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Job request: 15700

Organisation:
University of Bristol
Workspace:
post-covid-vaccinated
ID:
ssc2mp2umjfzc5e3

This page shows the technical details of what happened when authorised researcher Rochelle Knight requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show 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

  ## Post-exposure days to event histogram data - vaccinated 

  days_to_event_histogram_vaccinated:
    run: r:latest analysis/descriptives/histogram_data_post_exposure_days_to_event.R
      vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/histogram_data_vaccinated.csv

  ## Post-exposure days to event histogram data - electively_unvaccinated 

  days_to_event_histogram_electively_unvaccinated:
    run: r:latest analysis/descriptives/histogram_data_post_exposure_days_to_event.R
      electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/histogram_data_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 - 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 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_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 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 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 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_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 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 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 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_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 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 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 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_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 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 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 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_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 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 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 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_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 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 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 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_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 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_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 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_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 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 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 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_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 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 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 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_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

  ## 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 ami_unvax_sens - electively_unvaccinated 

  Analysis_cox_ami_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ami_unvax_sens 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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ami_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ami_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for stroke_isch_unvax_sens - electively_unvaccinated 

  Analysis_cox_stroke_isch_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_unvax_sens 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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_isch_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_isch_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for dvt_unvax_sens - electively_unvaccinated 

  Analysis_cox_dvt_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_unvax_sens 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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_dvt_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_dvt_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for pe_unvax_sens - electively_unvaccinated 

  Analysis_cox_pe_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R pe_unvax_sens 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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_pe_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_pe_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for tia_unvax_sens - electively_unvaccinated 

  Analysis_cox_tia_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R tia_unvax_sens 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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_tia_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_tia_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for stroke_sah_hs_unvax_sens - electively_unvaccinated 

  Analysis_cox_stroke_sah_hs_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_unvax_sens 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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_sah_hs_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_sah_hs_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for hf_unvax_sens - electively_unvaccinated 

  Analysis_cox_hf_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R hf_unvax_sens 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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_hf_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_hf_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for angina_unvax_sens - electively_unvaccinated 

  Analysis_cox_angina_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R angina_unvax_sens 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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_angina_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_angina_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for ate_unvax_sens - electively_unvaccinated 

  Analysis_cox_ate_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ate_unvax_sens 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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ate_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ate_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for vte_unvax_sens - electively_unvaccinated 

  Analysis_cox_vte_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R vte_unvax_sens 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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_vte_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_vte_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for ami_primary_position_unvax_sens - electively_unvaccinated

    

  Analysis_cox_ami_primary_position_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position_unvax_sens
      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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ami_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ami_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for stroke_isch_primary_position_unvax_sens - electively_unvaccinated

    

  Analysis_cox_stroke_isch_primary_position_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position_unvax_sens
      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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_isch_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_isch_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for dvt_primary_position_unvax_sens - electively_unvaccinated

    

  Analysis_cox_dvt_primary_position_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position_unvax_sens
      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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_dvt_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_dvt_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for pe_primary_position_unvax_sens - electively_unvaccinated 

  Analysis_cox_pe_primary_position_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position_unvax_sens
      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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_pe_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_pe_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for tia_primary_position_unvax_sens - electively_unvaccinated

    

  Analysis_cox_tia_primary_position_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position_unvax_sens
      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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_tia_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_tia_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for stroke_sah_hs_primary_position_unvax_sens - electively_unvaccinated

    

  Analysis_cox_stroke_sah_hs_primary_position_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position_unvax_sens
      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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_sah_hs_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_sah_hs_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for hf_primary_position_unvax_sens - electively_unvaccinated 

  Analysis_cox_hf_primary_position_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position_unvax_sens
      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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_hf_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_hf_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for angina_primary_position_unvax_sens - electively_unvaccinated

    

  Analysis_cox_angina_primary_position_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position_unvax_sens
      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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_angina_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_angina_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for ate_primary_position_unvax_sens - electively_unvaccinated

    

  Analysis_cox_ate_primary_position_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position_unvax_sens
      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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ate_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ate_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv

  ## Cox model for vte_primary_position_unvax_sens - electively_unvaccinated

    

  Analysis_cox_vte_primary_position_unvax_sens_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position_unvax_sens
      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_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_unvax_sens_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_unvax_sens_electively_unvaccinated.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_unvax_sens_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_vte_primary_position_unvax_sens_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_vte_primary_position_unvax_sens_*_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_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_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_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_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_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_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_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

  stata_cox_model_ami_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ami_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ami_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_stroke_isch_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_stroke_isch_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_dvt_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_dvt_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_dvt_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_pe_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_hf_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_hf_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_angina_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_angina_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_angina_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_ate_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ate_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_ate_primary_position_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_primary_position_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ate_primary_position_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_primary_position_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_primary_position_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_primary_position_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_primary_position_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_primary_position_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_primary_position_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_primary_position_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model.txt

  stata_cox_day_zero_ami_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ami_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ami_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_dvt_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_dvt_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_dvt_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_dvt_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_pe_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_hf_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_angina_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_angina_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_angina_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_angina_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ate_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ate_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_vte_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_primary_position_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_primary_position_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ami_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_primary_position_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ami_primary_position_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_primary_position_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_primary_position_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_primary_position_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_primary_position_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_primary_position_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_primary_position_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_pe_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_primary_position_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_pe_primary_position_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_primary_position_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_primary_position_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ate_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_primary_position_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ate_primary_position_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_primary_position_main_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_primary_position_main_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_primary_position_main_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_vte_primary_position_main_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_ami_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_dvt_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_dvt_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_angina_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_dvt_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_angina_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_primary_position_covid_pheno_hospitalised_vaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_vaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_ami_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_dvt_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_dvt_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_angina_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ami_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ami_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_covid_pheno_non_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_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_dvt_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_dvt_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_dvt_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_dvt_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_pe_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_angina_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_angina_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_angina_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_angina_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ate_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ate_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_vte_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_ami_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ami_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods
    needs:
    - Analysis_cox_pe_primary_position_electively_unvaccinated
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_pe_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.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_day_zero.csv
        stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_primary_position_covid_pheno_non_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_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_primary_position_covid_pheno_non_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_non_hospitalised_electively_unvaccinated_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced_time_periods_cox_model_day_zero.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_hf_main_electively_unvaccinated_reduced
    - stata_cox_model_hf_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_vte_sex_Male_electively_unvaccinated_reduced
    - stata_cox_model_vte_agegp_60_79_electively_unvaccinated_reduced
    - stata_cox_model_vte_ethnicity_Black_electively_unvaccinated_reduced
    - 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
    - stata_cox_model_ami_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_stroke_isch_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_dvt_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_pe_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_hf_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_angina_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_ate_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_vte_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_ate_primary_position_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_model_vte_primary_position_unvax_sens_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_ami_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_stroke_isch_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_dvt_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_pe_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_hf_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_angina_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_ate_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_vte_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_ami_primary_position_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_stroke_isch_primary_position_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_pe_primary_position_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_ate_primary_position_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_vte_primary_position_main_electively_unvaccinated_reduced
    - stata_cox_day_zero_ami_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_stroke_isch_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_dvt_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_pe_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_hf_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_angina_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_ate_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_vte_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_ami_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_dvt_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_pe_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_hf_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_angina_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_ate_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_vte_primary_position_covid_pheno_hospitalised_vaccinated_reduced
    - stata_cox_day_zero_ami_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_stroke_isch_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_dvt_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_pe_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_hf_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_angina_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_ate_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_vte_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_ate_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_vte_primary_position_covid_pheno_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_ami_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_stroke_isch_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_dvt_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_pe_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_hf_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_angina_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_ate_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_vte_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_ami_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_pe_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_hf_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_ate_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    - stata_cox_day_zero_vte_primary_position_covid_pheno_non_hospitalised_electively_unvaccinated_reduced
    outputs:
      moderately_sensitive:
        stata_output: output/stata_output.csv

  format_R_output:
    run: r:latest analysis/model/07_combine_HRs_to_one_file.R
    needs:
    - Analysis_cox_ami_electively_unvaccinated
    - Analysis_cox_ami_vaccinated
    - Analysis_cox_ami_primary_position_electively_unvaccinated
    - Analysis_cox_ami_primary_position_vaccinated
    - Analysis_cox_angina_electively_unvaccinated
    - Analysis_cox_angina_vaccinated
    - Analysis_cox_angina_primary_position_electively_unvaccinated
    - Analysis_cox_angina_primary_position_vaccinated
    - Analysis_cox_ate_electively_unvaccinated
    - Analysis_cox_ate_vaccinated
    - Analysis_cox_ate_primary_position_electively_unvaccinated
    - Analysis_cox_ate_primary_position_vaccinated
    - Analysis_cox_dvt_electively_unvaccinated
    - Analysis_cox_dvt_vaccinated
    - Analysis_cox_dvt_primary_position_electively_unvaccinated
    - Analysis_cox_dvt_primary_position_vaccinated
    - Analysis_cox_hf_electively_unvaccinated
    - Analysis_cox_hf_vaccinated
    - Analysis_cox_hf_primary_position_electively_unvaccinated
    - Analysis_cox_hf_primary_position_vaccinated
    - Analysis_cox_pe_electively_unvaccinated
    - Analysis_cox_pe_vaccinated
    - Analysis_cox_pe_primary_position_electively_unvaccinated
    - Analysis_cox_pe_primary_position_vaccinated
    - Analysis_cox_stroke_isch_electively_unvaccinated
    - Analysis_cox_stroke_isch_vaccinated
    - Analysis_cox_stroke_isch_primary_position_electively_unvaccinated
    - Analysis_cox_stroke_isch_primary_position_vaccinated
    - Analysis_cox_stroke_sah_hs_electively_unvaccinated
    - Analysis_cox_stroke_sah_hs_vaccinated
    - Analysis_cox_stroke_sah_hs_primary_position_electively_unvaccinated
    - Analysis_cox_stroke_sah_hs_primary_position_vaccinated
    - Analysis_cox_tia_electively_unvaccinated
    - Analysis_cox_tia_vaccinated
    - Analysis_cox_tia_primary_position_electively_unvaccinated
    - Analysis_cox_tia_primary_position_vaccinated
    - Analysis_cox_vte_electively_unvaccinated
    - Analysis_cox_vte_vaccinated
    - Analysis_cox_vte_primary_position_electively_unvaccinated
    - Analysis_cox_vte_primary_position_vaccinated
    - Analysis_cox_ami_unvax_sens_electively_unvaccinated
    - Analysis_cox_stroke_isch_unvax_sens_electively_unvaccinated
    - Analysis_cox_dvt_unvax_sens_electively_unvaccinated
    - Analysis_cox_pe_unvax_sens_electively_unvaccinated
    - Analysis_cox_tia_unvax_sens_electively_unvaccinated
    - Analysis_cox_stroke_sah_hs_unvax_sens_electively_unvaccinated
    - Analysis_cox_hf_unvax_sens_electively_unvaccinated
    - Analysis_cox_angina_unvax_sens_electively_unvaccinated
    - Analysis_cox_ate_unvax_sens_electively_unvaccinated
    - Analysis_cox_vte_unvax_sens_electively_unvaccinated
    - Analysis_cox_ami_primary_position_unvax_sens_electively_unvaccinated
    - Analysis_cox_stroke_isch_primary_position_unvax_sens_electively_unvaccinated
    - Analysis_cox_dvt_primary_position_unvax_sens_electively_unvaccinated
    - Analysis_cox_pe_primary_position_unvax_sens_electively_unvaccinated
    - Analysis_cox_tia_primary_position_unvax_sens_electively_unvaccinated
    - Analysis_cox_stroke_sah_hs_primary_position_unvax_sens_electively_unvaccinated
    - Analysis_cox_hf_primary_position_unvax_sens_electively_unvaccinated
    - Analysis_cox_angina_primary_position_unvax_sens_electively_unvaccinated
    - Analysis_cox_ate_primary_position_unvax_sens_electively_unvaccinated
    - Analysis_cox_vte_primary_position_unvax_sens_electively_unvaccinated
    outputs:
      moderately_sensitive:
        R_output: output/review/model/R_HR_output.csv
        R_event_counts: output/review/model/R_event_count_output.csv
        R_event_counts_day_zero: output/review/model/R_event_count_day_zero_output.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:13:27

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Job information

Status
Succeeded
Backend
TPP
Requested by
Rochelle Knight
Branch
main
Force run dependencies
No
Git commit hash
1fcffd0
Requested actions
  • stage2_missing_table1_both