project.yaml

version: "3.0"
expectations:
  population_size: 10000

actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  W2_generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_W2
    outputs:
      highly_sensitive:
        cohort: output/input_W2.csv

  worms_generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_worms
    outputs:
      highly_sensitive:
        cohort: output/input_worms.csv

  01_cr_analysis_dataset:
    needs: [generate_cohort]
    run: stata-mp:latest analysis/01_cr_analysis_dataset.do MAIN
    outputs:
      moderately_sensitive:
        log: log/01_cr_analysis_dataset.log
      highly_sensitive:
        check_data: "tempdata/analysis_datasetMAIN.dta"
        check_data2: "tempdata/analysis_dataset_ageband_*MAIN.dta"
        data: "tempdata/cr_create_analysis_dataset_STSET_*_ageband_*MAIN.dta"
        data_eth: "tempdata/analysis_dataset_with_missing_ethnicityMAIN.dta"

  01_cr_analysis_dataset_W2:
    needs: [W2_generate_cohort]
    run: stata-mp:latest analysis/01_cr_analysis_dataset.do W2
    outputs:
      moderately_sensitive:
        log: log/01_cr_analysis_dataset_W2.log
      highly_sensitive:
        check_data: "tempdata/analysis_datasetW2.dta"
        check_data2: "tempdata/analysis_dataset_ageband_*W2.dta"
        data: "tempdata/cr_create_analysis_dataset_STSET_*_ageband_*W2.dta"
        data_eth: "tempdata/analysis_dataset_with_missing_ethnicityW2.dta"

  WORMS_01_cr_analysis_dataset:
    needs: [worms_generate_cohort]
    run: stata-mp:latest analysis/WORMS_01_cr_analysis_dataset.do
    outputs:
      moderately_sensitive:
        log: log/WORMS_01_cr_analysis_dataset.log
      highly_sensitive:
        check_data: "tempdata/analysis_dataset_worms.dta"
        data: "tempdata/cr_create_analysis_dataset_STSET_worms_ageband_*.dta"
        ageband_data: "tempdata/analysis_dataset_worms_ageband_*.dta"

  02_an_data_checks:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/02_an_data_checks.do MAIN
    outputs:
      moderately_sensitive:
        log: log/02_an_data_checks.log
        histogram: "output/01_histogram_*MAIN.svg"

  02_an_data_checks_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/02_an_data_checks.do W2
    outputs:
      moderately_sensitive:
        log: log/02_an_data_checksW2.log
        histogram: "output/01_histogram_*W2.svg"

  WORMS_02_an_data_checks:
    needs: [WORMS_01_cr_analysis_dataset]
    run: stata-mp:latest analysis/WORMS_02_an_data_checks.do
    outputs:
      moderately_sensitive:
        log: log/WORMS_02_an_data_checks.log

  03a_an_descriptive_tables:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/03a_an_descriptive_tables.do MAIN
    outputs:
      moderately_sensitive:
        log: log/03a_an_descriptive_tablesMAIN.log
  
  03a_an_descriptive_tables_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/03a_an_descriptive_tables.do W2
    outputs:
      moderately_sensitive:
        log: log/03a_an_descriptive_tablesW2.log

  03b_an_descriptive_table_1:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/03b_an_descriptive_table_1.do MAIN
    outputs:
      moderately_sensitive:
        log: log/03b_an_descriptive_table_1MAIN.log
        data: "output/03b_an_descriptive_table_1_kids_cat4_ageband*MAIN.txt"
  
  03b_an_descriptive_table_1_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/03b_an_descriptive_table_1.do W2
    outputs:
      moderately_sensitive:
        log: log/03b_an_descriptive_table_1W2.log
        data: "output/03b_an_descriptive_table_1_kids_cat4_ageband*W2.txt"

  04a_an_descriptive_tables:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04a_an_descriptive_tables.do MAIN
    outputs:
      moderately_sensitive:
        log: log/04a_an_descriptive_tablesMAIN.log

  04a_an_descriptive_tables_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/04a_an_descriptive_tables.do W2
    outputs:
      moderately_sensitive:
        log: log/04a_an_descriptive_tablesW2.log

  04b_an_descriptive_table_2:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do MAIN
    outputs:
      moderately_sensitive:
        log: log/04b_an_descriptive_table_2_MAIN.log
        data: "output/04b_an_descriptive_table_2_MAIN_ageband*.txt"

  04b_an_descriptive_table_2_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do W2
    outputs:
      moderately_sensitive:
        log: log/04b_an_descriptive_table_2_W2.log
        data: "output/04b_an_descriptive_table_2_W2_ageband*.txt"

  06_univariate_analysis:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do MAIN
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_MAIN.log
        data: "output/an_univariable_cox_models_*_AGESEX_ageband_*MAIN.ster"

  06_univariate_analysis_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/06_univariate_analysis.do W2
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_W2.log
        data: "output/an_univariable_cox_models_*_AGESEX_ageband_*W2.ster"

  07a_an_multivariable_cox_models_demogADJ:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do MAIN
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_MAIN.log
        data: "output/an_multivariate_cox_models_*_DEMOGADJ_ageband_*MAIN.ster"

  07a_an_multivariable_cox_models_demogADJ_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do W2
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_W2.log
        data: "output/an_multivariate_cox_models_*_DEMOGADJ_ageband_*W2.ster"

  07b_an_multivariable_cox_models_FULL_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do non_covid_death MAIN
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_non_covid_deathMAIN.log
        data: "output/an_multivariate_cox_models_non_covid_death_*_MAINFULLYADJMODEL_ageband_*MAIN.ster"
        other_data: "output/an_sense_non_covid_death_plus_eth_12mo_ageband_*MAIN.ster"

  07b_an_multivariable_cox_models_FULL_non_covid_death_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do non_covid_death W2
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_non_covid_deathW2.log
        data: "output/an_multivariate_cox_models_non_covid_death_*_MAINFULLYADJMODEL_ageband_*W2.ster"
        other_data: "output/an_sense_non_covid_death_plus_eth_12mo_ageband_*W2.ster"

  07b_an_multivariable_cox_models_FULL_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covid_death MAIN
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_deathMAIN.log
        data: "output/an_multivariate_cox_models_covid_death_*_MAINFULLYADJMODEL_ageband_*MAIN.ster"
        other_data: "output/an_sense_covid_death_plus_eth_12mo_ageband_*MAIN.ster"

  07b_an_multivariable_cox_models_FULL_covid_death_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covid_death W2
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_deathW2.log
        data: "output/an_multivariate_cox_models_covid_death_*_MAINFULLYADJMODEL_ageband_*W2.ster"
        other_data: "output/an_sense_covid_death_plus_eth_12mo_ageband_*W2.ster"

  07b_an_multivariable_cox_models_FULL_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covid_tpp_prob MAIN
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_tpp_probMAIN.log
        data: "output/an_multivariate_cox_models_covid_tpp_prob_*_MAINFULLYADJMODEL_ageband_*MAIN.ster"
        other_data: "output/an_sense_covid_tpp_prob_plus_eth_12mo_ageband_*MAIN.ster"

  07b_an_multivariable_cox_models_FULL_covid_tpp_prob_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covid_tpp_prob W2
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_tpp_probW2.log
        data: "output/an_multivariate_cox_models_covid_tpp_prob_*_MAINFULLYADJMODEL_ageband_*W2.ster"
        other_data: "output/an_sense_covid_tpp_prob_plus_eth_12mo_ageband_*W2.ster"

  07b_an_multivariable_cox_models_FULL_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covid_icu MAIN
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_icuMAIN.log
        data: "output/an_multivariate_cox_models_covid_icu_*_MAINFULLYADJMODEL_ageband_*MAIN.ster"
        other_data: "output/an_sense_covid_icu_plus_eth_12mo_ageband_*MAIN.ster"

  07b_an_multivariable_cox_models_FULL_covid_icu_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covid_icu W2
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_icuW2.log
        data: "output/an_multivariate_cox_models_covid_icu_*_MAINFULLYADJMODEL_ageband_*W2.ster"
        other_data: "output/an_sense_covid_icu_plus_eth_12mo_ageband_*W2.ster"

  07b_an_multivariable_cox_models_FULL_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covidadmission MAIN
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covidadmissionMAIN.log
        data: "output/an_multivariate_cox_models_covidadmission_*_MAINFULLYADJMODEL_ageband_*MAIN.ster"
        other_data: "output/an_sense_covidadmission_plus_eth_12mo_ageband_*MAIN.ster"

  07b_an_multivariable_cox_models_FULL_covidadmission_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covidadmission W2
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covidadmissionW2.log
        data: "output/an_multivariate_cox_models_covidadmission_*_MAINFULLYADJMODEL_ageband_*W2.ster"
        other_data: "output/an_sense_covidadmission_plus_eth_12mo_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covid_death MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_deathMAIN.log
        data: "output/an_sense_covid_death_CCeth_bmi_smok_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covid_death_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covid_death W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_deathW2.log
        data: "output/an_sense_covid_death_CCeth_bmi_smok_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covid_icu MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_icuMAIN.log
        data: "output/an_sense_covid_icu_CCeth_bmi_smok_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covid_icu_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covid_icu W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_icuW2.log
        data: "output/an_sense_covid_icu_CCeth_bmi_smok_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covidadmission MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covidadmissionMAIN.log
        data: "output/an_sense_covidadmission_CCeth_bmi_smok_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covidadmission_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covidadmission W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covidadmissionW2.log
        data: "output/an_sense_covidadmission_CCeth_bmi_smok_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covid_tpp_prob MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_tpp_probMAIN.log
        data: "output/an_sense_covid_tpp_prob_CCeth_bmi_smok_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covid_tpp_prob_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covid_tpp_prob W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_tpp_probW2.log
        data: "output/an_sense_covid_tpp_prob_CCeth_bmi_smok_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covid_tpp_prob MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_tpp_prob_Sense4_*MAIN.log
        data: "output/an_sense_covid_tpp_prob_age_underlying_timescale_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covid_tpp_prob_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covid_tpp_prob W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_tpp_prob_Sense4_*W2.log
        data: "output/an_sense_covid_tpp_prob_age_underlying_timescale_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covid_death MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_death_Sense4_*MAIN.log
        data: "output/an_sense_covid_death_age_underlying_timescale_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covid_death_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covid_death W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_death_Sense4_*W2.log
        data: "output/an_sense_covid_death_age_underlying_timescale_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covid_icu MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_icu_Sense4_*MAIN.log
        data: "output/an_sense_covid_icu_age_underlying_timescale_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covid_icu_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covid_icu W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_icu_Sense4_*W2.log
        data: "output/an_sense_covid_icu_age_underlying_timescale_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covidadmission MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense4_*MAIN.log
        data: "output/an_sense_covidadmission_age_underlying_timescale_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covidadmission_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covidadmission W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense4_*W2.log
        data: "output/an_sense_covidadmission_age_underlying_timescale_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense5_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covid_tpp_prob MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_tpp_prob_Sense5_time_intsMAIN.log
        data: "output/an_sense_covid_tpp_prob_time_int_ageband_*MAIN.ster"  

  07d_an_multivariable_cox_models_FULL_Sense5_covid_tpp_prob_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covid_tpp_prob W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_tpp_prob_Sense5_time_intsW2.log
        data: "output/an_sense_covid_tpp_prob_time_int_ageband_*W2.ster" 

  07d_an_multivariable_cox_models_FULL_Sense5_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covidadmission MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense5_time_intsMAIN.log
        data: "output/an_sense_covidadmission_time_int_ageband_*MAIN.ster"  

  07d_an_multivariable_cox_models_FULL_Sense5_covidadmission_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covidadmission W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense5_time_intsW2.log
        data: "output/an_sense_covidadmission_time_int_ageband_*W2.ster" 

  07d_an_multivariable_cox_models_FULL_Sense5_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covid_icu MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_icu_Sense5_time_intsMAIN.log
        data: "output/an_sense_covid_icu_time_int_ageband_*MAIN.ster"  

  07d_an_multivariable_cox_models_FULL_Sense5_covid_icu_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covid_icu W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_icu_Sense5_time_intsW2.log
        data: "output/an_sense_covid_icu_time_int_ageband_*W2.ster"  

  07d_an_multivariable_cox_models_FULL_Sense5_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covid_death MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_death_Sense5_time_intsMAIN.log
        data: "output/an_sense_covid_death_time_int_ageband_*MAIN.ster"  

  07d_an_multivariable_cox_models_FULL_Sense5_covid_death_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covid_death W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_death_Sense5_time_intsW2.log
        data: "output/an_sense_covid_death_time_int_ageband_*W2.ster" 

  07d_an_multivariable_cox_models_FULL_Sense6_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense6.do covid_tpp_prob MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_tpp_prob_Sense6_*MAIN.log
        data: "output/an_sense_covid_tpp_prob_nursery_cat_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense6_covid_tpp_prob_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense6.do covid_tpp_prob W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_tpp_prob_Sense6_*W2.log
        data: "output/an_sense_covid_tpp_prob_nursery_cat_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense6_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense6.do covid_death MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_death_Sense6_*MAIN.log
        data: "output/an_sense_covid_death_nursery_cat_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense6_covid_death_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense6.do covid_death W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_death_Sense6_*W2.log
        data: "output/an_sense_covid_death_nursery_cat_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense6_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense6.do covid_icu MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_icu_Sense6_*MAIN.log
        data: "output/an_sense_covid_icu_nursery_cat_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense6_covid_icu_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense6.do covid_icu W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_icu_Sense6_*W2.log
        data: "output/an_sense_covid_icu_nursery_cat_ageband_*W2.ster"

  07d_an_multivariable_cox_models_FULL_Sense6_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense6.do covidadmission MAIN
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense6_*MAIN.log
        data: "output/an_sense_covidadmission_nursery_cat_ageband_*MAIN.ster"

  07d_an_multivariable_cox_models_FULL_Sense6_covidadmission_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense6.do covidadmission W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense6_*W2.log
        data: "output/an_sense_covidadmission_nursery_cat_ageband_*W2.ster" 

  07d_an_multivariable_cox_models_FULL_Sense7_covidadmission_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense7.do covidadmission W2
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense7_*W2.log
        data: "output/an_sense_covidadmission_SUS_censor_ageband_*W2.ster" 

  10_an_interaction_cox_models_shield_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covid_death MAIN
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_deathMAIN.log
        data: "output/an_interaction_cox_models_covid_death_kids_cat4_shield_MAINFULLYADJMODEL_*MAIN.ster"

  10_an_interaction_cox_models_sex_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covid_death MAIN
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_deathMAIN.log
        data: "output/an_interaction_cox_models_covid_death_kids_cat4_male_MAINFULLYADJMODEL_*MAIN.ster"

  10_an_interaction_cox_models_shield_covid_death_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covid_death W2
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_deathW2.log
        data: "output/an_interaction_cox_models_covid_death_kids_cat4_shield_MAINFULLYADJMODEL_*W2.ster"

  10_an_interaction_cox_models_sex_covid_death_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covid_death W2
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_deathW2.log
        data: "output/an_interaction_cox_models_covid_death_kids_cat4_male_MAINFULLYADJMODEL_*W2.ster"

  10_an_interaction_cox_models_shield_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covid_tpp_prob MAIN
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_tpp_probMAIN.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_kids_cat4_shield_MAINFULLYADJMODEL_*MAIN.ster"

  10_an_interaction_cox_models_sex_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covid_tpp_prob MAIN
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_tpp_probMAIN.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_kids_cat4_male_MAINFULLYADJMODEL_*MAIN.ster"

  10_an_interaction_cox_models_shield_covid_tpp_prob_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covid_tpp_prob W2
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_tpp_probW2.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_kids_cat4_shield_MAINFULLYADJMODEL_*W2.ster"

  10_an_interaction_cox_models_sex_covid_tpp_prob_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covid_tpp_prob W2
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_tpp_probW2.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_kids_cat4_male_MAINFULLYADJMODEL_*W2.ster"

  10_an_interaction_cox_models_shield_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covid_icu MAIN
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_icuMAIN.log
        data: "output/an_interaction_cox_models_covid_icu_kids_cat4_shield_MAINFULLYADJMODEL_*MAIN.ster"

  10_an_interaction_cox_models_sex_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covid_icu MAIN
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_icuMAIN.log
        data: "output/an_interaction_cox_models_covid_icu_kids_cat4_male_MAINFULLYADJMODEL_*MAIN.ster"

  10_an_interaction_cox_models_sex_covid_icu_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covid_icu W2
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_icuW2.log
        data: "output/an_interaction_cox_models_covid_icu_kids_cat4_male_MAINFULLYADJMODEL_*W2.ster"

  10_an_interaction_cox_models_shield_covid_icu_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covid_icu W2
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_icuW2.log
        data: "output/an_interaction_cox_models_covid_icu_kids_cat4_shield_MAINFULLYADJMODEL_*W2.ster"

  10_an_interaction_cox_models_shield_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covidadmission MAIN
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covidadmissionMAIN.log
        data: "output/an_interaction_cox_models_covidadmission_kids_cat4_shield_MAINFULLYADJMODEL_*MAIN.ster"

  10_an_interaction_cox_models_sex_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covidadmission MAIN
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covidadmissionMAIN.log
        data: "output/an_interaction_cox_models_covidadmission_kids_cat4_male_MAINFULLYADJMODEL_*MAIN.ster"

  10_an_interaction_cox_models_shield_covidadmission_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covidadmission W2
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covidadmissionW2.log
        data: "output/an_interaction_cox_models_covidadmission_kids_cat4_shield_MAINFULLYADJMODEL_*W2.ster"

  10_an_interaction_cox_models_sex_covidadmission_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covidadmission W2
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covidadmissionW2.log
        data: "output/an_interaction_cox_models_covidadmission_kids_cat4_male_MAINFULLYADJMODEL_*W2.ster"

  13_multiple_imputation_dataset_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/13_multiple_imputation_dataset.do covidadmission MAIN
    outputs:
      moderately_sensitive:
        log: log/13_multiple_imputation_dataset_covidadmissionMAIN.log
      highly_sensitive:
        data: "tempdata/cr_imputed_analysis_dataset_STSET_covidadmission_ageband_*MAIN.dta"

  14_multiple_imputation_analysis_covidadmission:
    needs: [13_multiple_imputation_dataset_covidadmission]
    run: stata-mp:latest analysis/14_multiple_imputation_analysis.do covidadmission MAIN
    outputs:
      moderately_sensitive:
        log: log/14_multiple_imputation_analysis_covidadmissionMAIN.log
        data: "output/an_sense_covidadmission_multiple_imputation_ageband_*MAIN.ster"

  13_multiple_imputation_dataset_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/13_multiple_imputation_dataset.do covid_tpp_prob MAIN
    outputs:
      moderately_sensitive:
        log: log/13_multiple_imputation_dataset_covid_tpp_probMAIN.log
      highly_sensitive:
        data: "tempdata/cr_imputed_analysis_dataset_STSET_covid_tpp_prob_ageband_*MAIN.dta"

  14_multiple_imputation_analysis_covid_tpp_prob:
    needs: [13_multiple_imputation_dataset_covid_tpp_prob]
    run: stata-mp:latest analysis/14_multiple_imputation_analysis.do covid_tpp_prob MAIN
    outputs:
      moderately_sensitive:
        log: log/14_multiple_imputation_analysis_covid_tpp_probMAIN.log
        data: "output/an_sense_covid_tpp_prob_multiple_imputation_ageband_*MAIN.ster"

  13_multiple_imputation_dataset_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/13_multiple_imputation_dataset.do covid_icu MAIN
    outputs:
      moderately_sensitive:
        log: log/13_multiple_imputation_dataset_covid_icuMAIN.log
      highly_sensitive:
        data: "tempdata/cr_imputed_analysis_dataset_STSET_covid_icu_ageband_*MAIN.dta"

  14_multiple_imputation_analysis_covid_icu:
    needs: [13_multiple_imputation_dataset_covid_icu]
    run: stata-mp:latest analysis/14_multiple_imputation_analysis.do covid_icu MAIN
    outputs:
      moderately_sensitive:
        log: log/14_multiple_imputation_analysis_covid_icuMAIN.log
        data: "output/an_sense_covid_icu_multiple_imputation_ageband_*MAIN.ster"

  13_multiple_imputation_dataset_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/13_multiple_imputation_dataset.do covid_death MAIN
    outputs:
      moderately_sensitive:
        log: log/13_multiple_imputation_dataset_covid_deathMAIN.log
      highly_sensitive:
        data: "tempdata/cr_imputed_analysis_dataset_STSET_covid_death_ageband_*MAIN.dta"

  14_multiple_imputation_analysis_covid_death:
    needs: [13_multiple_imputation_dataset_covid_death]
    run: stata-mp:latest analysis/14_multiple_imputation_analysis.do covid_death MAIN
    outputs:
      moderately_sensitive:
        log: log/14_multiple_imputation_analysis_covid_deathMAIN.log
        data: "output/an_sense_covid_death_multiple_imputation_ageband_*MAIN.ster"

  13_multiple_imputation_dataset_covid_tpp_prob_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/13_multiple_imputation_dataset.do covid_tpp_prob W2
    outputs:
      moderately_sensitive:
        log: log/13_multiple_imputation_dataset_covid_tpp_probW2.log
      highly_sensitive:
        data: "tempdata/cr_imputed_analysis_dataset_STSET_covid_tpp_prob_ageband_*W2.dta"

  14_multiple_imputation_analysis_covid_tpp_prob_W2:
    needs: [13_multiple_imputation_dataset_covid_tpp_prob_W2]
    run: stata-mp:latest analysis/14_multiple_imputation_analysis.do covid_tpp_prob W2
    outputs:
      moderately_sensitive:
        log: log/14_multiple_imputation_analysis_covid_tpp_probW2.log
        data: "output/an_sense_covid_tpp_prob_multiple_imputation_ageband_*W2.ster"

  13_multiple_imputation_dataset_covidadmission_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/13_multiple_imputation_dataset.do covidadmission W2
    outputs:
      moderately_sensitive:
        log: log/13_multiple_imputation_dataset_covidadmissionW2.log
      highly_sensitive:
        data: "tempdata/cr_imputed_analysis_dataset_STSET_covidadmission_ageband_*W2.dta"

  14_multiple_imputation_analysis_covidadmission_W2:
    needs: [13_multiple_imputation_dataset_covidadmission_W2]
    run: stata-mp:latest analysis/14_multiple_imputation_analysis.do covidadmission W2
    outputs:
      moderately_sensitive:
        log: log/14_multiple_imputation_analysis_covidadmissionW2.log
        data: "output/an_sense_covidadmission_multiple_imputation_ageband_*W2.ster"

  13_multiple_imputation_dataset_covid_icu_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/13_multiple_imputation_dataset.do covid_icu W2
    outputs:
      moderately_sensitive:
        log: log/13_multiple_imputation_dataset_covid_icuW2.log
      highly_sensitive:
        data: "tempdata/cr_imputed_analysis_dataset_STSET_covid_icu_ageband_*W2.dta"

  14_multiple_imputation_analysis_covid_icu_W2:
    needs: [13_multiple_imputation_dataset_covid_icu_W2]
    run: stata-mp:latest analysis/14_multiple_imputation_analysis.do covid_icu W2
    outputs:
      moderately_sensitive:
        log: log/14_multiple_imputation_analysis_covid_icuW2.log
        data: "output/an_sense_covid_icu_multiple_imputation_ageband_*W2.ster"

  13_multiple_imputation_dataset_covid_death_W2:
    needs: [01_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/13_multiple_imputation_dataset.do covid_death W2
    outputs:
      moderately_sensitive:
        log: log/13_multiple_imputation_dataset_covid_deathW2.log
      highly_sensitive:
        data: "tempdata/cr_imputed_analysis_dataset_STSET_covid_death_ageband_*W2.dta"

  14_multiple_imputation_analysis_covid_death_W2:
    needs: [13_multiple_imputation_dataset_covid_death_W2]
    run: stata-mp:latest analysis/14_multiple_imputation_analysis.do covid_death W2
    outputs:
      moderately_sensitive:
        log: log/14_multiple_imputation_analysis_covid_deathW2.log
        data: "output/an_sense_covid_death_multiple_imputation_ageband_*W2.ster"

  WORMS_06_univariate_analysis:
    needs: [WORMS_01_cr_analysis_dataset]
    run: stata-mp:latest analysis/WORMS_06_univariate_analysis.do worms kids_cat4 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/WORMS_06_univariate_analysis.log
        data: "output/an_univariable_cox_models_worms_AGESEX_*_ageband_*.ster"

  WORMS_07a_an_multivariable_cox_models_demogADJ:
    needs: [WORMS_01_cr_analysis_dataset]
    run: stata-mp:latest analysis/WORMS_07a_an_multivariable_cox_models_demogADJ.do worms
    outputs:
      moderately_sensitive:
        log: log/WORMS_07a_an_multivariable_cox_models_demogADJ.log
        data: "output/an_multivariate_cox_models_worms_*_DEMOGADJ_noeth_ageband_*.ster"

  WORMS_07b_an_multivariable_cox_models_FULL:
    needs: [WORMS_01_cr_analysis_dataset]
    run: stata-mp:latest analysis/WORMS_07b_an_multivariable_cox_models_FULL.do worms
    outputs:
      moderately_sensitive:
        log: log/WORMS_07b_an_multivariable_cox_models_FULL.log
        data: "output/an_multivariate_cox_models_worms_*_MAINFULLYADJMODEL_noeth_ageband_*.ster"

  08_an_tablecontent_HRtable_non_covid_death:
    needs:
      - 01_cr_analysis_dataset
      - 01_cr_analysis_dataset_W2
      - 06_univariate_analysis
      - 06_univariate_analysis_W2
      - 07a_an_multivariable_cox_models_demogADJ
      - 07a_an_multivariable_cox_models_demogADJ_W2
      - 07b_an_multivariable_cox_models_FULL_non_covid_death
      - 07b_an_multivariable_cox_models_FULL_non_covid_death_W2
    run: stata-mp:latest analysis/08_an_tablecontent_HRtable.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/08_an_tablecontent_HRtable_non_covid_death.log
        data: "output/an_tablecontents_HRtable_non_covid_death.txt"

  08_an_tablecontent_HRtable_covid_tpp_prob:
    needs:
      - 01_cr_analysis_dataset
      - 01_cr_analysis_dataset_W2
      - 06_univariate_analysis
      - 06_univariate_analysis_W2
      - 07a_an_multivariable_cox_models_demogADJ
      - 07a_an_multivariable_cox_models_demogADJ_W2
      - 07b_an_multivariable_cox_models_FULL_covid_tpp_prob
      - 07b_an_multivariable_cox_models_FULL_covid_tpp_prob_W2
    run: stata-mp:latest analysis/08_an_tablecontent_HRtable.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/08_an_tablecontent_HRtable_covid_tpp_prob.log
        data: "output/an_tablecontents_HRtable_covid_tpp_prob.txt"

  08_an_tablecontent_HRtable_covid_death:
    needs:
      - 01_cr_analysis_dataset
      - 01_cr_analysis_dataset_W2
      - 06_univariate_analysis
      - 06_univariate_analysis_W2
      - 07a_an_multivariable_cox_models_demogADJ
      - 07a_an_multivariable_cox_models_demogADJ_W2
      - 07b_an_multivariable_cox_models_FULL_covid_death
      - 07b_an_multivariable_cox_models_FULL_covid_death_W2
    run: stata-mp:latest analysis/08_an_tablecontent_HRtable.do covid_death
    outputs:
      moderately_sensitive:
        log: log/08_an_tablecontent_HRtable_covid_death.log
        data: "output/an_tablecontents_HRtable_covid_death.txt"

  08_an_tablecontent_HRtable_covid_icu:
    needs:
      - 01_cr_analysis_dataset
      - 01_cr_analysis_dataset_W2
      - 06_univariate_analysis
      - 06_univariate_analysis_W2
      - 07a_an_multivariable_cox_models_demogADJ
      - 07a_an_multivariable_cox_models_demogADJ_W2
      - 07b_an_multivariable_cox_models_FULL_covid_icu
      - 07b_an_multivariable_cox_models_FULL_covid_icu_W2
    run: stata-mp:latest analysis/08_an_tablecontent_HRtable.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/08_an_tablecontent_HRtable_covid_icu.log
        data: "output/an_tablecontents_HRtable_covid_icu.txt"

  08_an_tablecontent_HRtable_covidadmission:
    needs:
      - 01_cr_analysis_dataset
      - 01_cr_analysis_dataset_W2
      - 06_univariate_analysis
      - 06_univariate_analysis_W2
      - 07a_an_multivariable_cox_models_demogADJ
      - 07a_an_multivariable_cox_models_demogADJ_W2
      - 07b_an_multivariable_cox_models_FULL_covidadmission
      - 07b_an_multivariable_cox_models_FULL_covidadmission_W2
    run: stata-mp:latest analysis/08_an_tablecontent_HRtable.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/08_an_tablecontent_HRtable_covidadmission.log
        data: "output/an_tablecontents_HRtable_covidadmission.txt"

  WORMS_08_an_tablecontent_HRtable:
    needs:
      - WORMS_01_cr_analysis_dataset
      - WORMS_06_univariate_analysis
      - WORMS_07a_an_multivariable_cox_models_demogADJ
      - WORMS_07b_an_multivariable_cox_models_FULL
    run: stata-mp:latest analysis/WORMS_08_an_tablecontent_HRtable.do worms
    outputs:
      moderately_sensitive:
        log: log/WORMS_08_an_tablecontent_HRtable.log
        data: "output/an_tablecontents_HRtable_worms.txt"

  15_anHRfigure_all_outcomes:
    needs:
      - 07b_an_multivariable_cox_models_FULL_non_covid_death
      - 07b_an_multivariable_cox_models_FULL_covid_tpp_prob
      - 07b_an_multivariable_cox_models_FULL_covid_death
      - 07b_an_multivariable_cox_models_FULL_covid_icu
      - 07b_an_multivariable_cox_models_FULL_covidadmission
      - 07b_an_multivariable_cox_models_FULL_non_covid_death_W2
      - 07b_an_multivariable_cox_models_FULL_covid_tpp_prob_W2
      - 07b_an_multivariable_cox_models_FULL_covid_death_W2
      - 07b_an_multivariable_cox_models_FULL_covid_icu_W2
      - 07b_an_multivariable_cox_models_FULL_covidadmission_W2
    run: stata-mp:latest analysis/15_anHRfigure_all_outcomes.do 
    outputs:
      moderately_sensitive:
        data: "output/15_an_tablecontents_HRtable_all_outcomes_ANALYSES.txt"
        figure: "output/15_an_HRforest_all_outcomes_ageband_*.svg"

  15_anHRfigure_all_outcomes_nursery_cat:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense6_covidadmission
      - 07d_an_multivariable_cox_models_FULL_Sense6_covid_tpp_prob
      - 07d_an_multivariable_cox_models_FULL_Sense6_covid_death
      - 07d_an_multivariable_cox_models_FULL_Sense6_covid_icu
      - 07d_an_multivariable_cox_models_FULL_Sense6_covidadmission_W2
      - 07d_an_multivariable_cox_models_FULL_Sense6_covid_tpp_prob_W2
      - 07d_an_multivariable_cox_models_FULL_Sense6_covid_death_W2
      - 07d_an_multivariable_cox_models_FULL_Sense6_covid_icu_W2
    run: stata-mp:latest analysis/15_anHRfigure_all_outcomes_kids_cat5.do
    outputs:
      moderately_sensitive:
        data: "output/15_an_tablecontents_HRtable_all_outcomes_KIDS_CAT5.txt"
        figure: "output/15_an_HRforest_all_outcomes_ageband_*_KIDS_CAT5.svg"

  11_an_interaction_HR_tables_forest_covid_tpp_prob:
    needs:
      - 10_an_interaction_cox_models_shield_covid_tpp_prob
      - 10_an_interaction_cox_models_sex_covid_tpp_prob
      - 10_an_interaction_cox_models_shield_covid_tpp_prob_W2
      - 10_an_interaction_cox_models_sex_covid_tpp_prob_W2
    run: stata-mp:latest analysis/11_an_interaction_HR_tables_forest.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: 11_an_interaction_HR_tables_forest_covid_tpp_prob.log
        data: "output/11_an_int_tab_contents_HRtable_covid_tpp_prob.txt"

  11_an_interaction_HR_tables_forest_covid_death:
    needs:
      - 10_an_interaction_cox_models_shield_covid_death
      - 10_an_interaction_cox_models_sex_covid_death
      - 10_an_interaction_cox_models_shield_covid_death_W2
      - 10_an_interaction_cox_models_sex_covid_death_W2
    run: stata-mp:latest analysis/11_an_interaction_HR_tables_forest.do covid_death
    outputs:
      moderately_sensitive:
        log: 11_an_interaction_HR_tables_forest_covid_death.log
        data: "output/11_an_int_tab_contents_HRtable_covid_death.txt"

  11_an_interaction_HR_tables_forest_covid_icu:
    needs:
      - 10_an_interaction_cox_models_shield_covid_icu
      - 10_an_interaction_cox_models_sex_covid_icu
      - 10_an_interaction_cox_models_shield_covid_icu_W2
      - 10_an_interaction_cox_models_sex_covid_icu_W2
    run: stata-mp:latest analysis/11_an_interaction_HR_tables_forest.do covid_icu
    outputs:
      moderately_sensitive:
        log: 11_an_interaction_HR_tables_forest_covid_icu.log
        data: "output/11_an_int_tab_contents_HRtable_covid_icu.txt"

  11_an_interaction_HR_tables_forest_covidadmission:
    needs:
      - 10_an_interaction_cox_models_shield_covidadmission
      - 10_an_interaction_cox_models_sex_covidadmission
      - 10_an_interaction_cox_models_shield_covidadmission_W2
      - 10_an_interaction_cox_models_sex_covidadmission_W2
    run: stata-mp:latest analysis/11_an_interaction_HR_tables_forest.do covidadmission
    outputs:
      moderately_sensitive:
        log: 11_an_interaction_HR_tables_forest_covidadmission.log
        data: "output/11_an_int_tab_contents_HRtable_covidadmission.txt"

  12_an_tablecontent_HRtable_SENSE_covid_tpp_prob:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense3_covid_tpp_prob
      - 07d_an_multivariable_cox_models_FULL_Sense4_covid_tpp_prob
      - 07d_an_multivariable_cox_models_FULL_Sense5_covid_tpp_prob
      - 07b_an_multivariable_cox_models_FULL_covid_tpp_prob
      - 07d_an_multivariable_cox_models_FULL_Sense3_covid_tpp_prob_W2
      - 07d_an_multivariable_cox_models_FULL_Sense4_covid_tpp_prob_W2
      - 07d_an_multivariable_cox_models_FULL_Sense5_covid_tpp_prob_W2
      - 07b_an_multivariable_cox_models_FULL_covid_tpp_prob_W2
    run: stata-mp:latest analysis/12_an_tablecontent_HRtable_SENSE.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: 12_an_tablecontent_HRtable_SENSE_covid_tpp_prob.log
        data: "output/12_an_sense_HRtable_covid_tpp_prob_SENSE_ANALYSES.txt"
        figure: "output/12_an_HRforest_SENSE_covid_tpp_prob_ageband_*.svg"

  12_an_tablecontent_HRtable_SENSE_covid_death:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense3_covid_death
      - 07d_an_multivariable_cox_models_FULL_Sense4_covid_death
      - 07d_an_multivariable_cox_models_FULL_Sense5_covid_death
      - 07b_an_multivariable_cox_models_FULL_covid_death
      - 07d_an_multivariable_cox_models_FULL_Sense3_covid_death_W2
      - 07d_an_multivariable_cox_models_FULL_Sense4_covid_death_W2
      - 07d_an_multivariable_cox_models_FULL_Sense5_covid_death_W2
      - 07b_an_multivariable_cox_models_FULL_covid_death_W2
    run: stata-mp:latest analysis/12_an_tablecontent_HRtable_SENSE.do covid_death
    outputs:
      moderately_sensitive:
        log: 12_an_tablecontent_HRtable_SENSE_covid_death.log
        data: "output/12_an_sense_HRtable_covid_death_SENSE_ANALYSES.txt"
        figure: "output/12_an_HRforest_SENSE_covid_death_ageband_*.svg"

  12_an_tablecontent_HRtable_SENSE_covid_icu:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense3_covid_icu
      - 07d_an_multivariable_cox_models_FULL_Sense4_covid_icu
      - 07d_an_multivariable_cox_models_FULL_Sense5_covid_icu
      - 07b_an_multivariable_cox_models_FULL_covid_icu
      - 07d_an_multivariable_cox_models_FULL_Sense3_covid_icu_W2
      - 07d_an_multivariable_cox_models_FULL_Sense4_covid_icu_W2
      - 07d_an_multivariable_cox_models_FULL_Sense5_covid_icu_W2
      - 07b_an_multivariable_cox_models_FULL_covid_icu_W2
    run: stata-mp:latest analysis/12_an_tablecontent_HRtable_SENSE.do covid_icu
    outputs:
      moderately_sensitive:
        log: 12_an_tablecontent_HRtable_SENSE_covid_icu.log
        data: "output/12_an_sense_HRtable_covid_icu_SENSE_ANALYSES.txt"
        figure: "output/12_an_HRforest_SENSE_covid_icu_ageband_*.svg"

  12_an_tablecontent_HRtable_SENSE_covidadmission:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense3_covidadmission
      - 07d_an_multivariable_cox_models_FULL_Sense4_covidadmission
      - 07d_an_multivariable_cox_models_FULL_Sense5_covidadmission
      - 07b_an_multivariable_cox_models_FULL_covidadmission
      - 07d_an_multivariable_cox_models_FULL_Sense3_covidadmission_W2
      - 07d_an_multivariable_cox_models_FULL_Sense4_covidadmission_W2
      - 07d_an_multivariable_cox_models_FULL_Sense5_covidadmission_W2
      - 07d_an_multivariable_cox_models_FULL_Sense7_covidadmission_W2
      - 07b_an_multivariable_cox_models_FULL_covidadmission_W2
    run: stata-mp:latest analysis/12_an_tablecontent_HRtable_SENSE.do covidadmission
    outputs:
      moderately_sensitive:
        log: 12_an_tablecontent_HRtable_SENSE_covidadmission.log
        data: "output/12_an_sense_HRtable_covidadmission_SENSE_ANALYSES.txt"
        figure: "output/12_an_HRforest_SENSE_covidadmission_ageband_*.svg"

  run_all:
    needs:
      - 02_an_data_checks
      - 03a_an_descriptive_tables
      - 03b_an_descriptive_table_1
      - 04a_an_descriptive_tables
      - 04b_an_descriptive_table_2
      - 08_an_tablecontent_HRtable_covid_death
      - 08_an_tablecontent_HRtable_covid_icu
      - 08_an_tablecontent_HRtable_covid_tpp_prob
      - 08_an_tablecontent_HRtable_covidadmission
      - 08_an_tablecontent_HRtable_non_covid_death
      - 11_an_interaction_HR_tables_forest_covid_death
      - 11_an_interaction_HR_tables_forest_covid_icu
      - 11_an_interaction_HR_tables_forest_covid_tpp_prob
      - 11_an_interaction_HR_tables_forest_covidadmission
      - 12_an_tablecontent_HRtable_SENSE_covid_death
      - 12_an_tablecontent_HRtable_SENSE_covid_icu
      - 12_an_tablecontent_HRtable_SENSE_covid_tpp_prob
      - 12_an_tablecontent_HRtable_SENSE_covidadmission
      - 02_an_data_checks_W2
      - 03a_an_descriptive_tables_W2
      - 03b_an_descriptive_table_1_W2
      - 04a_an_descriptive_tables_W2
      - 04b_an_descriptive_table_2_W2
      - 15_anHRfigure_all_outcomes
      - 15_anHRfigure_all_outcomes_nursery_cat
      - WORMS_02_an_data_checks
      - WORMS_08_an_tablecontent_HRtable
    # In order to be valid this action needs to define a run commmand and
    # some output. We don't really care what these are but the below seems to
    # do the trick.
    run: cohortextractor:latest --version
    outputs:
      moderately_sensitive:
        whatever: project.yaml