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Job request: 16918

Organisation:
University of Bristol
Workspace:
post-covid-gastrointestinal
ID:
wobub4bp4srmejc2
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Marwa Al Arab 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.

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Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 200000

actions:

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

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

  ## Generate prelim study_definition 

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

  ## Generate dates for all study cohorts 

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

  ## Generate study population - prevax 

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

  ## Generate study population - unvax 

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

  ## Generate study population - vax 

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

  ## Preprocess data - prevax 

  preprocess_data_prevax:
    run: r:latest analysis/preprocess/preprocess_data.R prevax
    needs:
    - generate_index_dates
    - generate_study_population_prevax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_prevax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_prevax.txt
      highly_sensitive:
        cohort: output/input_prevax.rds
        venn: output/venn_prevax.rds

  ## Preprocess data - unvax 

  preprocess_data_unvax:
    run: r:latest analysis/preprocess/preprocess_data.R unvax
    needs:
    - generate_index_dates
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_unvax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_unvax.txt
      highly_sensitive:
        cohort: output/input_unvax.rds
        venn: output/venn_unvax.rds

  ## Preprocess data - vax 

  preprocess_data_vax:
    run: r:latest analysis/preprocess/preprocess_data.R vax
    needs:
    - generate_index_dates
    - generate_study_population_vax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_vax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_vax.txt
      highly_sensitive:
        cohort: output/input_vax.rds
        venn: output/venn_vax.rds

  count_study_def_variables:
    run: r:latest analysis/descriptives/intitial_input_counts.R
    needs:
    - generate_study_population_prevax
    - generate_study_population_unvax
    - generate_study_population_vax
    - preprocess_data_prevax
    - preprocess_data_unvax
    - preprocess_data_vax
    outputs:
      moderately_sensitive:
        counts: output/study_counts_prepro.txt
        vax_summary: output/describe_prepro_vax.txt
        prevax_summary: output/describe_prepro_prevax.txt
        unvax_summary: output/describe_prepro_unvax.txt

  ## Stage 1 - data cleaning - prevax 

  stage1_data_cleaning_prevax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
    needs:
    - vax_eligibility_inputs
    - preprocess_data_prevax
    outputs:
      moderately_sensitive:
        consort: output/consort_prevax.csv
        consort_rounded: output/consort_prevax_rounded.csv
      highly_sensitive:
        cohort: output/input_prevax_stage1.rds

  ## Stage 1 - data cleaning - unvax 

  stage1_data_cleaning_unvax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
    needs:
    - vax_eligibility_inputs
    - preprocess_data_unvax
    outputs:
      moderately_sensitive:
        consort: output/consort_unvax.csv
        consort_rounded: output/consort_unvax_rounded.csv
      highly_sensitive:
        cohort: output/input_unvax_stage1.rds

  ## Stage 1 - data cleaning - vax 

  stage1_data_cleaning_vax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R vax
    needs:
    - vax_eligibility_inputs
    - preprocess_data_vax
    outputs:
      moderately_sensitive:
        consort: output/consort_vax.csv
        consort_rounded: output/consort_vax_rounded.csv
      highly_sensitive:
        cohort: output/input_vax_stage1.rds

  ## Run models 

  make_model_input-cohort_prevax-main-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-acute_pancreatitis
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-acute_pancreatitis.rds

  cox_ipw-cohort_prevax-main-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_prevax-main-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-acute_pancreatitis.csv

  make_model_input-cohort_prevax-main-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-appendicitis
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-appendicitis.rds

  cox_ipw-cohort_prevax-main-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-appendicitis.csv
    needs:
    - make_model_input-cohort_prevax-main-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-appendicitis.csv

  make_model_input-cohort_prevax-main-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-dyspepsia
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-dyspepsia.rds

  cox_ipw-cohort_prevax-main-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-dyspepsia.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-dyspepsia.csv
    needs:
    - make_model_input-cohort_prevax-main-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-dyspepsia.csv

  make_model_input-cohort_prevax-main-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-gallstones_disease
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-gallstones_disease.rds

  cox_ipw-cohort_prevax-main-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-gallstones_disease.csv
    needs:
    - make_model_input-cohort_prevax-main-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-gallstones_disease.csv

  make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease.rds

  cox_ipw-cohort_prevax-main-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_prevax-main-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-ibs
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-ibs.rds

  cox_ipw-cohort_prevax-main-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-ibs.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-ibs.csv
    needs:
    - make_model_input-cohort_prevax-main-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-ibs.csv

  make_model_input-cohort_prevax-main-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-lower_gi_bleeding.rds

  cox_ipw-cohort_prevax-main-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-main-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-lower_gi_bleeding.csv

  make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-nonalcoholic_steatohepatitis.rds

  cox_ipw-cohort_prevax-main-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-nonvariceal_gi_bleeding.rds

  cox_ipw-cohort_prevax-main-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_prevax-main-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-peptic_ulcer
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-peptic_ulcer.rds

  cox_ipw-cohort_prevax-main-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_prevax-main-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-peptic_ulcer.csv

  make_model_input-cohort_prevax-main-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-upper_gi_bleeding.rds

  cox_ipw-cohort_prevax-main-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-main-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-upper_gi_bleeding.csv

  make_model_input-cohort_prevax-main-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-variceal_gi_bleeding.rds

  cox_ipw-cohort_prevax-main-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-main-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-variceal_gi_bleeding.csv

  make_model_input-cohort_unvax-main-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-acute_pancreatitis
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-acute_pancreatitis.rds

  cox_ipw-cohort_unvax-main-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_unvax-main-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-acute_pancreatitis.csv

  make_model_input-cohort_unvax-main-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-appendicitis
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-appendicitis.rds

  cox_ipw-cohort_unvax-main-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-appendicitis.csv
    needs:
    - make_model_input-cohort_unvax-main-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-appendicitis.csv

  make_model_input-cohort_unvax-main-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-dyspepsia
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-dyspepsia.rds

  cox_ipw-cohort_unvax-main-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-dyspepsia.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-dyspepsia.csv
    needs:
    - make_model_input-cohort_unvax-main-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-dyspepsia.csv

  make_model_input-cohort_unvax-main-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-gallstones_disease
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-gallstones_disease.rds

  cox_ipw-cohort_unvax-main-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-gallstones_disease.csv
    needs:
    - make_model_input-cohort_unvax-main-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-gallstones_disease.csv

  make_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease.rds

  cox_ipw-cohort_unvax-main-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_unvax-main-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-ibs
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-ibs.rds

  cox_ipw-cohort_unvax-main-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-ibs.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-ibs.csv
    needs:
    - make_model_input-cohort_unvax-main-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-ibs.csv

  make_model_input-cohort_unvax-main-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-lower_gi_bleeding.rds

  cox_ipw-cohort_unvax-main-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-main-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-lower_gi_bleeding.csv

  make_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-nonalcoholic_steatohepatitis.rds

  cox_ipw-cohort_unvax-main-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_unvax-main-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-nonvariceal_gi_bleeding.rds

  cox_ipw-cohort_unvax-main-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-main-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_unvax-main-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-peptic_ulcer
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-peptic_ulcer.rds

  cox_ipw-cohort_unvax-main-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_unvax-main-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-peptic_ulcer.csv

  make_model_input-cohort_unvax-main-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-upper_gi_bleeding.rds

  cox_ipw-cohort_unvax-main-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-main-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-upper_gi_bleeding.csv

  make_model_input-cohort_unvax-main-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-variceal_gi_bleeding.rds

  cox_ipw-cohort_unvax-main-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-main-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-variceal_gi_bleeding.csv

  make_model_input-cohort_vax-main-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-acute_pancreatitis
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-acute_pancreatitis.rds

  cox_ipw-cohort_vax-main-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_vax-main-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-acute_pancreatitis.csv

  make_model_input-cohort_vax-main-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-appendicitis
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-appendicitis.rds

  cox_ipw-cohort_vax-main-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-appendicitis.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-appendicitis.csv
    needs:
    - make_model_input-cohort_vax-main-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-appendicitis.csv

  make_model_input-cohort_vax-main-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-dyspepsia
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-dyspepsia.rds

  cox_ipw-cohort_vax-main-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-dyspepsia.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-dyspepsia.csv
    needs:
    - make_model_input-cohort_vax-main-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-dyspepsia.csv

  make_model_input-cohort_vax-main-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-gallstones_disease
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-gallstones_disease.rds

  cox_ipw-cohort_vax-main-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-gallstones_disease.csv
    needs:
    - make_model_input-cohort_vax-main-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-gallstones_disease.csv

  make_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-gastro_oesophageal_reflux_disease.rds

  cox_ipw-cohort_vax-main-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_vax-main-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-ibs
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-ibs.rds

  cox_ipw-cohort_vax-main-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-ibs.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-ibs.csv
    needs:
    - make_model_input-cohort_vax-main-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-ibs.csv

  make_model_input-cohort_vax-main-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-lower_gi_bleeding.rds

  cox_ipw-cohort_vax-main-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-main-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-lower_gi_bleeding.csv

  make_model_input-cohort_vax-main-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-nonalcoholic_steatohepatitis.rds

  cox_ipw-cohort_vax-main-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_vax-main-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_vax-main-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-nonvariceal_gi_bleeding.rds

  cox_ipw-cohort_vax-main-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-main-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_vax-main-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-peptic_ulcer
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-peptic_ulcer.rds

  cox_ipw-cohort_vax-main-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-peptic_ulcer.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_vax-main-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-peptic_ulcer.csv

  make_model_input-cohort_vax-main-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-upper_gi_bleeding.rds

  cox_ipw-cohort_vax-main-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-main-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-upper_gi_bleeding.csv

  make_model_input-cohort_vax-main-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-variceal_gi_bleeding.rds

  cox_ipw-cohort_vax-main-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-main-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-variceal_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_age_18_39-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-acute_pancreatitis
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-acute_pancreatitis.rds

  cox_ipw-cohort_prevax-sub_age_18_39-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-acute_pancreatitis.csv

  make_model_input-cohort_prevax-sub_age_18_39-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-appendicitis
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-appendicitis.rds

  cox_ipw-cohort_prevax-sub_age_18_39-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-appendicitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-appendicitis.csv

  make_model_input-cohort_prevax-sub_age_18_39-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-dyspepsia
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-dyspepsia.rds

  cox_ipw-cohort_prevax-sub_age_18_39-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-dyspepsia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-dyspepsia.csv

  make_model_input-cohort_prevax-sub_age_18_39-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-gallstones_disease
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-gallstones_disease.rds

  cox_ipw-cohort_prevax-sub_age_18_39-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-gallstones_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-gallstones_disease.csv

  make_model_input-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds

  cox_ipw-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_prevax-sub_age_18_39-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-ibs
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-ibs.rds

  cox_ipw-cohort_prevax-sub_age_18_39-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-ibs.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-ibs.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-ibs.csv

  make_model_input-cohort_prevax-sub_age_18_39-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-lower_gi_bleeding.rds

  cox_ipw-cohort_prevax-sub_age_18_39-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-lower_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis.rds

  cox_ipw-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding.rds

  cox_ipw-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_age_18_39-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-peptic_ulcer
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-peptic_ulcer.rds

  cox_ipw-cohort_prevax-sub_age_18_39-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-peptic_ulcer.csv

  make_model_input-cohort_prevax-sub_age_18_39-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-upper_gi_bleeding.rds

  cox_ipw-cohort_prevax-sub_age_18_39-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-upper_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_age_18_39-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-variceal_gi_bleeding.rds

  cox_ipw-cohort_prevax-sub_age_18_39-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-variceal_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_age_18_39-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-acute_pancreatitis
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-acute_pancreatitis.rds

  cox_ipw-cohort_unvax-sub_age_18_39-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-acute_pancreatitis.csv

  make_model_input-cohort_unvax-sub_age_18_39-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-appendicitis
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-appendicitis.rds

  cox_ipw-cohort_unvax-sub_age_18_39-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-appendicitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-appendicitis.csv

  make_model_input-cohort_unvax-sub_age_18_39-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-dyspepsia
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-dyspepsia.rds

  cox_ipw-cohort_unvax-sub_age_18_39-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-dyspepsia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-dyspepsia.csv

  make_model_input-cohort_unvax-sub_age_18_39-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-gallstones_disease
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-gallstones_disease.rds

  cox_ipw-cohort_unvax-sub_age_18_39-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-gallstones_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-gallstones_disease.csv

  make_model_input-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds

  cox_ipw-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_unvax-sub_age_18_39-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-ibs
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-ibs.rds

  cox_ipw-cohort_unvax-sub_age_18_39-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-ibs.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-ibs.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-ibs.csv

  make_model_input-cohort_unvax-sub_age_18_39-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-lower_gi_bleeding.rds

  cox_ipw-cohort_unvax-sub_age_18_39-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-lower_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis.rds

  cox_ipw-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding.rds

  cox_ipw-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_age_18_39-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-peptic_ulcer
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-peptic_ulcer.rds

  cox_ipw-cohort_unvax-sub_age_18_39-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-peptic_ulcer.csv

  make_model_input-cohort_unvax-sub_age_18_39-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-upper_gi_bleeding.rds

  cox_ipw-cohort_unvax-sub_age_18_39-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-upper_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_age_18_39-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-variceal_gi_bleeding.rds

  cox_ipw-cohort_unvax-sub_age_18_39-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-variceal_gi_bleeding.csv

  make_model_input-cohort_vax-sub_age_18_39-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-acute_pancreatitis
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-acute_pancreatitis.rds

  cox_ipw-cohort_vax-sub_age_18_39-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-acute_pancreatitis.csv

  make_model_input-cohort_vax-sub_age_18_39-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-appendicitis
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-appendicitis.rds

  cox_ipw-cohort_vax-sub_age_18_39-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-appendicitis.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-appendicitis.csv

  make_model_input-cohort_vax-sub_age_18_39-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-dyspepsia
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-dyspepsia.rds

  cox_ipw-cohort_vax-sub_age_18_39-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-dyspepsia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-dyspepsia.csv

  make_model_input-cohort_vax-sub_age_18_39-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-gallstones_disease
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-gallstones_disease.rds

  cox_ipw-cohort_vax-sub_age_18_39-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-gallstones_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-gallstones_disease.csv

  make_model_input-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds

  cox_ipw-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_vax-sub_age_18_39-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-ibs
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-ibs.rds

  cox_ipw-cohort_vax-sub_age_18_39-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-ibs.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-ibs.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-ibs.csv

  make_model_input-cohort_vax-sub_age_18_39-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-lower_gi_bleeding.rds

  cox_ipw-cohort_vax-sub_age_18_39-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-lower_gi_bleeding.csv

  make_model_input-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis.rds

  cox_ipw-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding.rds

  cox_ipw-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_vax-sub_age_18_39-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-peptic_ulcer
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-peptic_ulcer.rds

  cox_ipw-cohort_vax-sub_age_18_39-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-peptic_ulcer.csv

  make_model_input-cohort_vax-sub_age_18_39-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-upper_gi_bleeding.rds

  cox_ipw-cohort_vax-sub_age_18_39-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-upper_gi_bleeding.csv

  make_model_input-cohort_vax-sub_age_18_39-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_vax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-variceal_gi_bleeding.rds

  cox_ipw-cohort_vax-sub_age_18_39-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-variceal_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_age_40_59-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-acute_pancreatitis
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-acute_pancreatitis.rds

  cox_ipw-cohort_prevax-sub_age_40_59-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-acute_pancreatitis.csv

  make_model_input-cohort_prevax-sub_age_40_59-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-appendicitis
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-appendicitis.rds

  cox_ipw-cohort_prevax-sub_age_40_59-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-appendicitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-appendicitis.csv

  make_model_input-cohort_prevax-sub_age_40_59-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-dyspepsia
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-dyspepsia.rds

  cox_ipw-cohort_prevax-sub_age_40_59-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-dyspepsia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-dyspepsia.csv

  make_model_input-cohort_prevax-sub_age_40_59-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-gallstones_disease
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-gallstones_disease.rds

  cox_ipw-cohort_prevax-sub_age_40_59-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-gallstones_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-gallstones_disease.csv

  make_model_input-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease.rds

  cox_ipw-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_prevax-sub_age_40_59-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-ibs
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-ibs.rds

  cox_ipw-cohort_prevax-sub_age_40_59-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-ibs.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-ibs.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-ibs.csv

  make_model_input-cohort_prevax-sub_age_40_59-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-lower_gi_bleeding.rds

  cox_ipw-cohort_prevax-sub_age_40_59-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-lower_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis.rds

  cox_ipw-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding.rds

  cox_ipw-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_age_40_59-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-peptic_ulcer
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-peptic_ulcer.rds

  cox_ipw-cohort_prevax-sub_age_40_59-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-peptic_ulcer.csv

  make_model_input-cohort_prevax-sub_age_40_59-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-upper_gi_bleeding.rds

  cox_ipw-cohort_prevax-sub_age_40_59-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-upper_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_age_40_59-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-variceal_gi_bleeding.rds

  cox_ipw-cohort_prevax-sub_age_40_59-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-variceal_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_age_40_59-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-acute_pancreatitis
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-acute_pancreatitis.rds

  cox_ipw-cohort_unvax-sub_age_40_59-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-acute_pancreatitis.csv

  make_model_input-cohort_unvax-sub_age_40_59-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-appendicitis
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-appendicitis.rds

  cox_ipw-cohort_unvax-sub_age_40_59-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-appendicitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-appendicitis.csv

  make_model_input-cohort_unvax-sub_age_40_59-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-dyspepsia
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-dyspepsia.rds

  cox_ipw-cohort_unvax-sub_age_40_59-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-dyspepsia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-dyspepsia.csv

  make_model_input-cohort_unvax-sub_age_40_59-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-gallstones_disease
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-gallstones_disease.rds

  cox_ipw-cohort_unvax-sub_age_40_59-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-gallstones_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_outpu