthcare_use_ethnicity.csv

  2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2021
    outputs:
      highly_sensitive:
        cohort: output/input_2021.csv

  2021_ckd:
    run: stata-mp:latest analysis/ckd.do 2021
    needs: [2021]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2021_ckd.csv
      moderately_sensitive:
        log: logs/2021_ckd.log
  
  2021_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2021_ckd_complete
    needs: [2021, 2021_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2021_ckd_complete.csv

  2021_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2021
    needs: [2021, 2021_ckd, 2021_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2021_ckd_complete.dta
      moderately_sensitive:
        log: logs/2021_ckd_complete.log

  2021_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2021
    needs: [2021, 2021_ckd, 2021_ckd_complete, 2021_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2021_healthcare_use.log
        output: output/2021_healthcare_use.csv

  2021_healthcare_use_region:
    run: stata-mp:latest analysis/healthcare_use_region.do 2021
    needs: [2021, 2021_ckd, 2021_ckd_complete, 2021_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2021_ckd_complete_region.dta
      moderately_sensitive:
        log: logs/2021_healthcare_use_region.log
        output: output/2021_healthcare_use_region.csv

  2021_healthcare_use_imd:
    run: stata-mp:latest analysis/healthcare_use_imd.do 2021
    needs: [2021, 2021_ckd, 2021_ckd_complete, 2021_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2021_ckd_complete_imd.dta
      moderately_sensitive:
        log: logs/2021_healthcare_use_imd.log
        output: output/2021_healthcare_use_imd.csv

  2021_healthcare_use_ethnicity:
    run: stata-mp:latest analysis/healthcare_use_ethnicity.do 2021
    needs: [2021, 2021_ckd, 2021_ckd_complete, 2021_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2021_ckd_complete_ethnicity.dta
      moderately_sensitive:
        log: logs/2021_healthcare_use_ethnicity.log
        output: output/2021_healthcare_use_ethnicity.csv

  2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2022
    outputs:
      highly_sensitive:
        cohort: output/input_2022.csv

  2022_ckd:
    run: stata-mp:latest analysis/ckd.do 2022
    needs: [2022]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2022_ckd.csv
      moderately_sensitive:
        log: logs/2022_ckd.log
  
  2022_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2022_ckd_complete
    needs: [2022, 2022_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2022_ckd_complete.csv

  2022_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2022
    needs: [2022, 2022_ckd, 2022_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2022_ckd_complete.dta
      moderately_sensitive:
        log: logs/2022_ckd_complete.log

  2022_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2022
    needs: [2022, 2022_ckd, 2022_ckd_complete, 2022_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2022_healthcare_use.log
        output: output/2022_healthcare_use.csv

  2022_healthcare_use_region:
    run: stata-mp:latest analysis/healthcare_use_region.do 2022
    needs: [2022, 2022_ckd, 2022_ckd_complete, 2022_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2022_ckd_complete_region.dta
      moderately_sensitive:
        log: logs/2022_healthcare_use_region.log
        output: output/2022_healthcare_use_region.csv

  2022_healthcare_use_imd:
    run: stata-mp:latest analysis/healthcare_use_imd.do 2022
    needs: [2022, 2022_ckd, 2022_ckd_complete, 2022_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2022_ckd_complete_imd.dta
      moderately_sensitive:
        log: logs/2022_healthcare_use_imd.log
        output: output/2022_healthcare_use_imd.csv

  2022_healthcare_use_ethnicity:
    run: stata-mp:latest analysis/healthcare_use_ethnicity.do 2022
    needs: [2022, 2022_ckd, 2022_ckd_complete, 2022_clean_ckd_complete]
    outputs:
      highly_sensitive:
        dataset: output/2022_ckd_complete_ethnicity.dta
      moderately_sensitive:
        log: logs/2022_healthcare_use_ethnicity.log
        output: output/2022_healthcare_use_ethnicity.csv

  ckd_progression:
    run: stata-mp:latest analysis/ckd_progression.do
    needs: [2017_clean_ckd_complete, 2018_clean_ckd_complete, 2019_clean_ckd_complete, 2020_clean_ckd_complete, 2021_clean_ckd_complete, 2022_clean_ckd_complete, 2017_healthcare_use, 2018_healthcare_use, 2019_healthcare_use, 2020_healthcare_use, 2021_healthcare_use, 2022_healthcare_use]
    outputs:
      moderately_sensitive:
        log: logs/ckd_progression.log
        output: output/ckd_progression.csv

  ckd_progression_region:
    run: stata-mp:latest analysis/ckd_progression_region.do
    needs: [2017_clean_ckd_complete, 2018_clean_ckd_complete, 2019_clean_ckd_complete, 2020_clean_ckd_complete, 2021_clean_ckd_complete, 2022_clean_ckd_complete, 2017_healthcare_use, 2018_healthcare_use, 2019_healthcare_use, 2020_healthcare_use, 2021_healthcare_use, 2022_healthcare_use]
    outputs:
      moderately_sensitive:
        log: logs/ckd_progression_region.log
        output: output/ckd_progression_region.csv

  ckd_progression_ethnicity:
    run: stata-mp:latest analysis/ckd_progression_ethnicity.do
    needs: [2017_clean_ckd_complete, 2018_clean_ckd_complete, 2019_clean_ckd_complete, 2020_clean_ckd_complete, 2021_clean_ckd_complete, 2022_clean_ckd_complete, 2017_healthcare_use, 2018_healthcare_use, 2019_healthcare_use, 2020_healthcare_use, 2021_healthcare_use, 2022_healthcare_use]
    outputs:
      moderately_sensitive:
        log: logs/ckd_progression_ethnicity.log
        output: output/ckd_progression_ethnicity.csv

  ckd_progression_imd:
    run: stata-mp:latest analysis/ckd_progression_imd.do
    needs: [2017_clean_ckd_complete, 2018_clean_ckd_complete, 2019_clean_ckd_complete, 2020_clean_ckd_complete, 2021_clean_ckd_complete, 2022_clean_ckd_complete, 2017_healthcare_use, 2018_healthcare_use, 2019_healthcare_use, 2020_healthcare_use, 2021_healthcare_use, 2022_healthcare_use]
    outputs:
      moderately_sensitive:
        log: logs/ckd_progression_imd.log
        output: output/ckd_progression_imd.csv