project.yaml

version: "3.0"
expectations:
  population_size: 20000

actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.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
    outputs:
      moderately_sensitive:
        log: log/01_cr_analysis_dataset.log
      highly_sensitive:
        check_data: "tempdata/analysis_dataset.dta"
        data: "tempdata/cr_create_analysis_dataset_STSET_*_ageband_*.dta"
        ageband_data: "tempdata/analysis_dataset_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/02_an_data_checks.log
        histogram: "output/01_histogram_outcomes.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
    outputs:
      moderately_sensitive:
        log: log/03a_an_descriptive_tables.log

  03b_an_descriptive_table_1:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/03b_an_descriptive_table_1.do
    outputs:
      moderately_sensitive:
        log: log/03b_an_descriptive_table_1.log
        data: "output/03b_an_descriptive_table_1_kids_cat3_ageband*.txt"

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

  04b_an_descriptive_table_2_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do non_covid_death
    outputs:
      moderately_sensitive:
        log: 04b_an_descriptive_table_2_non_covid_death.log
        data: "output/04b_an_descriptive_table_2_non_covid_death_ageband*.txt"

  04b_an_descriptive_table_2_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: 04b_an_descriptive_table_2_covid_tpp_prob.log
        data: "output/04b_an_descriptive_table_2_covid_tpp_prob_ageband*.txt"

  04b_an_descriptive_table_2_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do covid_death
    outputs:
      moderately_sensitive:
        log: 04b_an_descriptive_table_2_covid_death.log
        data: "output/04b_an_descriptive_table_2_covid_death_ageband*.txt"

  04b_an_descriptive_table_2_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do covid_icu
    outputs:
      moderately_sensitive:
        log: 04b_an_descriptive_table_2_covid_icu.log
        data: "output/04b_an_descriptive_table_2_covid_icu_ageband*.txt"

  04b_an_descriptive_table_2_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do covidadmission
    outputs:
      moderately_sensitive:
        log: 04b_an_descriptive_table_2_covidadmission.log
        data: "output/04b_an_descriptive_table_2_covidadmission_ageband*.txt"

  06_univariate_analysis_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do non_covid_death kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_non_covid_death.log
        data: "output/an_univariable_cox_models_non_covid_death_AGESEX_*_ageband_*.ster"

  07a_an_multivariable_cox_models_demogADJ_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_non_covid_death.log
        data: "output/an_multivariate_cox_models_non_covid_death_*_DEMOGADJ_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_non_covid_death.log
        data: "output/an_multivariate_cox_models_non_covid_death_*_MAINFULLYADJMODEL_ageband_*.ster"
        other_data: "output/an_sense_non_covid_death_plus_eth_12mo_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_non_covid_death.log
        data: "output/an_sense_non_covid_death_CCeth_bmi_smok_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_non_covid_death_Sense4_*.log
        data: "output/an_sense_non_covid_death_age_underlying_timescale_ageband_*.ster"

  10_an_interaction_cox_models_shield_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_non_covid_death.log
        data: "output/an_interaction_cox_models_non_covid_death_kids_cat3_shield_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_time_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_time.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_time_non_covid_death.log
        data: "output/an_interaction_cox_models_non_covid_death_kids_cat3_cat_time_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_weeks_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_weeks.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_weeks_non_covid_death.log
        data: "output/an_interaction_cox_models_non_covid_death_week0_ageband_*.ster"

  10_an_interaction_cox_models_sex_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_non_covid_death.log
        data: "output/an_interaction_cox_models_non_covid_death_kids_cat3_male_MAINFULLYADJMODEL_*.ster"

  06_univariate_analysis_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do covid_tpp_prob kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_covid_tpp_prob.log
        data: "output/an_univariable_cox_models_covid_tpp_prob_AGESEX_*_ageband_*.ster"

  07a_an_multivariable_cox_models_demogADJ_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_covid_tpp_prob.log
        data: "output/an_multivariate_cox_models_covid_tpp_prob_*_DEMOGADJ_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_tpp_prob.log
        data: "output/an_multivariate_cox_models_covid_tpp_prob_*_MAINFULLYADJMODEL_ageband_*.ster"
        other_data: "output/an_sense_covid_tpp_prob_plus_eth_12mo_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_tpp_prob.log
        data: "output/an_sense_covid_tpp_prob_CCeth_bmi_smok_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_tpp_prob_Sense4_*.log
        data: "output/an_sense_covid_tpp_prob_age_underlying_timescale_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_tpp_prob.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_kids_cat3_shield_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_time_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_time.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_time_covid_tpp_prob.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_kids_cat3_cat_time_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_weeks_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_weeks.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_weeks_covid_tpp_prob.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_week0_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_tpp_prob.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_kids_cat3_male_MAINFULLYADJMODEL_*.ster"

  06_univariate_analysis_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do covid_death kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_covid_death.log
        data: "output/an_univariable_cox_models_covid_death_AGESEX_*_ageband_*.ster"

  07a_an_multivariable_cox_models_demogADJ_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do covid_death
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_covid_death.log
        data: "output/an_multivariate_cox_models_covid_death_*_DEMOGADJ_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_death.log
        data: "output/an_multivariate_cox_models_covid_death_*_MAINFULLYADJMODEL_ageband_*.ster"
        other_data: "output/an_sense_covid_death_plus_eth_12mo_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_death.log
        data: "output/an_sense_covid_death_CCeth_bmi_smok_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_death_Sense4_*.log
        data: "output/an_sense_covid_death_age_underlying_timescale_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_death.log
        data: "output/an_interaction_cox_models_covid_death_kids_cat3_shield_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_time_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_time.do covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_time_covid_death.log
        data: "output/an_interaction_cox_models_covid_death_kids_cat3_cat_time_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_weeks_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_weeks.do covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_weeks_covid_death.log
        data: "output/an_interaction_cox_models_covid_death_week0_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_death.log
        data: "output/an_interaction_cox_models_covid_death_kids_cat3_male_MAINFULLYADJMODEL_*.ster"

  06_univariate_analysis_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do covid_icu kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_covid_icu.log
        data: "output/an_univariable_cox_models_covid_icu_AGESEX_*_ageband_*.ster"

  07a_an_multivariable_cox_models_demogADJ_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_covid_icu.log
        data: "output/an_multivariate_cox_models_covid_icu_*_DEMOGADJ_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_icu.log
        data: "output/an_multivariate_cox_models_covid_icu_*_MAINFULLYADJMODEL_ageband_*.ster"
        other_data: "output/an_sense_covid_icu_plus_eth_12mo_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_icu.log
        data: "output/an_sense_covid_icu_CCeth_bmi_smok_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_icu_Sense4_*.log
        data: "output/an_sense_covid_icu_age_underlying_timescale_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_tpp_prob_Sense5_time_ints.log
        data: "output/an_sense_covid_tpp_prob_time_int_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense5_time_ints.log
        data: "output/an_sense_covidadmission_time_int_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_icu_Sense5_time_ints.log
        data: "output/an_sense_covid_icu_time_int_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_death_Sense5_time_ints.log
        data: "output/an_sense_covid_death_time_int_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_icu.log
        data: "output/an_interaction_cox_models_covid_icu_kids_cat3_shield_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_time_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_time.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_time_covid_icu.log
        data: "output/an_interaction_cox_models_covid_icu_kids_cat3_cat_time_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_weeks_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_weeks.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_weeks_covid_icu.log
        data: "output/an_interaction_cox_models_covid_icu_week0_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_icu.log
        data: "output/an_interaction_cox_models_covid_icu_kids_cat3_male_MAINFULLYADJMODEL_*.ster"

  06_univariate_analysis_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do covidadmission kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_covidadmission.log
        data: "output/an_univariable_cox_models_covidadmission_AGESEX_*_ageband_*.ster"

  07a_an_multivariable_cox_models_demogADJ_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_covidadmission.log
        data: "output/an_multivariate_cox_models_covidadmission_*_DEMOGADJ_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covidadmission.log
        data: "output/an_multivariate_cox_models_covidadmission_*_MAINFULLYADJMODEL_ageband_*.ster"
        other_data: "output/an_sense_covidadmission_plus_eth_12mo_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covidadmission.log
        data: "output/an_sense_covidadmission_CCeth_bmi_smok_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense4_*.log
        data: "output/an_sense_covidadmission_age_underlying_timescale_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covidadmission.log
        data: "output/an_interaction_cox_models_covidadmission_kids_cat3_shield_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_time_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_time.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_time_covidadmission.log
        data: "output/an_interaction_cox_models_covidadmission_kids_cat3_cat_time_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_weeks_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10a_an_interaction_cox_models_weeks_covidad.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_weeks_covidadmission.log
        data: "output/an_interaction_cox_models_covidadmission_week*_ageband_*.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
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covidadmission.log
        data: "output/an_interaction_cox_models_covidadmission_kids_cat3_male_MAINFULLYADJMODEL_*.ster"

  WORMS_06_univariate_analysis:
    needs: [WORMS_01_cr_analysis_dataset]
    run: stata-mp:latest analysis/WORMS_06_univariate_analysis.do worms kids_cat3 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
      - 06_univariate_analysis_non_covid_death
      - 07a_an_multivariable_cox_models_demogADJ_non_covid_death
      - 07b_an_multivariable_cox_models_FULL_non_covid_death
    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
      - 06_univariate_analysis_covid_tpp_prob
      - 07a_an_multivariable_cox_models_demogADJ_covid_tpp_prob
      - 07b_an_multivariable_cox_models_FULL_covid_tpp_prob
    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
      - 06_univariate_analysis_covid_death
      - 07a_an_multivariable_cox_models_demogADJ_covid_death
      - 07b_an_multivariable_cox_models_FULL_covid_death
    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
      - 06_univariate_analysis_covid_icu
      - 07a_an_multivariable_cox_models_demogADJ_covid_icu
      - 07b_an_multivariable_cox_models_FULL_covid_icu
    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
      - 06_univariate_analysis_covidadmission
      - 07a_an_multivariable_cox_models_demogADJ_covidadmission
      - 07b_an_multivariable_cox_models_FULL_covidadmission
    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_covidadmission:
    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
    run: stata-mp:latest analysis/15_anHRfigure_all_outcomes.do covidadmission
    outputs:
      moderately_sensitive:
        log: 15_anHRfigure_all_outcomes.log
        data: "output/15_an_tablecontents_HRtable_all_outcomes_ANALYSES.txt"
        figure: "output/15_an_HRforest_all_outcomes_ageband_*.svg"

  11_an_interaction_HR_tables_forest_non_covid_death:
    needs:
      - 10_an_interaction_cox_models_shield_non_covid_death
      - 10_an_interaction_cox_models_time_non_covid_death
      - 10_an_interaction_cox_models_weeks_non_covid_death
      - 10_an_interaction_cox_models_sex_non_covid_death
    run: stata-mp:latest analysis/11_an_interaction_HR_tables_forest.do non_covid_death
    outputs:
      moderately_sensitive:
        log: 11_an_interaction_HR_tables_forest_non_covid_death.log
        data: "output/11_an_int_tab_contents_HRtable_non_covid_death.txt"

  11_an_interaction_HR_tables_forest_covid_tpp_prob:
    needs:
      - 10_an_interaction_cox_models_shield_covid_tpp_prob
      - 10_an_interaction_cox_models_time_covid_tpp_prob
      - 10_an_interaction_cox_models_weeks_covid_tpp_prob
      - 10_an_interaction_cox_models_sex_covid_tpp_prob
    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_time_covid_death
      - 10_an_interaction_cox_models_weeks_covid_death
      - 10_an_interaction_cox_models_sex_covid_death
    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_time_covid_icu
      - 10_an_interaction_cox_models_weeks_covid_icu
      - 10_an_interaction_cox_models_sex_covid_icu
    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_time_covidadmission
      - 10_an_interaction_cox_models_weeks_covidadmission
      - 10_an_interaction_cox_models_sex_covidadmission
    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"

  11a_an_interaction_HR_tables_forest_WEEKS_covidadmission:
    needs:
      - 10_an_interaction_cox_models_shield_non_covid_death
      - 10_an_interaction_cox_models_shield_covid_tpp_prob
      - 10_an_interaction_cox_models_shield_covid_death
      - 10_an_interaction_cox_models_shield_covid_icu
      - 10_an_interaction_cox_models_shield_covidadmission
      - 10_an_interaction_cox_models_time_non_covid_death
      - 10_an_interaction_cox_models_time_covid_tpp_prob
      - 10_an_interaction_cox_models_time_covid_death
      - 10_an_interaction_cox_models_time_covid_icu
      - 10_an_interaction_cox_models_time_covidadmission
      - 10_an_interaction_cox_models_weeks_non_covid_death
      - 10_an_interaction_cox_models_weeks_covid_tpp_prob
      - 10_an_interaction_cox_models_weeks_covid_death
      - 10_an_interaction_cox_models_weeks_covid_icu
      - 10_an_interaction_cox_models_weeks_covidadmission
      - 10_an_interaction_cox_models_sex_non_covid_death
      - 10_an_interaction_cox_models_sex_covid_tpp_prob
      - 10_an_interaction_cox_models_sex_covid_death
      - 10_an_interaction_cox_models_sex_covid_icu
      - 10_an_interaction_cox_models_sex_covidadmission
    run: stata-mp:latest analysis/11a_an_interaction_HR_tables_forest_WEEKS.do covidadmission
    outputs:
      moderately_sensitive:
        log: 11a_an_interaction_HR_tables_forest_WEEKS.log
        data: "output/an_int_tab_contents_HRtable_WEEKS.txt"

  12_an_tablecontent_HRtable_SENSE_non_covid_death:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense3_non_covid_death
      - 07d_an_multivariable_cox_models_FULL_Sense4_non_covid_death
      - 07b_an_multivariable_cox_models_FULL_non_covid_death
    run: stata-mp:latest analysis/12_an_tablecontent_HRtable_SENSE.do non_covid_death
    outputs:
      moderately_sensitive:
        log: 12_an_tablecontent_HRtable_SENSE_non_covid_death.log
        data: "output/12_an_sense_HRtable_non_covid_death_SENSE_ANALYSES.txt"
        figure: "output/12_an_HRforest_SENSE_non_covid_death_ageband_*.svg"

  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
    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
    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
    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
    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_covid_death
      - 04b_an_descriptive_table_2_covid_icu
      - 04b_an_descriptive_table_2_covid_tpp_prob
      - 04b_an_descriptive_table_2_covidadmission
      - 04b_an_descriptive_table_2_non_covid_death
      - 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
      - 11_an_interaction_HR_tables_forest_non_covid_death
      - 11a_an_interaction_HR_tables_forest_WEEKS_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
      - 12_an_tablecontent_HRtable_SENSE_non_covid_death
      - 15_anHRfigure_all_outcomes_covidadmission
      - 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