project.yaml

version: '3.0'

expectations:

  population_size: 100000

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/vax_eligibility_inputs.R
    outputs:
      highly_sensitive:
        vax_study_dates_json: output/vax_study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population_electively_unvaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_electively_unvaccinated
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_electively_unvaccinated.feather

  generate_study_population_vaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
      --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_vaccinated.feather

  generate_study_population_index:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_index
      --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_index.feather

  preprocess_data_vaccinated:
    run: r:latest analysis/preprocess/preprocess_data.R vaccinated
    needs:
    - generate_study_population_index
    - generate_study_population_vaccinated
    - generate_study_population_electively_unvaccinated
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_vaccinated_*.txt
        describe_index: output/not-for-review/describe_tmp_index_vaccinated.txt
        describe_cohort: output/not-for-review/describe_tmp_vaccinated.txt
        descrive_venn: output/not-for-review/describe_venn_vaccinated.txt
      highly_sensitive:
        cohort: output/input_vaccinated.rds
        venn: output/venn_vaccinated.rds

  preprocess_data_electively_unvaccinated:
    run: r:latest analysis/preprocess/preprocess_data.R electively_unvaccinated
    needs:
    - generate_study_population_index
    - generate_study_population_vaccinated
    - generate_study_population_electively_unvaccinated
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_electively_unvaccinated_*.txt
        describe_index: output/not-for-review/describe_tmp_index_electively_unvaccinated.txt
        describe_cohort: output/not-for-review/describe_tmp_electively_unvaccinated.txt
        descrive_venn: output/not-for-review/describe_venn_electively_unvaccinated.txt
      highly_sensitive:
        cohort: output/input_electively_unvaccinated.rds
        venn: output/venn_electively_unvaccinated.rds

  stage1_data_cleaning_both:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R both
    needs:
    - preprocess_data_vaccinated
    - preprocess_data_electively_unvaccinated
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_*.csv
        QA_rules: output/review/descriptives/QA_summary_*.csv
        IE_criteria: output/review/descriptives/Cohort_flow_*.csv
        histograms: output/not-for-review/numeric_histograms_*.svg
      highly_sensitive:
        cohort: output/input_*_stage1.rds

  stage1_end_date_table_vaccinated:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R vaccinated
    needs:
    - preprocess_data_vaccinated
    - preprocess_data_electively_unvaccinated
    - stage1_data_cleaning_both
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates_vaccinated.rds

  stage1_end_date_table_electively_unvaccinated:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R electively_unvaccinated
    needs:
    - preprocess_data_vaccinated
    - preprocess_data_electively_unvaccinated
    - stage1_data_cleaning_both
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates_electively_unvaccinated.rds

  stage2_missing_table1_both:
    run: r:latest analysis/descriptives/Stage2_missing_table1.R both
    needs:
    - stage1_data_cleaning_both
    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

  ## Stage 4 - Table 2 - vaccinated cohort 

  stage4_table_2_vaccinated:
    run: r:latest analysis/descriptives/table_2.R vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_vaccinated.csv

  ## Stage 4 - Table 2 - electively_unvaccinated cohort 

  stage4_table_2_electively_unvaccinated:
    run: r:latest analysis/descriptives/table_2.R electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_electively_unvaccinated.csv

  event_counts_by_time_period_vaccinated:
    run: r:latest analysis/descriptives/event_counts_by_time_period.R vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        event_counts: output/review/descriptives/event_counts_by_time_period_vaccinated.csv

  event_counts_by_time_period_electively_unvaccinated:
    run: r:latest analysis/descriptives/event_counts_by_time_period.R electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        event_counts: output/review/descriptives/event_counts_by_time_period_electively_unvaccinated.csv

  stage4_venn_diagram_both:
    run: r:latest analysis/descriptives/venn_diagram.R both
    needs:
    - preprocess_data_vaccinated
    - preprocess_data_electively_unvaccinated
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_*

  ## Cox model for ami - vaccinated 

  Analysis_cox_ami_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ami vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ami_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ami_*_vaccinated_*_time_periods.csv

  ## Cox model for ami - electively_unvaccinated 

  Analysis_cox_ami_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ami electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ami_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ami_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for stroke_isch - vaccinated 

  Analysis_cox_stroke_isch_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_isch_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_isch_*_vaccinated_*_time_periods.csv

  ## Cox model for stroke_isch - electively_unvaccinated 

  Analysis_cox_stroke_isch_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_isch_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_isch_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for dvt - vaccinated 

  Analysis_cox_dvt_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R dvt vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_dvt_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_dvt_*_vaccinated_*_time_periods.csv

  ## Cox model for dvt - electively_unvaccinated 

  Analysis_cox_dvt_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R dvt electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_dvt_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_dvt_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for pe - vaccinated 

  Analysis_cox_pe_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R pe vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_pe_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_pe_*_vaccinated_*_time_periods.csv

  ## Cox model for pe - electively_unvaccinated 

  Analysis_cox_pe_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R pe electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_pe_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_pe_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for tia - vaccinated 

  Analysis_cox_tia_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R tia vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_tia_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_tia_*_vaccinated_*_time_periods.csv

  ## Cox model for tia - electively_unvaccinated 

  Analysis_cox_tia_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R tia electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_tia_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_tia_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for stroke_sah_hs - vaccinated 

  Analysis_cox_stroke_sah_hs_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_sah_hs_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_sah_hs_*_vaccinated_*_time_periods.csv

  ## Cox model for stroke_sah_hs - electively_unvaccinated 

  Analysis_cox_stroke_sah_hs_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_sah_hs_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_sah_hs_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for hf - vaccinated 

  Analysis_cox_hf_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R hf vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_hf_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_hf_*_vaccinated_*_time_periods.csv

  ## Cox model for hf - electively_unvaccinated 

  Analysis_cox_hf_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R hf electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_hf_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_hf_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for angina - vaccinated 

  Analysis_cox_angina_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R angina vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_angina_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_angina_*_vaccinated_*_time_periods.csv

  ## Cox model for angina - electively_unvaccinated 

  Analysis_cox_angina_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R angina electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_angina_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_angina_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for ate - vaccinated 

  Analysis_cox_ate_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ate vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ate_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ate_*_vaccinated_*_time_periods.csv

  ## Cox model for ate - electively_unvaccinated 

  Analysis_cox_ate_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ate electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ate_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ate_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for vte - vaccinated 

  Analysis_cox_vte_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R vte vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_vte_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_vte_*_vaccinated_*_time_periods.csv

  ## Cox model for vte - electively_unvaccinated 

  Analysis_cox_vte_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R vte electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_vte_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_vte_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for ami_primary_position - vaccinated 

  Analysis_cox_ami_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ami_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ami_primary_position_*_vaccinated_*_time_periods.csv

  ## Cox model for ami_primary_position - electively_unvaccinated 

  Analysis_cox_ami_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ami_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ami_primary_position_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for stroke_isch_primary_position - vaccinated 

  Analysis_cox_stroke_isch_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_isch_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_isch_primary_position_*_vaccinated_*_time_periods.csv

  ## Cox model for stroke_isch_primary_position - electively_unvaccinated 

  Analysis_cox_stroke_isch_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_isch_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_isch_primary_position_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for dvt_primary_position - vaccinated 

  Analysis_cox_dvt_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_dvt_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_dvt_primary_position_*_vaccinated_*_time_periods.csv

  ## Cox model for dvt_primary_position - electively_unvaccinated 

  Analysis_cox_dvt_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_dvt_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_dvt_primary_position_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for pe_primary_position - vaccinated 

  Analysis_cox_pe_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_pe_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_pe_primary_position_*_vaccinated_*_time_periods.csv

  ## Cox model for pe_primary_position - electively_unvaccinated 

  Analysis_cox_pe_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_pe_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_pe_primary_position_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for tia_primary_position - vaccinated 

  Analysis_cox_tia_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_tia_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_tia_primary_position_*_vaccinated_*_time_periods.csv

  ## Cox model for tia_primary_position - electively_unvaccinated 

  Analysis_cox_tia_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_tia_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_tia_primary_position_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for stroke_sah_hs_primary_position - vaccinated 

  Analysis_cox_stroke_sah_hs_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
      vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_sah_hs_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_sah_hs_primary_position_*_vaccinated_*_time_periods.csv

  ## Cox model for stroke_sah_hs_primary_position - electively_unvaccinated 

  Analysis_cox_stroke_sah_hs_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
      electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_sah_hs_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_sah_hs_primary_position_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for hf_primary_position - vaccinated 

  Analysis_cox_hf_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_hf_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_hf_primary_position_*_vaccinated_*_time_periods.csv

  ## Cox model for hf_primary_position - electively_unvaccinated 

  Analysis_cox_hf_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_hf_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_hf_primary_position_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for angina_primary_position - vaccinated 

  Analysis_cox_angina_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_angina_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_angina_primary_position_*_vaccinated_*_time_periods.csv

  ## Cox model for angina_primary_position - electively_unvaccinated 

  Analysis_cox_angina_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_angina_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_angina_primary_position_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for ate_primary_position - vaccinated 

  Analysis_cox_ate_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ate_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ate_primary_position_*_vaccinated_*_time_periods.csv

  ## Cox model for ate_primary_position - electively_unvaccinated 

  Analysis_cox_ate_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ate_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ate_primary_position_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for vte_primary_position - vaccinated 

  Analysis_cox_vte_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_vaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_vte_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_vte_primary_position_*_vaccinated_*_time_periods.csv

  ## Cox model for vte_primary_position - electively_unvaccinated 

  Analysis_cox_vte_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_vte_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_vte_primary_position_*_electively_unvaccinated_*_time_periods.csv

  stata_cox_model_ami_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ami_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ami_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_stroke_isch_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_dvt_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_dvt_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_dvt_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_pe_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_hf_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_hf_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_angina_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_angina_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_ate_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ate_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_ami_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ami_primary_position_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_stroke_isch_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_primary_position_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_dvt_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_dvt_primary_position_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_pe_primary_position_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_hf_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_hf_primary_position_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_angina_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_angina_primary_position_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_ate_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ate_primary_position_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_primary_position_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_covid_pheno_hospitalised_vaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_covid_pheno_hospitalised_vaccinated_normal_time_periods
    needs:
    - Analysis_cox_pe_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_covid_pheno_hospitalised_vaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_vaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_hf_covid_pheno_hospitalised_vaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_covid_pheno_hospitalised_vaccinated_normal_time_periods
    needs:
    - Analysis_cox_hf_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_covid_pheno_hospitalised_vaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_vaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_angina_covid_pheno_hospitalised_vaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_covid_pheno_hospitalised_vaccinated_normal_time_periods
    needs:
    - Analysis_cox_angina_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_covid_pheno_hospitalised_vaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_vaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_ate_covid_pheno_hospitalised_vaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_covid_pheno_hospitalised_vaccinated_normal_time_periods
    needs:
    - Analysis_cox_ate_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_covid_pheno_hospitalised_vaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_vaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_vte_covid_pheno_hospitalised_vaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_covid_pheno_hospitalised_vaccinated_normal_time_periods
    needs:
    - Analysis_cox_vte_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_covid_pheno_hospitalised_vaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_vaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_ami_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ami_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ami_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_stroke_isch_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_dvt_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_dvt_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_dvt_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_pe_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_hf_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_hf_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_angina_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_angina_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_ate_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ate_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_ate_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ate_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_covid_pheno_hospitalised_electively_unvaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_covid_pheno_hospitalised_electively_unvaccinated_normal_time_periods
    needs:
    - Analysis_cox_pe_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_covid_pheno_hospitalised_electively_unvaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_electively_unvaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_vte_covid_pheno_hospitalised_electively_unvaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_covid_pheno_hospitalised_electively_unvaccinated_normal_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_covid_pheno_hospitalised_electively_unvaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_electively_unvaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_angina_covid_history_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_covid_history_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_angina_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_covid_history_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_angina_covid_history_vaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_pe_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_main_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_main_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_main_electively_unvaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_main_electively_unvaccinated_normal_time_periods
    needs:
    - Analysis_cox_pe_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_main_electively_unvaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_main_electively_unvaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_hf_main_electively_unvaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_main_electively_unvaccinated_normal_time_periods
    needs:
    - Analysis_cox_hf_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_main_electively_unvaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_main_electively_unvaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_hf_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_hf_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_main_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_main_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_hf_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_hf_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_sex_Male_electively_unvaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_sex_Male_electively_unvaccinated_normal_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_sex_Male_electively_unvaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_sex_Male_electively_unvaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_vte_sex_Male_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_sex_Male_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_sex_Male_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_sex_Male_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_agegp_40_59_electively_unvaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_agegp_40_59_electively_unvaccinated_normal_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_agegp_40_59_electively_unvaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_agegp_40_59_electively_unvaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_vte_agegp_60_79_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_agegp_60_79_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_agegp_60_79_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_agegp_60_79_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_ethnicity_White_electively_unvaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_ethnicity_White_electively_unvaccinated_normal_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_ethnicity_White_electively_unvaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_ethnicity_White_electively_unvaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_vte_ethnicity_Black_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_ethnicity_Black_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_ethnicity_Black_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_ethnicity_Black_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_prior_history_FALSE_electively_unvaccinated_normal:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_prior_history_FALSE_electively_unvaccinated_normal_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_prior_history_FALSE_electively_unvaccinated_normal_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_prior_history_FALSE_electively_unvaccinated_normal_time_periods_cox_model.txt

  stata_cox_model_hf_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_hf_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_aer_Female_60_79_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_aer_Female_60_79_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_aer_Female_60_79_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_aer_Female_60_79_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_aer_Male_60_79_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_aer_Male_60_79_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_aer_Male_60_79_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_aer_Male_60_79_electively_unvaccinated_reduced_time_periods_cox_model.txt

  format_stata_output:
    run: r:latest analysis/format_stata_output.R
    needs:
    - stata_cox_model_ami_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_stroke_isch_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_dvt_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_pe_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_hf_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_angina_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_ate_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_vte_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_ami_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_stroke_isch_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_dvt_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_pe_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_hf_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_angina_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_ate_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_vte_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_model_ami_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_stroke_isch_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_dvt_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_pe_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_hf_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_angina_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_ate_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_vte_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_ate_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_vte_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_angina_covid_history_vaccinated_reduced
    - stata_cox_model_pe_main_electively_unvaccinated_reduced
    - stata_cox_model_pe_main_electively_unvaccinated_normal
    - stata_cox_model_hf_main_electively_unvaccinated_normal
    - stata_cox_model_hf_main_electively_unvaccinated_reduced
    - stata_cox_model_hf_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_vte_sex_Male_electively_unvaccinated_normal
    - stata_cox_model_vte_sex_Male_electively_unvaccinated_reduced
    - stata_cox_model_vte_agegp_40_59_electively_unvaccinated_normal
    - stata_cox_model_vte_agegp_60_79_electively_unvaccinated_reduced
    - stata_cox_model_vte_ethnicity_White_electively_unvaccinated_normal
    - stata_cox_model_vte_ethnicity_Black_electively_unvaccinated_reduced
    - stata_cox_model_vte_prior_history_FALSE_electively_unvaccinated_normal
    - stata_cox_model_hf_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_vte_aer_Female_60_79_electively_unvaccinated_reduced
    - stata_cox_model_vte_aer_Male_60_79_electively_unvaccinated_reduced
    outputs:
      moderately_sensitive:
        stata_output: output/stata_output.csv

  tmp_ate_main_vaccinated_stata:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_main_vaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ate_vaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_main_vaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_main_vaccinated_reduced_time_periods_cox_model.txt