project.yaml

version: '3.0'

expectations:

  population_size: 200000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  vax_eligibility_inputs:
    run: r:latest analysis/metadates.R
    outputs:
      highly_sensitive:
        study_dates_json: output/study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population_prelim:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_prelim.feather

  generate_index_dates:
    run: r:latest analysis/prelim.R
    needs:
    - vax_eligibility_inputs
    - generate_study_population_prelim
    outputs:
      highly_sensitive:
        index_dates: output/index_dates.csv

  generate_study_population_prevax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_prevax.feather

  generate_study_population_vax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
      --output-format feather
    needs:
    - generate_index_dates
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_vax.feather

  generate_study_population_unvax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_unvax.feather

  preprocess_data_prevax:
    run: r:latest analysis/preprocess/preprocess_data.R prevax
    needs:
    - generate_index_dates
    - generate_study_population_prelim
    - generate_study_population_prevax
    - generate_study_population_vax
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_prevax_*.txt
      highly_sensitive:
        cohort: output/input_prevax.rds
        venn: output/venn_prevax.rds

  preprocess_data_vax:
    run: r:latest analysis/preprocess/preprocess_data.R vax
    needs:
    - generate_index_dates
    - generate_study_population_prelim
    - generate_study_population_prevax
    - generate_study_population_vax
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_vax_*.txt
      highly_sensitive:
        cohort: output/input_vax.rds
        venn: output/venn_vax.rds

  preprocess_data_unvax:
    run: r:latest analysis/preprocess/preprocess_data.R unvax
    needs:
    - generate_index_dates
    - generate_study_population_prelim
    - generate_study_population_prevax
    - generate_study_population_vax
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_unvax_*.txt
      highly_sensitive:
        cohort: output/input_unvax.rds
        venn: output/venn_unvax.rds

  stage1_data_cleaning_prevax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_prevax.csv
        QA_rules: output/review/descriptives/QA_summary_prevax_*.csv
        IE_criteria: output/review/descriptives/Cohort_flow_prevax_*.csv
        histograms: output/not-for-review/numeric_histograms_prevax_*.svg
      highly_sensitive:
        cohort: output/input_prevax_*.rds
        cohort_csv: output/input_prevax_*.csv.gz

  stage1_data_cleaning_vax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R vax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_vax.csv
        QA_rules: output/review/descriptives/QA_summary_vax_*.csv
        IE_criteria: output/review/descriptives/Cohort_flow_vax_*.csv
        histograms: output/not-for-review/numeric_histograms_vax_*.svg
      highly_sensitive:
        cohort: output/input_vax_*.rds
        cohort_csv: output/input_vax_*.csv.gz

  stage1_data_cleaning_unvax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_unvax.csv
        QA_rules: output/review/descriptives/QA_summary_unvax_*.csv
        IE_criteria: output/review/descriptives/Cohort_flow_unvax_*.csv
        histograms: output/not-for-review/numeric_histograms_unvax_*.svg
      highly_sensitive:
        cohort: output/input_unvax_*.rds
        cohort_csv: output/input_unvax_*.csv.gz

  stage1_end_date_table_prevax:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R prevax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - stage1_data_cleaning_prevax
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates_prevax_*.rds
        end_date_table_csv: output/follow_up_end_dates_prevax_*.csv.gz

  stage1_end_date_table_vax:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R vax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - stage1_data_cleaning_vax
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates_vax_*.rds
        end_date_table_csv: output/follow_up_end_dates_vax_*.csv.gz

  stage1_end_date_table_unvax:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R unvax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - stage1_data_cleaning_unvax
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates_unvax_*.rds
        end_date_table_csv: output/follow_up_end_dates_unvax_*.csv.gz

  generate_study_population_prevax_diabetes_analyis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_diabetes_analysis
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - stage1_data_cleaning_prevax
    - stage1_end_date_table_prevax
    outputs:
      highly_sensitive:
        cohort: output/input_prevax_diabetes_analysis.feather

  generate_study_population_vax_diabetes_analyis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax_diabetes_analysis
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - stage1_data_cleaning_vax
    - stage1_end_date_table_vax
    outputs:
      highly_sensitive:
        cohort: output/input_vax_diabetes_analysis.feather

  generate_study_population_unvax_diabetes_analyis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax_diabetes_analysis
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    outputs:
      highly_sensitive:
        cohort: output/input_unvax_diabetes_analysis.feather

  diabetes_post_hoc_prevax:
    run: r:latest analysis/descriptives/diabetes-follow-up-analysis.R prevax
    needs:
    - generate_study_population_prevax_diabetes_analyis
    - generate_study_population_vax_diabetes_analyis
    - generate_study_population_unvax_diabetes_analyis
    - vax_eligibility_inputs
    - stage1_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_prevax.csv
        histograms: output/review/descriptives/days_*_prevax.png
      highly_sensitive:
        cohort_new: output/input_prevax_stage1_diabetes.rds

  diabetes_post_hoc_vax:
    run: r:latest analysis/descriptives/diabetes-follow-up-analysis.R vax
    needs:
    - generate_study_population_prevax_diabetes_analyis
    - generate_study_population_vax_diabetes_analyis
    - generate_study_population_unvax_diabetes_analyis
    - vax_eligibility_inputs
    - stage1_data_cleaning_vax
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_vax.csv
        histograms: output/review/descriptives/days_*_vax.png
      highly_sensitive:
        cohort_new: output/input_vax_stage1_diabetes.rds

  diabetes_post_hoc_unvax:
    run: r:latest analysis/descriptives/diabetes-follow-up-analysis.R unvax
    needs:
    - generate_study_population_prevax_diabetes_analyis
    - generate_study_population_vax_diabetes_analyis
    - generate_study_population_unvax_diabetes_analyis
    - vax_eligibility_inputs
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_unvax.csv
        histograms: output/review/descriptives/days_*_unvax.png
      highly_sensitive:
        cohort_new: output/input_unvax_stage1_diabetes.rds

  diabetes_post_hoc_prevax_extended_follow_up:
    run: r:latest analysis/descriptives/diabetes-follow-up-analysis-extended-follow-up.R
      prevax
    needs:
    - generate_study_population_prevax_diabetes_analyis
    - generate_study_population_vax_diabetes_analyis
    - generate_study_population_unvax_diabetes_analyis
    - vax_eligibility_inputs
    - stage1_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_EXTENDED_*_prevax.csv

  stage2_missing_table1_all:
    run: r:latest analysis/descriptives/Stage2_missing_table1.R all
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/not-for-review/Check_missing_range_*.csv
        DateChecks: output/not-for-review/Check_dates_range_*.csv
        Descriptive_Table: output/review/descriptives/Table1_*.csv

  stage3_diabetes_flow_prevax:
    run: r:latest analysis/descriptives/diabetes_flowchart.R prevax
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values_prevax_*.csv

  stage3_diabetes_flow_vax:
    run: r:latest analysis/descriptives/diabetes_flowchart.R vax
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values_vax_*.csv

  stage3_diabetes_flow_unvax:
    run: r:latest analysis/descriptives/diabetes_flowchart.R unvax
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values_unvax_*.csv

  ## Stage 4 - Table 2 - prevax cohort 

  stage4_table_2_prevax:
    run: r:latest analysis/descriptives/table_2.R prevax
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_prevax_*.csv

  ## Stage 4 - Table 2 - vax cohort 

  stage4_table_2_vax:
    run: r:latest analysis/descriptives/table_2.R vax
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_vax_*.csv

  ## Stage 4 - Table 2 - unvax cohort 

  stage4_table_2_unvax:
    run: r:latest analysis/descriptives/table_2.R unvax
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_unvax_*.csv

  ## Cox model for t1dm - prevax 

  Analysis_cox_t1dm_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t1dm_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t1dm_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t1dm_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t1dm_*_prevax_*_time_periods.csv

  ## Cox model for t1dm - vax 

  Analysis_cox_t1dm_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm vax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t1dm_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t1dm_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t1dm_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t1dm_*_vax_*_time_periods.csv

  ## Cox model for t1dm - unvax 

  Analysis_cox_t1dm_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm unvax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t1dm_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t1dm_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t1dm_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t1dm_*_unvax_*_time_periods.csv

  ## Cox model for t2dm - prevax 

  Analysis_cox_t2dm_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm prevax TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_*_prevax_*_time_periods.csv

  ## Cox model for t2dm - vax 

  Analysis_cox_t2dm_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm vax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_*_vax_*_time_periods.csv

  ## Cox model for t2dm - unvax 

  Analysis_cox_t2dm_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm unvax TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_rec - prevax 

  Analysis_cox_t2dm_rec_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_rec prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_rec_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_rec_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_rec_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_rec_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_rec_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_rec_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_rec_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_rec_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pre_rec - prevax 

  Analysis_cox_t2dm_pre_rec_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pre_rec prevax TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pre_rec_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pre_rec_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pre_rec_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pre_rec_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pre_rec_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pre_rec_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pre_rec - vax 

  Analysis_cox_t2dm_pre_rec_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pre_rec vax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pre_rec_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pre_rec_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pre_rec_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pre_rec_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pre_rec_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pre_rec_*_vax_*_time_periods.csv

  ## Cox model for t2dm_pre_rec - unvax 

  Analysis_cox_t2dm_pre_rec_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pre_rec unvax TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pre_rec_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pre_rec_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pre_rec_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pre_rec_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pre_rec_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pre_rec_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_post_rec - prevax 

  Analysis_cox_t2dm_post_rec_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_post_rec prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_post_rec_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_post_rec_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_post_rec_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_post_rec_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_post_rec_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_post_rec_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_post_rec_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_post_rec_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_follow - prevax 

  Analysis_cox_t2dm_follow_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_follow prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_follow_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_follow_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_follow_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_follow_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_follow_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_follow_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pd - prevax 

  Analysis_cox_t2dm_pd_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pd - vax 

  Analysis_cox_t2dm_pd_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd vax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_*_vax_*_time_periods.csv

  ## Cox model for t2dm_pd - unvax 

  Analysis_cox_t2dm_pd_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd unvax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_pd_no - prevax 

  Analysis_cox_t2dm_pd_no_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no prevax TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_no_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_no_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pd_no - vax 

  Analysis_cox_t2dm_pd_no_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no vax TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_no_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_no_*_vax_*_time_periods.csv

  ## Cox model for t2dm_pd_no - unvax 

  Analysis_cox_t2dm_pd_no_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no unvax TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_no_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_no_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_obes - prevax 

  Analysis_cox_t2dm_obes_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_obes - vax 

  Analysis_cox_t2dm_obes_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes vax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_*_vax_*_time_periods.csv

  ## Cox model for t2dm_obes - unvax 

  Analysis_cox_t2dm_obes_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes unvax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_obes_no - prevax 

  Analysis_cox_t2dm_obes_no_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no prevax TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_no_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_no_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_obes_no - vax 

  Analysis_cox_t2dm_obes_no_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no vax TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_no_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_no_*_vax_*_time_periods.csv

  ## Cox model for t2dm_obes_no - unvax 

  Analysis_cox_t2dm_obes_no_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no unvax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_no_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_no_*_unvax_*_time_periods.csv

  ## Cox model for otherdm - prevax 

  Analysis_cox_otherdm_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_otherdm_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_otherdm_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_otherdm_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_otherdm_*_prevax_*_time_periods.csv

  ## Cox model for otherdm - vax 

  Analysis_cox_otherdm_vax:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm vax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_otherdm_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_otherdm_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_otherdm_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_otherdm_*_vax_*_time_periods.csv

  ## Cox model for otherdm - unvax 

  Analysis_cox_otherdm_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm unvax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_otherdm_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_otherdm_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_otherdm_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_otherdm_*_unvax_*_time_periods.csv

  ## Cox model for gestationaldm - prevax 

  Analysis_cox_gestationaldm_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R gestationaldm prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_gestationaldm_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_gestationaldm_*_prevax_*_time_periods.csv

  ## Cox model for gestationaldm - vax 

  Analysis_cox_gestationaldm_vax:
    run: r:latest analysis/model/01_cox_pipeline.R gestationaldm vax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_gestationaldm_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_gestationaldm_*_vax_*_time_periods.csv

  ## Cox model for gestationaldm - unvax 

  Analysis_cox_gestationaldm_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R gestationaldm unvax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_gestationaldm_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_gestationaldm_*_unvax_*_time_periods.csv

  ## Cox model for t1dm_extended_follow_up - prevax 

  Analysis_cox_t1dm_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t1dm_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t1dm_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t1dm_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t1dm_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_extended_follow_up - prevax 

  Analysis_cox_t2dm_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for otherdm_extended_follow_up - prevax 

  Analysis_cox_otherdm_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_otherdm_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_otherdm_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_otherdm_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_otherdm_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for gestationaldm_extended_follow_up - prevax 

  Analysis_cox_gestationaldm_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R gestationaldm_extended_follow_up
      prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_gestationaldm_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_gestationaldm_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_follow_extended_follow_up - prevax 

  Analysis_cox_t2dm_follow_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_follow_extended_follow_up
      prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_follow_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_follow_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_follow_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_follow_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_follow_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_follow_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pd_extended_follow_up - prevax 

  Analysis_cox_t2dm_pd_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pd_no_extended_follow_up - prevax 

  Analysis_cox_t2dm_pd_no_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_no_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_no_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_obes_extended_follow_up - prevax 

  Analysis_cox_t2dm_obes_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_obes_no_extended_follow_up - prevax 

  Analysis_cox_t2dm_obes_no_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no_extended_follow_up
      prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_no_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_no_extended_follow_up_*_prevax_*_time_periods.csv

  stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_hospitalised_vax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_vax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_main_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_main_vax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_vax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_vax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_vax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_main_unvax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_unvax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_follow_main_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_main_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_pre_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_post_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_rec_main_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_main_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_rec_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_rec_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_pre_rec_main_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_main_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_pre_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_pre_rec_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_pre_rec_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_post_rec_main_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_main_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_post_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_post_rec_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_post_rec_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t1dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_otherdm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_gestationaldm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_main_vax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_vax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_vax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_vax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_main_unvax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_unvax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_unvax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_unvax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_follow_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_main_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_pre_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_post_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_main_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_rec_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_rec_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_pre_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_main_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_pre_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_pre_rec_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_pre_rec_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_post_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_main_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_post_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_post_rec_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_post_rec_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  format_stata_output:
    run: r:latest analysis/format_stata_output.R
    needs:
    - stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_hospitalised_vax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_main_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_main_vax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_main_unvax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_follow_main_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_rec_main_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_pre_rec_main_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_post_rec_main_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
    - stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
    - stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_main_vax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_main_unvax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_follow_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_pre_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_post_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
    outputs:
      moderately_sensitive:
        stata_output: output/stata_output.csv

  format_hazard_ratios:
    run: r:latest analysis/model/format_hazard_ratio_outputs.R
    needs:
    - format_stata_output
    - stage4_table_2_prevax
    - stage4_table_2_vax
    - stage4_table_2_unvax
    - Analysis_cox_t1dm_prevax
    - Analysis_cox_t1dm_vax
    - Analysis_cox_t1dm_unvax
    - Analysis_cox_t2dm_prevax
    - Analysis_cox_t2dm_vax
    - Analysis_cox_t2dm_unvax
    - Analysis_cox_t2dm_pre_rec_prevax
    - Analysis_cox_t2dm_pre_rec_vax
    - Analysis_cox_t2dm_pre_rec_unvax
    - Analysis_cox_t2dm_pd_prevax
    - Analysis_cox_t2dm_pd_vax
    - Analysis_cox_t2dm_pd_unvax
    - Analysis_cox_t2dm_pd_no_prevax
    - Analysis_cox_t2dm_pd_no_vax
    - Analysis_cox_t2dm_pd_no_unvax
    - Analysis_cox_t2dm_obes_prevax
    - Analysis_cox_t2dm_obes_vax
    - Analysis_cox_t2dm_obes_unvax
    - Analysis_cox_t2dm_obes_no_prevax
    - Analysis_cox_t2dm_obes_no_vax
    - Analysis_cox_t2dm_obes_no_unvax
    - Analysis_cox_otherdm_prevax
    - Analysis_cox_otherdm_vax
    - Analysis_cox_otherdm_unvax
    - Analysis_cox_gestationaldm_prevax
    - Analysis_cox_gestationaldm_vax
    - Analysis_cox_gestationaldm_unvax
    - Analysis_cox_t2dm_rec_prevax
    - Analysis_cox_t2dm_post_rec_prevax
    - Analysis_cox_t2dm_follow_prevax
    - Analysis_cox_t1dm_extended_follow_up_prevax
    - Analysis_cox_t2dm_extended_follow_up_prevax
    - Analysis_cox_otherdm_extended_follow_up_prevax
    - Analysis_cox_gestationaldm_extended_follow_up_prevax
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    - Analysis_cox_t2dm_pd_extended_follow_up_prevax
    - Analysis_cox_t2dm_pd_no_extended_follow_up_prevax
    - Analysis_cox_t2dm_obes_extended_follow_up_prevax
    - Analysis_cox_t2dm_obes_no_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        hr_output: output/review/model/hr_output_formatted.csv
        hr_output_no_events: output/review/model/hr_output_formatted_no_event_counts.csv
        table2_output: output/review/model/table2_output_formatted_no_hrs.csv