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Job request: 14516

Organisation:
University of Bristol
Workspace:
post-covid-pre-vaccinated-cardiovascular
ID:
cqdx6nsjza3or57n
View repo View project.yaml

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:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  preprocess_data:
    run: r:latest analysis/preprocess/preprocess_data.R
    needs:
    - generate_study_population
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_stage0.txt
      highly_sensitive:
        cohort: output/input.rds
        venn: output/venn.rds

  stage1_data_cleaning:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R
    needs:
    - preprocess_data
    outputs:
      moderately_sensitive:
        QA_rules: output/review/descriptives/QA_summary.csv
        refactoring: output/not-for-review/meta_data_factors.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:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates.rds

  stage2_missing_table1:
    run: r:latest analysis/descriptives/Stage2_Missing_Table1.R
    needs:
    - stage1_data_cleaning
    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_pre_vaccination_cvd.csv

  table_2_original_follow_up_any_position_events:
    run: r:latest analysis/descriptives/table_2.R original_follow_up any_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        table_2: output/review/descriptives/table2_pre_vaccination_original_follow_up_any_position_events.csv

  table_2_extended_follow_up_any_position_events:
    run: r:latest analysis/descriptives/table_2.R extended_follow_up any_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        table_2: output/review/descriptives/table2_pre_vaccination_extended_follow_up_any_position_events.csv

  table_2_original_follow_up_primary_position_events:
    run: r:latest analysis/descriptives/table_2.R original_follow_up primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        table_2: output/review/descriptives/table2_pre_vaccination_original_follow_up_primary_position_events.csv

  table_2_extended_follow_up_primary_position_events:
    run: r:latest analysis/descriptives/table_2.R extended_follow_up primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        table_2: output/review/descriptives/table2_pre_vaccination_extended_follow_up_primary_position_events.csv

  venn_diagram:
    run: r:latest analysis/descriptives/venn_diagram.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_*

  days_to_event_histogram_original_follow_up:
    run: r:latest analysis/descriptives/histogram_data_post_exposure_days_to_event.R
      original_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        histogram_data: output/review/descriptives/histogram_data_pre_vaccination_original_follow_up.csv

  days_to_event_histogram_extended_follow_up:
    run: r:latest analysis/descriptives/histogram_data_post_exposure_days_to_event.R
      extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        histogram_data: output/review/descriptives/histogram_data_pre_vaccination_extended_follow_up.csv

  ## Apply cox model for ami 

  Analysis_cox_ami:
    run: r:latest analysis/model/01_cox_pipeline.R ami
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_ami_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ami_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ami_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_isch 

  Analysis_cox_stroke_isch:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_stroke_isch_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_isch_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_isch_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for dvt 

  Analysis_cox_dvt:
    run: r:latest analysis/model/01_cox_pipeline.R dvt
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_dvt_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_dvt_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_dvt_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for pe 

  Analysis_cox_pe:
    run: r:latest analysis/model/01_cox_pipeline.R pe
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_pe_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_pe_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_pe_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for tia 

  Analysis_cox_tia:
    run: r:latest analysis/model/01_cox_pipeline.R tia
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_tia_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_tia_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_tia_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_sah_hs 

  Analysis_cox_stroke_sah_hs:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_stroke_sah_hs_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_sah_hs_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_sah_hs_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for hf 

  Analysis_cox_hf:
    run: r:latest analysis/model/01_cox_pipeline.R hf
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_hf_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_hf_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_hf_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for angina 

  Analysis_cox_angina:
    run: r:latest analysis/model/01_cox_pipeline.R angina
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_angina_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_angina_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_angina_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for ami_extended_follow_up 

  Analysis_cox_ami_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R ami_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_ami_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ami_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ami_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_isch_extended_follow_up 

  Analysis_cox_stroke_isch_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_stroke_isch_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_isch_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_isch_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for dvt_extended_follow_up 

  Analysis_cox_dvt_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_dvt_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_dvt_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_dvt_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for pe_extended_follow_up 

  Analysis_cox_pe_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R pe_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_pe_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_pe_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_pe_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for tia_extended_follow_up 

  Analysis_cox_tia_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R tia_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_tia_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_tia_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_tia_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_sah_hs_extended_follow_up 

  Analysis_cox_stroke_sah_hs_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_stroke_sah_hs_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_sah_hs_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_sah_hs_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for hf_extended_follow_up 

  Analysis_cox_hf_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R hf_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_hf_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_hf_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_hf_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for angina_extended_follow_up 

  Analysis_cox_angina_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R angina_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_angina_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_angina_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_angina_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for ate 

  Analysis_cox_ate:
    run: r:latest analysis/model/01_cox_pipeline.R ate
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_ate_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ate_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ate_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for vte 

  Analysis_cox_vte:
    run: r:latest analysis/model/01_cox_pipeline.R vte
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_vte_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_vte_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_vte_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for ate_extended_follow_up 

  Analysis_cox_ate_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R ate_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_ate_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ate_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ate_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for vte_extended_follow_up 

  Analysis_cox_vte_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R vte_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_vte_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_vte_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_vte_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for ami_primary_position 

  Analysis_cox_ami_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_ami_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ami_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ami_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_isch_primary_position 

  Analysis_cox_stroke_isch_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_stroke_isch_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_isch_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_isch_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for dvt_primary_position 

  Analysis_cox_dvt_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_dvt_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_dvt_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_dvt_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for pe_primary_position 

  Analysis_cox_pe_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_pe_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_pe_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_pe_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for tia_primary_position 

  Analysis_cox_tia_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_tia_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_tia_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_tia_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_sah_hs_primary_position 

  Analysis_cox_stroke_sah_hs_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_stroke_sah_hs_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_sah_hs_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_sah_hs_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for hf_primary_position 

  Analysis_cox_hf_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_hf_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_hf_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_hf_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for angina_primary_position 

  Analysis_cox_angina_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_angina_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_angina_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_angina_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for ami_primary_position_extended_follow_up 

  Analysis_cox_ami_primary_position_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_ami_primary_position_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ami_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ami_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_isch_primary_position_extended_follow_up 

  Analysis_cox_stroke_isch_primary_position_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_stroke_isch_primary_position_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_isch_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_isch_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for dvt_primary_position_extended_follow_up 

  Analysis_cox_dvt_primary_position_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_dvt_primary_position_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_dvt_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_dvt_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for pe_primary_position_extended_follow_up 

  Analysis_cox_pe_primary_position_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_pe_primary_position_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_pe_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_pe_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for tia_primary_position_extended_follow_up 

  Analysis_cox_tia_primary_position_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_tia_primary_position_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_tia_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_tia_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_sah_hs_primary_position_extended_follow_up 

  Analysis_cox_stroke_sah_hs_primary_position_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_stroke_sah_hs_primary_position_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_sah_hs_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_sah_hs_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for hf_primary_position_extended_follow_up 

  Analysis_cox_hf_primary_position_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_hf_primary_position_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_hf_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_hf_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for angina_primary_position_extended_follow_up 

  Analysis_cox_angina_primary_position_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_angina_primary_position_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_angina_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_angina_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for ate_primary_position 

  Analysis_cox_ate_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_ate_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ate_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ate_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for vte_primary_position 

  Analysis_cox_vte_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_vte_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_vte_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_vte_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for ate_primary_position_extended_follow_up 

  Analysis_cox_ate_primary_position_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_ate_primary_position_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ate_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ate_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for vte_primary_position_extended_follow_up 

  Analysis_cox_vte_primary_position_extended_follow_up:
    run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position_extended_follow_up
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_extended_follow_up_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_extended_follow_up_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_extended_follow_up_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_vte_primary_position_extended_follow_up_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_vte_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_vte_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv

  stata_cox_model_ami_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_dvt_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_dvt
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_tia_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_tia
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_sah_hs
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_hf_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_angina_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_angina
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_ate_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_dvt_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_tia_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_angina_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_agegp_60_79_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_agegp_60_79_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_agegp_60_79_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_agegp_60_79_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_ethnicity_Other_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_ethnicity_Other_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_ethnicity_Other_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_ethnicity_Other_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_aer_Male_60_79_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_aer_Male_60_79_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_aer_Male_60_79_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_aer_Male_60_79_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_day_zero_ami_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_dvt_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_dvt
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_tia_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_tia
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_sah_hs
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_angina_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_angina
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_dvt_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_tia_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_angina_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ami_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_dvt_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_dvt_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_dvt
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_dvt_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_pe_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_tia_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_tia_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_tia
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_tia_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_tia_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_sah_hs_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_sah_hs_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_sah_hs
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_sah_hs_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_sah_hs_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_hf_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_angina_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_angina_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_angina
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_angina_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ate_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_vte_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_primary_position_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_primary_position_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ami_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_primary_position_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_primary_position_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_primary_position_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_primary_position_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_pe_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_primary_position_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_primary_position_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_hf_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_primary_position_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_primary_position_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ate_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_primary_position_main_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_primary_position_main_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_vte_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ami_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_dvt_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_dvt_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_dvt
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_dvt_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_sah_hs_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_sah_hs_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_sah_hs
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_sah_hs_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_sah_hs_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_angina_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_angina_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_angina
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_angina_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ate_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ami_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ami_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_pe_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_pe_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_stroke_sah_hs_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_sah_hs_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_sah_hs_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_sah_hs_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_stroke_sah_hs_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_hf_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_ate_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_day_zero_vte_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
        stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt

  stata_cox_extended_ami_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_ami_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_ami_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_stroke_isch_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_stroke_isch_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_stroke_isch_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_dvt_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_dvt_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_dvt_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_dvt_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_pe_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_pe_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_pe_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_tia_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_tia_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_tia_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_tia_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_tia_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_stroke_sah_hs_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_stroke_sah_hs_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_sah_hs_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_sah_hs_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_stroke_sah_hs_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_hf_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_hf_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_hf_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_angina_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_angina_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_angina_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_angina_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_ate_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_ate_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_ate_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_vte_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_vte_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_vte_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_ami_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_ami_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami_primary_position_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_ami_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_stroke_isch_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_stroke_isch_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_primary_position_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_stroke_isch_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_dvt_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_dvt_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_dvt_primary_position_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_dvt_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_pe_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_pe_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe_primary_position_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_pe_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_tia_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_tia_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_tia_primary_position_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_tia_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_tia_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_hf_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_hf_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf_primary_position_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_hf_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_angina_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_angina_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_angina_primary_position_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_angina_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_ate_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_ate_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate_primary_position_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_ate_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  stata_cox_extended_vte_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_vte_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte_primary_position_extended_follow_up
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
        stata_output: output/input_sampled_data_vte_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt

  format_stata_output:
    run: r:latest analysis/format_stata_output.R
    needs:
    - stata_cox_model_ami_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_dvt_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_pe_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_tia_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_hf_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_angina_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_ate_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_vte_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_vte_agegp_60_79_pre_vaccination_reduced
    - stata_cox_model_vte_ethnicity_Other_pre_vaccination_reduced
    - stata_cox_model_vte_aer_Male_60_79_pre_vaccination_reduced
    - stata_cox_day_zero_ami_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_dvt_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_pe_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_tia_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_hf_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_angina_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_ate_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_vte_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_ami_main_pre_vaccination_reduced
    - stata_cox_day_zero_stroke_isch_main_pre_vaccination_reduced
    - stata_cox_day_zero_dvt_main_pre_vaccination_reduced
    - stata_cox_day_zero_pe_main_pre_vaccination_reduced
    - stata_cox_day_zero_tia_main_pre_vaccination_reduced
    - stata_cox_day_zero_stroke_sah_hs_main_pre_vaccination_reduced
    - stata_cox_day_zero_hf_main_pre_vaccination_reduced
    - stata_cox_day_zero_angina_main_pre_vaccination_reduced
    - stata_cox_day_zero_ate_main_pre_vaccination_reduced
    - stata_cox_day_zero_vte_main_pre_vaccination_reduced
    - stata_cox_day_zero_ami_primary_position_main_pre_vaccination_reduced
    - stata_cox_day_zero_stroke_isch_primary_position_main_pre_vaccination_reduced
    - stata_cox_day_zero_pe_primary_position_main_pre_vaccination_reduced
    - stata_cox_day_zero_hf_primary_position_main_pre_vaccination_reduced
    - stata_cox_day_zero_ate_primary_position_main_pre_vaccination_reduced
    - stata_cox_day_zero_vte_primary_position_main_pre_vaccination_reduced
    - stata_cox_day_zero_ami_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_stroke_isch_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_dvt_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_pe_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_stroke_sah_hs_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_hf_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_angina_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_ate_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_vte_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_ami_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_pe_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_stroke_sah_hs_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_hf_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_ate_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_day_zero_vte_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_ami_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_stroke_isch_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_dvt_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_pe_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_tia_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_stroke_sah_hs_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_hf_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_angina_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_ate_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_vte_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_ami_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_stroke_isch_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_dvt_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_pe_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_tia_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_hf_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_angina_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_ate_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_extended_vte_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_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
    - Analysis_cox_stroke_isch
    - Analysis_cox_dvt
    - Analysis_cox_pe
    - Analysis_cox_tia
    - Analysis_cox_stroke_sah_hs
    - Analysis_cox_hf
    - Analysis_cox_angina
    - Analysis_cox_ami_extended_follow_up
    - Analysis_cox_stroke_isch_extended_follow_up
    - Analysis_cox_dvt_extended_follow_up
    - Analysis_cox_pe_extended_follow_up
    - Analysis_cox_tia_extended_follow_up
    - Analysis_cox_stroke_sah_hs_extended_follow_up
    - Analysis_cox_hf_extended_follow_up
    - Analysis_cox_angina_extended_follow_up
    - Analysis_cox_ate
    - Analysis_cox_vte
    - Analysis_cox_ate_extended_follow_up
    - Analysis_cox_vte_extended_follow_up
    - Analysis_cox_ami_primary_position
    - Analysis_cox_stroke_isch_primary_position
    - Analysis_cox_dvt_primary_position
    - Analysis_cox_pe_primary_position
    - Analysis_cox_tia_primary_position
    - Analysis_cox_stroke_sah_hs_primary_position
    - Analysis_cox_hf_primary_position
    - Analysis_cox_angina_primary_position
    - Analysis_cox_ami_primary_position_extended_follow_up
    - Analysis_cox_stroke_isch_primary_position_extended_follow_up
    - Analysis_cox_dvt_primary_position_extended_follow_up
    - Analysis_cox_pe_primary_position_extended_follow_up
    - Analysis_cox_tia_primary_position_extended_follow_up
    - Analysis_cox_stroke_sah_hs_primary_position_extended_follow_up
    - Analysis_cox_hf_primary_position_extended_follow_up
    - Analysis_cox_angina_primary_position_extended_follow_up
    - Analysis_cox_ate_primary_position
    - Analysis_cox_vte_primary_position
    - Analysis_cox_ate_primary_position_extended_follow_up
    - Analysis_cox_vte_primary_position_extended_follow_up
    outputs:
      moderately_sensitive:
        R_output: output/review/model/R_HR_output.csv
        R_event_counts: output/review/model/R_event_count_output.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:18:53

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Failed
Backend
TPP
Workspace
post-covid-pre-vaccinated-cardiovascular
Requested by
Rochelle Knight
Branch
main
Force run dependencies
No
Git commit hash
5c0d2f4
Requested actions
  • days_to_event_histogram_original_follow_up
  • days_to_event_histogram_extended_follow_up