project.yaml

version: '3.0'

expectations:

  population_size: 150000

actions:

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

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

  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_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

  ## Generate study population history - prevax 

  generate_study_population_history_prevax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_history
      --output-format csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_prevax_history.csv.gz

  ## Generate study population history - unvax 

  generate_study_population_history_unvax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax_history
      --output-format csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_unvax_history.csv.gz

  ## Generate study population history - vax 

  generate_study_population_history_vax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax_history
      --output-format csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_vax_history.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:
      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:
      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:
      highly_sensitive:
        cohort: output/input_vax.rds
        venn: output/venn_vax.rds

  ## 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_midpoint6: output/consort_prevax_midpoint6.csv
      highly_sensitive:
        cohort: output/input_prevax_stage1.rds

  describe_stage1_data_cleaning_prevax:
    run: r:latest analysis/model/describe_file.R input_prevax_stage1 rds
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_prevax_stage1.txt

  ## 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_midpoint6: output/consort_unvax_midpoint6.csv
      highly_sensitive:
        cohort: output/input_unvax_stage1.rds

  describe_stage1_data_cleaning_unvax:
    run: r:latest analysis/model/describe_file.R input_unvax_stage1 rds
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_unvax_stage1.txt

  ## 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_midpoint6: output/consort_vax_midpoint6.csv
      highly_sensitive:
        cohort: output/input_vax_stage1.rds

  describe_stage1_data_cleaning_vax:
    run: r:latest analysis/model/describe_file.R input_vax_stage1 rds
    needs:
    - stage1_data_cleaning_vax
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_vax_stage1.txt

  ## Join stage1 and history data - prevax 

  preprocess_stage1_history_data_cleaning_prevax:
    run: r:latest analysis/preprocess/preprocess_stage1_history_data_cleaning.R prevax
    needs:
    - stage1_data_cleaning_prevax
    - generate_study_population_history_prevax
    outputs:
      highly_sensitive:
        cohort_final: output/input_prevax_new_stage1.rds

  ## Join stage1 and history data - unvax 

  preprocess_stage1_history_data_cleaning_unvax:
    run: r:latest analysis/preprocess/preprocess_stage1_history_data_cleaning.R unvax
    needs:
    - stage1_data_cleaning_unvax
    - generate_study_population_history_unvax
    outputs:
      highly_sensitive:
        cohort_final: output/input_unvax_new_stage1.rds

  ## Join stage1 and history data - vax 

  preprocess_stage1_history_data_cleaning_vax:
    run: r:latest analysis/preprocess/preprocess_stage1_history_data_cleaning.R vax
    needs:
    - stage1_data_cleaning_vax
    - generate_study_population_history_vax
    outputs:
      highly_sensitive:
        cohort_final: output/input_vax_new_stage1.rds

  make_consort_output:
    run: r:latest analysis/model/make_other_output.R consort prevax;vax;unvax
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        consort_output_midpoint6: output/consort_output_midpoint6.csv

  make_table1_output:
    run: r:latest analysis/model/make_other_output.R table1 prevax;vax;unvax
    needs:
    - table1_prevax
    - table1_vax
    - table1_unvax
    outputs:
      moderately_sensitive:
        table1_output_midpoint6: output/table1_output_midpoint6.csv

  make_extendedtable1_part1_output:
    run: r:latest analysis/model/make_other_output.R extendedtable1_part1 prevax;vax;unvax
    needs:
    - extendedtable1_part1_prevax
    - extendedtable1_part1_vax
    - extendedtable1_part1_unvax
    outputs:
      moderately_sensitive:
        table1_output_midpoint6: output/extendedtable1_part1_output_midpoint6.csv

  make_extendedtable1_part2_output:
    run: r:latest analysis/model/make_other_output.R extendedtable1_part2 prevax;vax;unvax
    needs:
    - extendedtable1_part2_prevax
    - extendedtable1_part2_vax
    - extendedtable1_part2_unvax
    outputs:
      moderately_sensitive:
        table1_output_midpoint6: output/extendedtable1_part2_output_midpoint6.csv

  make_table2_output:
    run: r:latest analysis/model/make_other_output.R table2 prevax;vax;unvax
    needs:
    - table2_prevax
    - table2_vax
    - table2_unvax
    outputs:
      moderately_sensitive:
        table2_output_midpoint6: output/table2_output_midpoint6.csv

  ## Table 1 - prevax 

  table1_prevax:
    run: r:latest analysis/descriptives/table1.R prevax
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        table1: output/table1_prevax.csv
        table1_midpoint6: output/table1_prevax_midpoint6.csv

  extendedtable1_part1_prevax:
    run: r:latest analysis/descriptives/extendedtable1_part1.R prevax
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        extendedtable1_part1: output/extendedtable1_part1_prevax.csv
        extendedtable1_part1_midpoint6: output/extendedtable1_part1_prevax_midpoint6.csv

  extendedtable1_part2_prevax:
    run: r:latest analysis/descriptives/extendedtable1_part2.R prevax
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        extendedtable1_part2: output/extendedtable1_part2_prevax.csv
        extendedtable1_part2_midpoint6: output/extendedtable1_part2_prevax_midpoint6.csv

  ## Table 1 - unvax 

  table1_unvax:
    run: r:latest analysis/descriptives/table1.R unvax
    needs:
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        table1: output/table1_unvax.csv
        table1_midpoint6: output/table1_unvax_midpoint6.csv

  extendedtable1_part1_unvax:
    run: r:latest analysis/descriptives/extendedtable1_part1.R unvax
    needs:
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        extendedtable1_part1: output/extendedtable1_part1_unvax.csv
        extendedtable1_part1_midpoint6: output/extendedtable1_part1_unvax_midpoint6.csv

  extendedtable1_part2_unvax:
    run: r:latest analysis/descriptives/extendedtable1_part2.R unvax
    needs:
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        extendedtable1_part2: output/extendedtable1_part2_unvax.csv
        extendedtable1_part2_midpoint6: output/extendedtable1_part2_unvax_midpoint6.csv

  ## Table 1 - vax 

  table1_vax:
    run: r:latest analysis/descriptives/table1.R vax
    needs:
    - preprocess_stage1_history_data_cleaning_vax
    outputs:
      moderately_sensitive:
        table1: output/table1_vax.csv
        table1_midpoint6: output/table1_vax_midpoint6.csv

  extendedtable1_part1_vax:
    run: r:latest analysis/descriptives/extendedtable1_part1.R vax
    needs:
    - preprocess_stage1_history_data_cleaning_vax
    outputs:
      moderately_sensitive:
        extendedtable1_part1: output/extendedtable1_part1_vax.csv
        extendedtable1_part1_midpoint6: output/extendedtable1_part1_vax_midpoint6.csv

  extendedtable1_part2_vax:
    run: r:latest analysis/descriptives/extendedtable1_part2.R vax
    needs:
    - preprocess_stage1_history_data_cleaning_vax
    outputs:
      moderately_sensitive:
        extendedtable1_part2: output/extendedtable1_part2_vax.csv
        extendedtable1_part2_midpoint6: output/extendedtable1_part2_vax_midpoint6.csv

  ## Stage 5 - Run models 

  make_model_input-cohort_prevax-sub_age_18_39-addison:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-addison.rds

  cox_ipw-cohort_prevax-sub_age_18_39-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-addison.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-addison.csv

  make_model_input-cohort_prevax-sub_age_18_39-apa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-apa.rds

  cox_ipw-cohort_prevax-sub_age_18_39-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-apa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-apa.csv

  make_model_input-cohort_prevax-sub_age_18_39-axial:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-axial.rds

  cox_ipw-cohort_prevax-sub_age_18_39-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-axial.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-axial.csv

  make_model_input-cohort_prevax-sub_age_18_39-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-celiac.rds

  cox_ipw-cohort_prevax-sub_age_18_39-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-celiac.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-celiac.csv

  make_model_input-cohort_prevax-sub_age_18_39-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-composite_ai.rds

  cox_ipw-cohort_prevax-sub_age_18_39-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-composite_ai.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-composite_ai.csv

  make_model_input-cohort_prevax-sub_age_18_39-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-crohn.rds

  cox_ipw-cohort_prevax-sub_age_18_39-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-crohn.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-crohn.csv

  make_model_input-cohort_prevax-sub_age_18_39-grave:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-grave.rds

  cox_ipw-cohort_prevax-sub_age_18_39-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grave.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-grave.csv

  make_model_input-cohort_prevax-sub_age_18_39-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-grp1_ifa.rds

  cox_ipw-cohort_prevax-sub_age_18_39-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp1_ifa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-grp1_ifa.csv

  make_model_input-cohort_prevax-sub_age_18_39-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-grp2_ctd.rds

  cox_ipw-cohort_prevax-sub_age_18_39-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp2_ctd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-grp2_ctd.csv

  make_model_input-cohort_prevax-sub_age_18_39-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-grp3_isd.rds

  cox_ipw-cohort_prevax-sub_age_18_39-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp3_isd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-grp3_isd.csv

  make_model_input-cohort_prevax-sub_age_18_39-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-grp4_agi_ibd.rds

  cox_ipw-cohort_prevax-sub_age_18_39-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-grp4_agi_ibd.csv

  make_model_input-cohort_prevax-sub_age_18_39-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-grp5_atv.rds

  cox_ipw-cohort_prevax-sub_age_18_39-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp5_atv.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-grp5_atv.csv

  make_model_input-cohort_prevax-sub_age_18_39-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-grp6_trd.rds

  cox_ipw-cohort_prevax-sub_age_18_39-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp6_trd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-grp6_trd.csv

  make_model_input-cohort_prevax-sub_age_18_39-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-grp7_htd.rds

  cox_ipw-cohort_prevax-sub_age_18_39-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp7_htd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-grp7_htd.csv

  make_model_input-cohort_prevax-sub_age_18_39-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-grp8_ind.rds

  cox_ipw-cohort_prevax-sub_age_18_39-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp8_ind.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-grp8_ind.csv

  make_model_input-cohort_prevax-sub_age_18_39-hs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-hs.rds

  cox_ipw-cohort_prevax-sub_age_18_39-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-hs.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-hs.csv

  make_model_input-cohort_prevax-sub_age_18_39-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-ibd.rds

  cox_ipw-cohort_prevax-sub_age_18_39-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-ibd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-ibd.csv

  make_model_input-cohort_prevax-sub_age_18_39-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-immune_thromb.rds

  cox_ipw-cohort_prevax-sub_age_18_39-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-immune_thromb.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-immune_thromb.csv

  make_model_input-cohort_prevax-sub_age_18_39-ms:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-ms.rds

  cox_ipw-cohort_prevax-sub_age_18_39-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-ms.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-ms.csv

  make_model_input-cohort_prevax-sub_age_18_39-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-myasthenia.rds

  cox_ipw-cohort_prevax-sub_age_18_39-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-myasthenia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-myasthenia.csv

  make_model_input-cohort_prevax-sub_age_18_39-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-pern_anaemia.rds

  cox_ipw-cohort_prevax-sub_age_18_39-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-pern_anaemia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-pern_anaemia.csv

  make_model_input-cohort_prevax-sub_age_18_39-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-pmr.rds

  cox_ipw-cohort_prevax-sub_age_18_39-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-pmr.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-pmr.csv

  make_model_input-cohort_prevax-sub_age_18_39-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-psoa.rds

  cox_ipw-cohort_prevax-sub_age_18_39-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-psoa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-psoa.csv

  make_model_input-cohort_prevax-sub_age_18_39-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-psoriasis.rds

  cox_ipw-cohort_prevax-sub_age_18_39-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-psoriasis.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-psoriasis.csv

  make_model_input-cohort_prevax-sub_age_18_39-ra:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-ra.rds

  cox_ipw-cohort_prevax-sub_age_18_39-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-ra.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-ra.csv

  make_model_input-cohort_prevax-sub_age_18_39-uc:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-uc.rds

  cox_ipw-cohort_prevax-sub_age_18_39-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_18_39-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-uc.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-uc.csv

  make_model_input-cohort_unvax-sub_age_18_39-addison:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-addison.rds

  cox_ipw-cohort_unvax-sub_age_18_39-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-addison.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-addison.csv

  make_model_input-cohort_unvax-sub_age_18_39-apa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-apa.rds

  cox_ipw-cohort_unvax-sub_age_18_39-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-apa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-apa.csv

  make_model_input-cohort_unvax-sub_age_18_39-axial:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-axial.rds

  cox_ipw-cohort_unvax-sub_age_18_39-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-axial.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-axial.csv

  make_model_input-cohort_unvax-sub_age_18_39-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-celiac.rds

  cox_ipw-cohort_unvax-sub_age_18_39-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-celiac.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-celiac.csv

  make_model_input-cohort_unvax-sub_age_18_39-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-composite_ai.rds

  cox_ipw-cohort_unvax-sub_age_18_39-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-composite_ai.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-composite_ai.csv

  make_model_input-cohort_unvax-sub_age_18_39-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-crohn.rds

  cox_ipw-cohort_unvax-sub_age_18_39-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-crohn.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-crohn.csv

  make_model_input-cohort_unvax-sub_age_18_39-grave:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-grave.rds

  cox_ipw-cohort_unvax-sub_age_18_39-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grave.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-grave.csv

  make_model_input-cohort_unvax-sub_age_18_39-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-grp1_ifa.rds

  cox_ipw-cohort_unvax-sub_age_18_39-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp1_ifa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-grp1_ifa.csv

  make_model_input-cohort_unvax-sub_age_18_39-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-grp2_ctd.rds

  cox_ipw-cohort_unvax-sub_age_18_39-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp2_ctd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-grp2_ctd.csv

  make_model_input-cohort_unvax-sub_age_18_39-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-grp3_isd.rds

  cox_ipw-cohort_unvax-sub_age_18_39-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp3_isd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-grp3_isd.csv

  make_model_input-cohort_unvax-sub_age_18_39-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-grp4_agi_ibd.rds

  cox_ipw-cohort_unvax-sub_age_18_39-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-grp4_agi_ibd.csv

  make_model_input-cohort_unvax-sub_age_18_39-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-grp5_atv.rds

  cox_ipw-cohort_unvax-sub_age_18_39-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp5_atv.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-grp5_atv.csv

  make_model_input-cohort_unvax-sub_age_18_39-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-grp6_trd.rds

  cox_ipw-cohort_unvax-sub_age_18_39-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp6_trd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-grp6_trd.csv

  make_model_input-cohort_unvax-sub_age_18_39-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-grp7_htd.rds

  cox_ipw-cohort_unvax-sub_age_18_39-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp7_htd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-grp7_htd.csv

  make_model_input-cohort_unvax-sub_age_18_39-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-grp8_ind.rds

  cox_ipw-cohort_unvax-sub_age_18_39-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp8_ind.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-grp8_ind.csv

  make_model_input-cohort_unvax-sub_age_18_39-hs:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-hs.rds

  cox_ipw-cohort_unvax-sub_age_18_39-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-hs.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-hs.csv

  make_model_input-cohort_unvax-sub_age_18_39-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-ibd.rds

  cox_ipw-cohort_unvax-sub_age_18_39-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-ibd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-ibd.csv

  make_model_input-cohort_unvax-sub_age_18_39-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-immune_thromb.rds

  cox_ipw-cohort_unvax-sub_age_18_39-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-immune_thromb.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-immune_thromb.csv

  make_model_input-cohort_unvax-sub_age_18_39-ms:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-ms.rds

  cox_ipw-cohort_unvax-sub_age_18_39-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-ms.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-ms.csv

  make_model_input-cohort_unvax-sub_age_18_39-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-myasthenia.rds

  cox_ipw-cohort_unvax-sub_age_18_39-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-myasthenia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-myasthenia.csv

  make_model_input-cohort_unvax-sub_age_18_39-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-pern_anaemia.rds

  cox_ipw-cohort_unvax-sub_age_18_39-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-pern_anaemia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-pern_anaemia.csv

  make_model_input-cohort_unvax-sub_age_18_39-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-pmr.rds

  cox_ipw-cohort_unvax-sub_age_18_39-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-pmr.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-pmr.csv

  make_model_input-cohort_unvax-sub_age_18_39-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-psoa.rds

  cox_ipw-cohort_unvax-sub_age_18_39-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-psoa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-psoa.csv

  make_model_input-cohort_unvax-sub_age_18_39-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-psoriasis.rds

  cox_ipw-cohort_unvax-sub_age_18_39-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-psoriasis.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-psoriasis.csv

  make_model_input-cohort_unvax-sub_age_18_39-ra:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-ra.rds

  cox_ipw-cohort_unvax-sub_age_18_39-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-ra.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-ra.csv

  make_model_input-cohort_unvax-sub_age_18_39-uc:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-uc.rds

  cox_ipw-cohort_unvax-sub_age_18_39-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-uc.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-uc.csv

  make_model_input-cohort_vax-sub_age_18_39-addison:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-addison.rds

  cox_ipw-cohort_vax-sub_age_18_39-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-addison.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-addison.csv

  make_model_input-cohort_vax-sub_age_18_39-apa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-apa.rds

  cox_ipw-cohort_vax-sub_age_18_39-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-apa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-apa.csv

  make_model_input-cohort_vax-sub_age_18_39-axial:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-axial.rds

  cox_ipw-cohort_vax-sub_age_18_39-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-axial.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-axial.csv

  make_model_input-cohort_vax-sub_age_18_39-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-celiac.rds

  cox_ipw-cohort_vax-sub_age_18_39-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-celiac.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-celiac.csv

  make_model_input-cohort_vax-sub_age_18_39-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-composite_ai.rds

  cox_ipw-cohort_vax-sub_age_18_39-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-composite_ai.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-composite_ai.csv

  make_model_input-cohort_vax-sub_age_18_39-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-crohn.rds

  cox_ipw-cohort_vax-sub_age_18_39-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-crohn.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-crohn.csv

  make_model_input-cohort_vax-sub_age_18_39-grave:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-grave.rds

  cox_ipw-cohort_vax-sub_age_18_39-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grave.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-grave.csv

  make_model_input-cohort_vax-sub_age_18_39-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-grp1_ifa.rds

  cox_ipw-cohort_vax-sub_age_18_39-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp1_ifa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-grp1_ifa.csv

  make_model_input-cohort_vax-sub_age_18_39-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-grp2_ctd.rds

  cox_ipw-cohort_vax-sub_age_18_39-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp2_ctd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-grp2_ctd.csv

  make_model_input-cohort_vax-sub_age_18_39-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-grp3_isd.rds

  cox_ipw-cohort_vax-sub_age_18_39-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp3_isd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-grp3_isd.csv

  make_model_input-cohort_vax-sub_age_18_39-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-grp4_agi_ibd.rds

  cox_ipw-cohort_vax-sub_age_18_39-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-grp4_agi_ibd.csv

  make_model_input-cohort_vax-sub_age_18_39-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-grp5_atv.rds

  cox_ipw-cohort_vax-sub_age_18_39-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp5_atv.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-grp5_atv.csv

  make_model_input-cohort_vax-sub_age_18_39-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-grp6_trd.rds

  cox_ipw-cohort_vax-sub_age_18_39-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp6_trd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-grp6_trd.csv

  make_model_input-cohort_vax-sub_age_18_39-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-grp7_htd.rds

  cox_ipw-cohort_vax-sub_age_18_39-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp7_htd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-grp7_htd.csv

  make_model_input-cohort_vax-sub_age_18_39-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-grp8_ind.rds

  cox_ipw-cohort_vax-sub_age_18_39-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp8_ind.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-grp8_ind.csv

  make_model_input-cohort_vax-sub_age_18_39-hs:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-hs.rds

  cox_ipw-cohort_vax-sub_age_18_39-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-hs.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-hs.csv

  make_model_input-cohort_vax-sub_age_18_39-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-ibd.rds

  cox_ipw-cohort_vax-sub_age_18_39-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-ibd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-ibd.csv

  make_model_input-cohort_vax-sub_age_18_39-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-immune_thromb.rds

  cox_ipw-cohort_vax-sub_age_18_39-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-immune_thromb.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-immune_thromb.csv

  make_model_input-cohort_vax-sub_age_18_39-ms:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-ms.rds

  cox_ipw-cohort_vax-sub_age_18_39-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-ms.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-ms.csv

  make_model_input-cohort_vax-sub_age_18_39-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-myasthenia.rds

  cox_ipw-cohort_vax-sub_age_18_39-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-myasthenia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-myasthenia.csv

  make_model_input-cohort_vax-sub_age_18_39-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-pern_anaemia.rds

  cox_ipw-cohort_vax-sub_age_18_39-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-pern_anaemia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-pern_anaemia.csv

  make_model_input-cohort_vax-sub_age_18_39-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-pmr.rds

  cox_ipw-cohort_vax-sub_age_18_39-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-pmr.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-pmr.csv

  make_model_input-cohort_vax-sub_age_18_39-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-psoa.rds

  cox_ipw-cohort_vax-sub_age_18_39-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-psoa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-psoa.csv

  make_model_input-cohort_vax-sub_age_18_39-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-psoriasis.rds

  cox_ipw-cohort_vax-sub_age_18_39-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-psoriasis.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-psoriasis.csv

  make_model_input-cohort_vax-sub_age_18_39-ra:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-ra.rds

  cox_ipw-cohort_vax-sub_age_18_39-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-ra.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-ra.csv

  make_model_input-cohort_vax-sub_age_18_39-uc:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-uc.rds

  cox_ipw-cohort_vax-sub_age_18_39-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-uc.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-uc.csv

  make_model_input-cohort_prevax-sub_age_40_59-addison:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-addison.rds

  cox_ipw-cohort_prevax-sub_age_40_59-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-addison.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-addison.csv

  make_model_input-cohort_prevax-sub_age_40_59-apa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-apa.rds

  cox_ipw-cohort_prevax-sub_age_40_59-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-apa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-apa.csv

  make_model_input-cohort_prevax-sub_age_40_59-axial:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-axial.rds

  cox_ipw-cohort_prevax-sub_age_40_59-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-axial.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-axial.csv

  make_model_input-cohort_prevax-sub_age_40_59-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-celiac.rds

  cox_ipw-cohort_prevax-sub_age_40_59-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-celiac.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-celiac.csv

  make_model_input-cohort_prevax-sub_age_40_59-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-composite_ai.rds

  cox_ipw-cohort_prevax-sub_age_40_59-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-composite_ai.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-composite_ai.csv

  make_model_input-cohort_prevax-sub_age_40_59-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-crohn.rds

  cox_ipw-cohort_prevax-sub_age_40_59-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-crohn.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-crohn.csv

  make_model_input-cohort_prevax-sub_age_40_59-grave:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-grave.rds

  cox_ipw-cohort_prevax-sub_age_40_59-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grave.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-grave.csv

  make_model_input-cohort_prevax-sub_age_40_59-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-grp1_ifa.rds

  cox_ipw-cohort_prevax-sub_age_40_59-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp1_ifa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-grp1_ifa.csv

  make_model_input-cohort_prevax-sub_age_40_59-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-grp2_ctd.rds

  cox_ipw-cohort_prevax-sub_age_40_59-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp2_ctd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-grp2_ctd.csv

  make_model_input-cohort_prevax-sub_age_40_59-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-grp3_isd.rds

  cox_ipw-cohort_prevax-sub_age_40_59-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp3_isd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-grp3_isd.csv

  make_model_input-cohort_prevax-sub_age_40_59-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-grp4_agi_ibd.rds

  cox_ipw-cohort_prevax-sub_age_40_59-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-grp4_agi_ibd.csv

  make_model_input-cohort_prevax-sub_age_40_59-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-grp5_atv.rds

  cox_ipw-cohort_prevax-sub_age_40_59-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp5_atv.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-grp5_atv.csv

  make_model_input-cohort_prevax-sub_age_40_59-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-grp6_trd.rds

  cox_ipw-cohort_prevax-sub_age_40_59-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp6_trd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-grp6_trd.csv

  make_model_input-cohort_prevax-sub_age_40_59-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-grp7_htd.rds

  cox_ipw-cohort_prevax-sub_age_40_59-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp7_htd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-grp7_htd.csv

  make_model_input-cohort_prevax-sub_age_40_59-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-grp8_ind.rds

  cox_ipw-cohort_prevax-sub_age_40_59-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-grp8_ind.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-grp8_ind.csv

  make_model_input-cohort_prevax-sub_age_40_59-hs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-hs.rds

  cox_ipw-cohort_prevax-sub_age_40_59-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-hs.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-hs.csv

  make_model_input-cohort_prevax-sub_age_40_59-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-ibd.rds

  cox_ipw-cohort_prevax-sub_age_40_59-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-ibd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-ibd.csv

  make_model_input-cohort_prevax-sub_age_40_59-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-immune_thromb.rds

  cox_ipw-cohort_prevax-sub_age_40_59-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-immune_thromb.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-immune_thromb.csv

  make_model_input-cohort_prevax-sub_age_40_59-ms:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-ms.rds

  cox_ipw-cohort_prevax-sub_age_40_59-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-ms.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-ms.csv

  make_model_input-cohort_prevax-sub_age_40_59-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-myasthenia.rds

  cox_ipw-cohort_prevax-sub_age_40_59-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-myasthenia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-myasthenia.csv

  make_model_input-cohort_prevax-sub_age_40_59-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-pern_anaemia.rds

  cox_ipw-cohort_prevax-sub_age_40_59-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-pern_anaemia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-pern_anaemia.csv

  make_model_input-cohort_prevax-sub_age_40_59-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-pmr.rds

  cox_ipw-cohort_prevax-sub_age_40_59-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-pmr.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-pmr.csv

  make_model_input-cohort_prevax-sub_age_40_59-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-psoa.rds

  cox_ipw-cohort_prevax-sub_age_40_59-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-psoa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-psoa.csv

  make_model_input-cohort_prevax-sub_age_40_59-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-psoriasis.rds

  cox_ipw-cohort_prevax-sub_age_40_59-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-psoriasis.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-psoriasis.csv

  make_model_input-cohort_prevax-sub_age_40_59-ra:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-ra.rds

  cox_ipw-cohort_prevax-sub_age_40_59-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-ra.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-ra.csv

  make_model_input-cohort_prevax-sub_age_40_59-uc:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-uc.rds

  cox_ipw-cohort_prevax-sub_age_40_59-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_40_59-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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-uc.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-uc.csv

  make_model_input-cohort_unvax-sub_age_40_59-addison:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-addison.rds

  cox_ipw-cohort_unvax-sub_age_40_59-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-addison.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-addison.csv

  make_model_input-cohort_unvax-sub_age_40_59-apa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-apa.rds

  cox_ipw-cohort_unvax-sub_age_40_59-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-apa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-apa.csv

  make_model_input-cohort_unvax-sub_age_40_59-axial:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-axial.rds

  cox_ipw-cohort_unvax-sub_age_40_59-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-axial.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-axial.csv

  make_model_input-cohort_unvax-sub_age_40_59-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-celiac.rds

  cox_ipw-cohort_unvax-sub_age_40_59-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-celiac.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-celiac.csv

  make_model_input-cohort_unvax-sub_age_40_59-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-composite_ai.rds

  cox_ipw-cohort_unvax-sub_age_40_59-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-composite_ai.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-composite_ai.csv

  make_model_input-cohort_unvax-sub_age_40_59-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-crohn.rds

  cox_ipw-cohort_unvax-sub_age_40_59-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-crohn.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-crohn.csv

  make_model_input-cohort_unvax-sub_age_40_59-grave:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-grave.rds

  cox_ipw-cohort_unvax-sub_age_40_59-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grave.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-grave.csv

  make_model_input-cohort_unvax-sub_age_40_59-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-grp1_ifa.rds

  cox_ipw-cohort_unvax-sub_age_40_59-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp1_ifa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-grp1_ifa.csv

  make_model_input-cohort_unvax-sub_age_40_59-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-grp2_ctd.rds

  cox_ipw-cohort_unvax-sub_age_40_59-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp2_ctd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-grp2_ctd.csv

  make_model_input-cohort_unvax-sub_age_40_59-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-grp3_isd.rds

  cox_ipw-cohort_unvax-sub_age_40_59-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp3_isd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-grp3_isd.csv

  make_model_input-cohort_unvax-sub_age_40_59-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-grp4_agi_ibd.rds

  cox_ipw-cohort_unvax-sub_age_40_59-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-grp4_agi_ibd.csv

  make_model_input-cohort_unvax-sub_age_40_59-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-grp5_atv.rds

  cox_ipw-cohort_unvax-sub_age_40_59-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp5_atv.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-grp5_atv.csv

  make_model_input-cohort_unvax-sub_age_40_59-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-grp6_trd.rds

  cox_ipw-cohort_unvax-sub_age_40_59-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp6_trd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-grp6_trd.csv

  make_model_input-cohort_unvax-sub_age_40_59-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-grp7_htd.rds

  cox_ipw-cohort_unvax-sub_age_40_59-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp7_htd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-grp7_htd.csv

  make_model_input-cohort_unvax-sub_age_40_59-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-grp8_ind.rds

  cox_ipw-cohort_unvax-sub_age_40_59-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-grp8_ind.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-grp8_ind.csv

  make_model_input-cohort_unvax-sub_age_40_59-hs:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-hs.rds

  cox_ipw-cohort_unvax-sub_age_40_59-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-hs.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-hs.csv

  make_model_input-cohort_unvax-sub_age_40_59-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-ibd.rds

  cox_ipw-cohort_unvax-sub_age_40_59-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-ibd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-ibd.csv

  make_model_input-cohort_unvax-sub_age_40_59-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-immune_thromb.rds

  cox_ipw-cohort_unvax-sub_age_40_59-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-immune_thromb.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-immune_thromb.csv

  make_model_input-cohort_unvax-sub_age_40_59-ms:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-ms.rds

  cox_ipw-cohort_unvax-sub_age_40_59-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-ms.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-ms.csv

  make_model_input-cohort_unvax-sub_age_40_59-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-myasthenia.rds

  cox_ipw-cohort_unvax-sub_age_40_59-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-myasthenia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-myasthenia.csv

  make_model_input-cohort_unvax-sub_age_40_59-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-pern_anaemia.rds

  cox_ipw-cohort_unvax-sub_age_40_59-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-pern_anaemia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-pern_anaemia.csv

  make_model_input-cohort_unvax-sub_age_40_59-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-pmr.rds

  cox_ipw-cohort_unvax-sub_age_40_59-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-pmr.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-pmr.csv

  make_model_input-cohort_unvax-sub_age_40_59-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-psoa.rds

  cox_ipw-cohort_unvax-sub_age_40_59-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-psoa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-psoa.csv

  make_model_input-cohort_unvax-sub_age_40_59-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-psoriasis.rds

  cox_ipw-cohort_unvax-sub_age_40_59-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-psoriasis.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-psoriasis.csv

  make_model_input-cohort_unvax-sub_age_40_59-ra:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-ra.rds

  cox_ipw-cohort_unvax-sub_age_40_59-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-ra.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-ra.csv

  make_model_input-cohort_unvax-sub_age_40_59-uc:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-uc.rds

  cox_ipw-cohort_unvax-sub_age_40_59-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-uc.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-uc.csv

  make_model_input-cohort_vax-sub_age_40_59-addison:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-addison.rds

  cox_ipw-cohort_vax-sub_age_40_59-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-addison.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-addison.csv

  make_model_input-cohort_vax-sub_age_40_59-apa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-apa.rds

  cox_ipw-cohort_vax-sub_age_40_59-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-apa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-apa.csv

  make_model_input-cohort_vax-sub_age_40_59-axial:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-axial.rds

  cox_ipw-cohort_vax-sub_age_40_59-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-axial.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-axial.csv

  make_model_input-cohort_vax-sub_age_40_59-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-celiac.rds

  cox_ipw-cohort_vax-sub_age_40_59-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-celiac.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-celiac.csv

  make_model_input-cohort_vax-sub_age_40_59-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-composite_ai.rds

  cox_ipw-cohort_vax-sub_age_40_59-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-composite_ai.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-composite_ai.csv

  make_model_input-cohort_vax-sub_age_40_59-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-crohn.rds

  cox_ipw-cohort_vax-sub_age_40_59-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-crohn.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-crohn.csv

  make_model_input-cohort_vax-sub_age_40_59-grave:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-grave.rds

  cox_ipw-cohort_vax-sub_age_40_59-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-grave.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-grave.csv

  make_model_input-cohort_vax-sub_age_40_59-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-grp1_ifa.rds

  cox_ipw-cohort_vax-sub_age_40_59-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-grp1_ifa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-grp1_ifa.csv

  make_model_input-cohort_vax-sub_age_40_59-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-grp2_ctd.rds

  cox_ipw-cohort_vax-sub_age_40_59-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-grp2_ctd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-grp2_ctd.csv

  make_model_input-cohort_vax-sub_age_40_59-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-grp3_isd.rds

  cox_ipw-cohort_vax-sub_age_40_59-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-grp3_isd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-grp3_isd.csv

  make_model_input-cohort_vax-sub_age_40_59-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-grp4_agi_ibd.rds

  cox_ipw-cohort_vax-sub_age_40_59-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-grp4_agi_ibd.csv

  make_model_input-cohort_vax-sub_age_40_59-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-grp5_atv.rds

  cox_ipw-cohort_vax-sub_age_40_59-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-grp5_atv.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-grp5_atv.csv

  make_model_input-cohort_vax-sub_age_40_59-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-grp6_trd.rds

  cox_ipw-cohort_vax-sub_age_40_59-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-grp6_trd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-grp6_trd.csv

  make_model_input-cohort_vax-sub_age_40_59-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-grp7_htd.rds

  cox_ipw-cohort_vax-sub_age_40_59-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-grp7_htd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-grp7_htd.csv

  make_model_input-cohort_vax-sub_age_40_59-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-grp8_ind.rds

  cox_ipw-cohort_vax-sub_age_40_59-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-grp8_ind.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-grp8_ind.csv

  make_model_input-cohort_vax-sub_age_40_59-hs:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-hs.rds

  cox_ipw-cohort_vax-sub_age_40_59-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-hs.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-hs.csv

  make_model_input-cohort_vax-sub_age_40_59-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-ibd.rds

  cox_ipw-cohort_vax-sub_age_40_59-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-ibd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-ibd.csv

  make_model_input-cohort_vax-sub_age_40_59-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-immune_thromb.rds

  cox_ipw-cohort_vax-sub_age_40_59-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-immune_thromb.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-immune_thromb.csv

  make_model_input-cohort_vax-sub_age_40_59-ms:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-ms.rds

  cox_ipw-cohort_vax-sub_age_40_59-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-ms.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-ms.csv

  make_model_input-cohort_vax-sub_age_40_59-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-myasthenia.rds

  cox_ipw-cohort_vax-sub_age_40_59-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-myasthenia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-myasthenia.csv

  make_model_input-cohort_vax-sub_age_40_59-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-pern_anaemia.rds

  cox_ipw-cohort_vax-sub_age_40_59-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-pern_anaemia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-pern_anaemia.csv

  make_model_input-cohort_vax-sub_age_40_59-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-pmr.rds

  cox_ipw-cohort_vax-sub_age_40_59-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-pmr.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-pmr.csv

  make_model_input-cohort_vax-sub_age_40_59-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-psoa.rds

  cox_ipw-cohort_vax-sub_age_40_59-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-psoa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-psoa.csv

  make_model_input-cohort_vax-sub_age_40_59-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-psoriasis.rds

  cox_ipw-cohort_vax-sub_age_40_59-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-psoriasis.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-psoriasis.csv

  make_model_input-cohort_vax-sub_age_40_59-ra:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-ra.rds

  cox_ipw-cohort_vax-sub_age_40_59-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-ra.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-ra.csv

  make_model_input-cohort_vax-sub_age_40_59-uc:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-uc.rds

  cox_ipw-cohort_vax-sub_age_40_59-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_40_59-uc.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-uc.csv

  make_model_input-cohort_prevax-sub_age_60_79-addison:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-addison.rds

  cox_ipw-cohort_prevax-sub_age_60_79-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-addison.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-addison.csv

  make_model_input-cohort_prevax-sub_age_60_79-apa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-apa.rds

  cox_ipw-cohort_prevax-sub_age_60_79-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-apa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-apa.csv

  make_model_input-cohort_prevax-sub_age_60_79-axial:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-axial.rds

  cox_ipw-cohort_prevax-sub_age_60_79-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-axial.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-axial.csv

  make_model_input-cohort_prevax-sub_age_60_79-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-celiac.rds

  cox_ipw-cohort_prevax-sub_age_60_79-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-celiac.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-celiac.csv

  make_model_input-cohort_prevax-sub_age_60_79-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-composite_ai.rds

  cox_ipw-cohort_prevax-sub_age_60_79-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-composite_ai.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-composite_ai.csv

  make_model_input-cohort_prevax-sub_age_60_79-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-crohn.rds

  cox_ipw-cohort_prevax-sub_age_60_79-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-crohn.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-crohn.csv

  make_model_input-cohort_prevax-sub_age_60_79-grave:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-grave.rds

  cox_ipw-cohort_prevax-sub_age_60_79-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grave.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-grave.csv

  make_model_input-cohort_prevax-sub_age_60_79-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-grp1_ifa.rds

  cox_ipw-cohort_prevax-sub_age_60_79-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp1_ifa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-grp1_ifa.csv

  make_model_input-cohort_prevax-sub_age_60_79-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-grp2_ctd.rds

  cox_ipw-cohort_prevax-sub_age_60_79-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp2_ctd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-grp2_ctd.csv

  make_model_input-cohort_prevax-sub_age_60_79-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-grp3_isd.rds

  cox_ipw-cohort_prevax-sub_age_60_79-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp3_isd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-grp3_isd.csv

  make_model_input-cohort_prevax-sub_age_60_79-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-grp4_agi_ibd.rds

  cox_ipw-cohort_prevax-sub_age_60_79-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-grp4_agi_ibd.csv

  make_model_input-cohort_prevax-sub_age_60_79-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-grp5_atv.rds

  cox_ipw-cohort_prevax-sub_age_60_79-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp5_atv.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-grp5_atv.csv

  make_model_input-cohort_prevax-sub_age_60_79-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-grp6_trd.rds

  cox_ipw-cohort_prevax-sub_age_60_79-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp6_trd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-grp6_trd.csv

  make_model_input-cohort_prevax-sub_age_60_79-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-grp7_htd.rds

  cox_ipw-cohort_prevax-sub_age_60_79-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp7_htd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-grp7_htd.csv

  make_model_input-cohort_prevax-sub_age_60_79-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-grp8_ind.rds

  cox_ipw-cohort_prevax-sub_age_60_79-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp8_ind.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-grp8_ind.csv

  make_model_input-cohort_prevax-sub_age_60_79-hs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-hs.rds

  cox_ipw-cohort_prevax-sub_age_60_79-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-hs.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-hs.csv

  make_model_input-cohort_prevax-sub_age_60_79-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-ibd.rds

  cox_ipw-cohort_prevax-sub_age_60_79-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-ibd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-ibd.csv

  make_model_input-cohort_prevax-sub_age_60_79-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-immune_thromb.rds

  cox_ipw-cohort_prevax-sub_age_60_79-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-immune_thromb.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-immune_thromb.csv

  make_model_input-cohort_prevax-sub_age_60_79-ms:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-ms.rds

  cox_ipw-cohort_prevax-sub_age_60_79-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-ms.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-ms.csv

  make_model_input-cohort_prevax-sub_age_60_79-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-myasthenia.rds

  cox_ipw-cohort_prevax-sub_age_60_79-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-myasthenia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-myasthenia.csv

  make_model_input-cohort_prevax-sub_age_60_79-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-pern_anaemia.rds

  cox_ipw-cohort_prevax-sub_age_60_79-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-pern_anaemia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-pern_anaemia.csv

  make_model_input-cohort_prevax-sub_age_60_79-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-pmr.rds

  cox_ipw-cohort_prevax-sub_age_60_79-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-pmr.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-pmr.csv

  make_model_input-cohort_prevax-sub_age_60_79-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-psoa.rds

  cox_ipw-cohort_prevax-sub_age_60_79-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-psoa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-psoa.csv

  make_model_input-cohort_prevax-sub_age_60_79-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-psoriasis.rds

  cox_ipw-cohort_prevax-sub_age_60_79-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-psoriasis.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-psoriasis.csv

  make_model_input-cohort_prevax-sub_age_60_79-ra:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-ra.rds

  cox_ipw-cohort_prevax-sub_age_60_79-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-ra.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-ra.csv

  make_model_input-cohort_prevax-sub_age_60_79-uc:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-uc.rds

  cox_ipw-cohort_prevax-sub_age_60_79-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_60_79-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-uc.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-uc.csv

  make_model_input-cohort_unvax-sub_age_60_79-addison:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-addison.rds

  cox_ipw-cohort_unvax-sub_age_60_79-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-addison.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-addison.csv

  make_model_input-cohort_unvax-sub_age_60_79-apa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-apa.rds

  cox_ipw-cohort_unvax-sub_age_60_79-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-apa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-apa.csv

  make_model_input-cohort_unvax-sub_age_60_79-axial:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-axial.rds

  cox_ipw-cohort_unvax-sub_age_60_79-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-axial.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-axial.csv

  make_model_input-cohort_unvax-sub_age_60_79-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-celiac.rds

  cox_ipw-cohort_unvax-sub_age_60_79-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-celiac.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-celiac.csv

  make_model_input-cohort_unvax-sub_age_60_79-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-composite_ai.rds

  cox_ipw-cohort_unvax-sub_age_60_79-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-composite_ai.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-composite_ai.csv

  make_model_input-cohort_unvax-sub_age_60_79-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-crohn.rds

  cox_ipw-cohort_unvax-sub_age_60_79-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-crohn.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-crohn.csv

  make_model_input-cohort_unvax-sub_age_60_79-grave:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-grave.rds

  cox_ipw-cohort_unvax-sub_age_60_79-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grave.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-grave.csv

  make_model_input-cohort_unvax-sub_age_60_79-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-grp1_ifa.rds

  cox_ipw-cohort_unvax-sub_age_60_79-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp1_ifa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-grp1_ifa.csv

  make_model_input-cohort_unvax-sub_age_60_79-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-grp2_ctd.rds

  cox_ipw-cohort_unvax-sub_age_60_79-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp2_ctd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-grp2_ctd.csv

  make_model_input-cohort_unvax-sub_age_60_79-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-grp3_isd.rds

  cox_ipw-cohort_unvax-sub_age_60_79-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp3_isd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-grp3_isd.csv

  make_model_input-cohort_unvax-sub_age_60_79-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-grp4_agi_ibd.rds

  cox_ipw-cohort_unvax-sub_age_60_79-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-grp4_agi_ibd.csv

  make_model_input-cohort_unvax-sub_age_60_79-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-grp5_atv.rds

  cox_ipw-cohort_unvax-sub_age_60_79-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp5_atv.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-grp5_atv.csv

  make_model_input-cohort_unvax-sub_age_60_79-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-grp6_trd.rds

  cox_ipw-cohort_unvax-sub_age_60_79-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp6_trd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-grp6_trd.csv

  make_model_input-cohort_unvax-sub_age_60_79-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-grp7_htd.rds

  cox_ipw-cohort_unvax-sub_age_60_79-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp7_htd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-grp7_htd.csv

  make_model_input-cohort_unvax-sub_age_60_79-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-grp8_ind.rds

  cox_ipw-cohort_unvax-sub_age_60_79-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp8_ind.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-grp8_ind.csv

  make_model_input-cohort_unvax-sub_age_60_79-hs:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-hs.rds

  cox_ipw-cohort_unvax-sub_age_60_79-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-hs.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-hs.csv

  make_model_input-cohort_unvax-sub_age_60_79-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-ibd.rds

  cox_ipw-cohort_unvax-sub_age_60_79-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-ibd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-ibd.csv

  make_model_input-cohort_unvax-sub_age_60_79-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-immune_thromb.rds

  cox_ipw-cohort_unvax-sub_age_60_79-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-immune_thromb.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-immune_thromb.csv

  make_model_input-cohort_unvax-sub_age_60_79-ms:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-ms.rds

  cox_ipw-cohort_unvax-sub_age_60_79-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-ms.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-ms.csv

  make_model_input-cohort_unvax-sub_age_60_79-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-myasthenia.rds

  cox_ipw-cohort_unvax-sub_age_60_79-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-myasthenia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-myasthenia.csv

  make_model_input-cohort_unvax-sub_age_60_79-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-pern_anaemia.rds

  cox_ipw-cohort_unvax-sub_age_60_79-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-pern_anaemia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-pern_anaemia.csv

  make_model_input-cohort_unvax-sub_age_60_79-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-pmr.rds

  cox_ipw-cohort_unvax-sub_age_60_79-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-pmr.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-pmr.csv

  make_model_input-cohort_unvax-sub_age_60_79-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-psoa.rds

  cox_ipw-cohort_unvax-sub_age_60_79-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-psoa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-psoa.csv

  make_model_input-cohort_unvax-sub_age_60_79-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-psoriasis.rds

  cox_ipw-cohort_unvax-sub_age_60_79-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-psoriasis.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-psoriasis.csv

  make_model_input-cohort_unvax-sub_age_60_79-ra:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-ra.rds

  cox_ipw-cohort_unvax-sub_age_60_79-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-ra.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-ra.csv

  make_model_input-cohort_unvax-sub_age_60_79-uc:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-uc.rds

  cox_ipw-cohort_unvax-sub_age_60_79-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-uc.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-uc.csv

  make_model_input-cohort_vax-sub_age_60_79-addison:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-addison.rds

  cox_ipw-cohort_vax-sub_age_60_79-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-addison.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-addison.csv

  make_model_input-cohort_vax-sub_age_60_79-apa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-apa.rds

  cox_ipw-cohort_vax-sub_age_60_79-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-apa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-apa.csv

  make_model_input-cohort_vax-sub_age_60_79-axial:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-axial.rds

  cox_ipw-cohort_vax-sub_age_60_79-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-axial.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-axial.csv

  make_model_input-cohort_vax-sub_age_60_79-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-celiac.rds

  cox_ipw-cohort_vax-sub_age_60_79-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-celiac.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-celiac.csv

  make_model_input-cohort_vax-sub_age_60_79-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-composite_ai.rds

  cox_ipw-cohort_vax-sub_age_60_79-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-composite_ai.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-composite_ai.csv

  make_model_input-cohort_vax-sub_age_60_79-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-crohn.rds

  cox_ipw-cohort_vax-sub_age_60_79-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-crohn.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-crohn.csv

  make_model_input-cohort_vax-sub_age_60_79-grave:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-grave.rds

  cox_ipw-cohort_vax-sub_age_60_79-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grave.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-grave.csv

  make_model_input-cohort_vax-sub_age_60_79-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-grp1_ifa.rds

  cox_ipw-cohort_vax-sub_age_60_79-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp1_ifa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-grp1_ifa.csv

  make_model_input-cohort_vax-sub_age_60_79-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-grp2_ctd.rds

  cox_ipw-cohort_vax-sub_age_60_79-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp2_ctd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-grp2_ctd.csv

  make_model_input-cohort_vax-sub_age_60_79-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-grp3_isd.rds

  cox_ipw-cohort_vax-sub_age_60_79-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp3_isd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-grp3_isd.csv

  make_model_input-cohort_vax-sub_age_60_79-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-grp4_agi_ibd.rds

  cox_ipw-cohort_vax-sub_age_60_79-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-grp4_agi_ibd.csv

  make_model_input-cohort_vax-sub_age_60_79-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-grp5_atv.rds

  cox_ipw-cohort_vax-sub_age_60_79-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp5_atv.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-grp5_atv.csv

  make_model_input-cohort_vax-sub_age_60_79-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-grp6_trd.rds

  cox_ipw-cohort_vax-sub_age_60_79-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp6_trd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-grp6_trd.csv

  make_model_input-cohort_vax-sub_age_60_79-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-grp7_htd.rds

  cox_ipw-cohort_vax-sub_age_60_79-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp7_htd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-grp7_htd.csv

  make_model_input-cohort_vax-sub_age_60_79-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-grp8_ind.rds

  cox_ipw-cohort_vax-sub_age_60_79-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-grp8_ind.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-grp8_ind.csv

  make_model_input-cohort_vax-sub_age_60_79-hs:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-hs.rds

  cox_ipw-cohort_vax-sub_age_60_79-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-hs.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-hs.csv

  make_model_input-cohort_vax-sub_age_60_79-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-ibd.rds

  cox_ipw-cohort_vax-sub_age_60_79-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-ibd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-ibd.csv

  make_model_input-cohort_vax-sub_age_60_79-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-immune_thromb.rds

  cox_ipw-cohort_vax-sub_age_60_79-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-immune_thromb.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-immune_thromb.csv

  make_model_input-cohort_vax-sub_age_60_79-ms:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-ms.rds

  cox_ipw-cohort_vax-sub_age_60_79-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-ms.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-ms.csv

  make_model_input-cohort_vax-sub_age_60_79-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-myasthenia.rds

  cox_ipw-cohort_vax-sub_age_60_79-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-myasthenia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-myasthenia.csv

  make_model_input-cohort_vax-sub_age_60_79-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-pern_anaemia.rds

  cox_ipw-cohort_vax-sub_age_60_79-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-pern_anaemia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-pern_anaemia.csv

  make_model_input-cohort_vax-sub_age_60_79-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-pmr.rds

  cox_ipw-cohort_vax-sub_age_60_79-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-pmr.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-pmr.csv

  make_model_input-cohort_vax-sub_age_60_79-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-psoa.rds

  cox_ipw-cohort_vax-sub_age_60_79-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-psoa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-psoa.csv

  make_model_input-cohort_vax-sub_age_60_79-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-psoriasis.rds

  cox_ipw-cohort_vax-sub_age_60_79-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-psoriasis.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-psoriasis.csv

  make_model_input-cohort_vax-sub_age_60_79-ra:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-ra.rds

  cox_ipw-cohort_vax-sub_age_60_79-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-ra.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-ra.csv

  make_model_input-cohort_vax-sub_age_60_79-uc:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-uc.rds

  cox_ipw-cohort_vax-sub_age_60_79-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_60_79-uc.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-uc.csv

  make_model_input-cohort_prevax-sub_age_80_110-addison:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-addison.rds

  cox_ipw-cohort_prevax-sub_age_80_110-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-addison.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-addison.csv

  make_model_input-cohort_prevax-sub_age_80_110-apa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-apa.rds

  cox_ipw-cohort_prevax-sub_age_80_110-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-apa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-apa.csv

  make_model_input-cohort_prevax-sub_age_80_110-axial:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-axial.rds

  cox_ipw-cohort_prevax-sub_age_80_110-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-axial.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-axial.csv

  make_model_input-cohort_prevax-sub_age_80_110-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-celiac.rds

  cox_ipw-cohort_prevax-sub_age_80_110-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-celiac.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-celiac.csv

  make_model_input-cohort_prevax-sub_age_80_110-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-composite_ai.rds

  cox_ipw-cohort_prevax-sub_age_80_110-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-composite_ai.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-composite_ai.csv

  make_model_input-cohort_prevax-sub_age_80_110-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-crohn.rds

  cox_ipw-cohort_prevax-sub_age_80_110-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-crohn.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-crohn.csv

  make_model_input-cohort_prevax-sub_age_80_110-grave:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-grave.rds

  cox_ipw-cohort_prevax-sub_age_80_110-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grave.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-grave.csv

  make_model_input-cohort_prevax-sub_age_80_110-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-grp1_ifa.rds

  cox_ipw-cohort_prevax-sub_age_80_110-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp1_ifa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-grp1_ifa.csv

  make_model_input-cohort_prevax-sub_age_80_110-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-grp2_ctd.rds

  cox_ipw-cohort_prevax-sub_age_80_110-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp2_ctd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-grp2_ctd.csv

  make_model_input-cohort_prevax-sub_age_80_110-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-grp3_isd.rds

  cox_ipw-cohort_prevax-sub_age_80_110-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp3_isd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-grp3_isd.csv

  make_model_input-cohort_prevax-sub_age_80_110-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-grp4_agi_ibd.rds

  cox_ipw-cohort_prevax-sub_age_80_110-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-grp4_agi_ibd.csv

  make_model_input-cohort_prevax-sub_age_80_110-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-grp5_atv.rds

  cox_ipw-cohort_prevax-sub_age_80_110-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp5_atv.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-grp5_atv.csv

  make_model_input-cohort_prevax-sub_age_80_110-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-grp6_trd.rds

  cox_ipw-cohort_prevax-sub_age_80_110-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp6_trd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-grp6_trd.csv

  make_model_input-cohort_prevax-sub_age_80_110-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-grp7_htd.rds

  cox_ipw-cohort_prevax-sub_age_80_110-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp7_htd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-grp7_htd.csv

  make_model_input-cohort_prevax-sub_age_80_110-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-grp8_ind.rds

  cox_ipw-cohort_prevax-sub_age_80_110-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp8_ind.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-grp8_ind.csv

  make_model_input-cohort_prevax-sub_age_80_110-hs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-hs.rds

  cox_ipw-cohort_prevax-sub_age_80_110-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-hs.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-hs.csv

  make_model_input-cohort_prevax-sub_age_80_110-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-ibd.rds

  cox_ipw-cohort_prevax-sub_age_80_110-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-ibd.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-ibd.csv

  make_model_input-cohort_prevax-sub_age_80_110-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-immune_thromb.rds

  cox_ipw-cohort_prevax-sub_age_80_110-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-immune_thromb.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-immune_thromb.csv

  make_model_input-cohort_prevax-sub_age_80_110-ms:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-ms.rds

  cox_ipw-cohort_prevax-sub_age_80_110-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-ms.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-ms.csv

  make_model_input-cohort_prevax-sub_age_80_110-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-myasthenia.rds

  cox_ipw-cohort_prevax-sub_age_80_110-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-myasthenia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-myasthenia.csv

  make_model_input-cohort_prevax-sub_age_80_110-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-pern_anaemia.rds

  cox_ipw-cohort_prevax-sub_age_80_110-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-pern_anaemia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-pern_anaemia.csv

  make_model_input-cohort_prevax-sub_age_80_110-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-pmr.rds

  cox_ipw-cohort_prevax-sub_age_80_110-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-pmr.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-pmr.csv

  make_model_input-cohort_prevax-sub_age_80_110-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-psoa.rds

  cox_ipw-cohort_prevax-sub_age_80_110-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-psoa.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-psoa.csv

  make_model_input-cohort_prevax-sub_age_80_110-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-psoriasis.rds

  cox_ipw-cohort_prevax-sub_age_80_110-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-psoriasis.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-psoriasis.csv

  make_model_input-cohort_prevax-sub_age_80_110-ra:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-ra.rds

  cox_ipw-cohort_prevax-sub_age_80_110-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-ra.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-ra.csv

  make_model_input-cohort_prevax-sub_age_80_110-uc:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-uc.rds

  cox_ipw-cohort_prevax-sub_age_80_110-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-sub_age_80_110-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-uc.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-uc.csv

  make_model_input-cohort_unvax-sub_age_80_110-addison:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-addison.rds

  cox_ipw-cohort_unvax-sub_age_80_110-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-addison.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-addison.csv

  make_model_input-cohort_unvax-sub_age_80_110-apa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-apa.rds

  cox_ipw-cohort_unvax-sub_age_80_110-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-apa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-apa.csv

  make_model_input-cohort_unvax-sub_age_80_110-axial:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-axial.rds

  cox_ipw-cohort_unvax-sub_age_80_110-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-axial.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-axial.csv

  make_model_input-cohort_unvax-sub_age_80_110-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-celiac.rds

  cox_ipw-cohort_unvax-sub_age_80_110-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-celiac.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-celiac.csv

  make_model_input-cohort_unvax-sub_age_80_110-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-composite_ai.rds

  cox_ipw-cohort_unvax-sub_age_80_110-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-composite_ai.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-composite_ai.csv

  make_model_input-cohort_unvax-sub_age_80_110-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-crohn.rds

  cox_ipw-cohort_unvax-sub_age_80_110-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-crohn.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-crohn.csv

  make_model_input-cohort_unvax-sub_age_80_110-grave:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-grave.rds

  cox_ipw-cohort_unvax-sub_age_80_110-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grave.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-grave.csv

  make_model_input-cohort_unvax-sub_age_80_110-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-grp1_ifa.rds

  cox_ipw-cohort_unvax-sub_age_80_110-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp1_ifa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-grp1_ifa.csv

  make_model_input-cohort_unvax-sub_age_80_110-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-grp2_ctd.rds

  cox_ipw-cohort_unvax-sub_age_80_110-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp2_ctd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-grp2_ctd.csv

  make_model_input-cohort_unvax-sub_age_80_110-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-grp3_isd.rds

  cox_ipw-cohort_unvax-sub_age_80_110-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp3_isd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-grp3_isd.csv

  make_model_input-cohort_unvax-sub_age_80_110-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-grp4_agi_ibd.rds

  cox_ipw-cohort_unvax-sub_age_80_110-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-grp4_agi_ibd.csv

  make_model_input-cohort_unvax-sub_age_80_110-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-grp5_atv.rds

  cox_ipw-cohort_unvax-sub_age_80_110-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp5_atv.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-grp5_atv.csv

  make_model_input-cohort_unvax-sub_age_80_110-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-grp6_trd.rds

  cox_ipw-cohort_unvax-sub_age_80_110-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp6_trd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-grp6_trd.csv

  make_model_input-cohort_unvax-sub_age_80_110-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-grp7_htd.rds

  cox_ipw-cohort_unvax-sub_age_80_110-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp7_htd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-grp7_htd.csv

  make_model_input-cohort_unvax-sub_age_80_110-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-grp8_ind.rds

  cox_ipw-cohort_unvax-sub_age_80_110-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp8_ind.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-grp8_ind.csv

  make_model_input-cohort_unvax-sub_age_80_110-hs:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-hs.rds

  cox_ipw-cohort_unvax-sub_age_80_110-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-hs.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-hs.csv

  make_model_input-cohort_unvax-sub_age_80_110-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-ibd.rds

  cox_ipw-cohort_unvax-sub_age_80_110-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-ibd.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-ibd.csv

  make_model_input-cohort_unvax-sub_age_80_110-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-immune_thromb.rds

  cox_ipw-cohort_unvax-sub_age_80_110-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-immune_thromb.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-immune_thromb.csv

  make_model_input-cohort_unvax-sub_age_80_110-ms:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-ms.rds

  cox_ipw-cohort_unvax-sub_age_80_110-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-ms.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-ms.csv

  make_model_input-cohort_unvax-sub_age_80_110-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-myasthenia.rds

  cox_ipw-cohort_unvax-sub_age_80_110-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-myasthenia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-myasthenia.csv

  make_model_input-cohort_unvax-sub_age_80_110-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-pern_anaemia.rds

  cox_ipw-cohort_unvax-sub_age_80_110-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-pern_anaemia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-pern_anaemia.csv

  make_model_input-cohort_unvax-sub_age_80_110-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-pmr.rds

  cox_ipw-cohort_unvax-sub_age_80_110-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-pmr.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-pmr.csv

  make_model_input-cohort_unvax-sub_age_80_110-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-psoa.rds

  cox_ipw-cohort_unvax-sub_age_80_110-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-psoa.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-psoa.csv

  make_model_input-cohort_unvax-sub_age_80_110-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-psoriasis.rds

  cox_ipw-cohort_unvax-sub_age_80_110-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-psoriasis.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-psoriasis.csv

  make_model_input-cohort_unvax-sub_age_80_110-ra:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-ra.rds

  cox_ipw-cohort_unvax-sub_age_80_110-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-ra.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-ra.csv

  make_model_input-cohort_unvax-sub_age_80_110-uc:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-uc.rds

  cox_ipw-cohort_unvax-sub_age_80_110-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-uc.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-uc.csv

  make_model_input-cohort_vax-sub_age_80_110-addison:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-addison
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-addison.rds

  cox_ipw-cohort_vax-sub_age_80_110-addison:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-addison.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-addison.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-addison
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-addison.csv

  make_model_input-cohort_vax-sub_age_80_110-apa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-apa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-apa.rds

  cox_ipw-cohort_vax-sub_age_80_110-apa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-apa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-apa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-apa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-apa.csv

  make_model_input-cohort_vax-sub_age_80_110-axial:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-axial
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-axial.rds

  cox_ipw-cohort_vax-sub_age_80_110-axial:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-axial.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-axial.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-axial
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-axial.csv

  make_model_input-cohort_vax-sub_age_80_110-celiac:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-celiac
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-celiac.rds

  cox_ipw-cohort_vax-sub_age_80_110-celiac:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-celiac.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-celiac.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-celiac
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-celiac.csv

  make_model_input-cohort_vax-sub_age_80_110-composite_ai:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-composite_ai
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-composite_ai.rds

  cox_ipw-cohort_vax-sub_age_80_110-composite_ai:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-composite_ai.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-composite_ai.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-composite_ai
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-composite_ai.csv

  make_model_input-cohort_vax-sub_age_80_110-crohn:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-crohn
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-crohn.rds

  cox_ipw-cohort_vax-sub_age_80_110-crohn:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-crohn.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-crohn.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-crohn
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-crohn.csv

  make_model_input-cohort_vax-sub_age_80_110-grave:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-grave
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-grave.rds

  cox_ipw-cohort_vax-sub_age_80_110-grave:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-grave.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grave.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-grave
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-grave.csv

  make_model_input-cohort_vax-sub_age_80_110-grp1_ifa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-grp1_ifa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-grp1_ifa.rds

  cox_ipw-cohort_vax-sub_age_80_110-grp1_ifa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-grp1_ifa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp1_ifa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-grp1_ifa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-grp1_ifa.csv

  make_model_input-cohort_vax-sub_age_80_110-grp2_ctd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-grp2_ctd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-grp2_ctd.rds

  cox_ipw-cohort_vax-sub_age_80_110-grp2_ctd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-grp2_ctd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp2_ctd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-grp2_ctd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-grp2_ctd.csv

  make_model_input-cohort_vax-sub_age_80_110-grp3_isd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-grp3_isd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-grp3_isd.rds

  cox_ipw-cohort_vax-sub_age_80_110-grp3_isd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-grp3_isd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp3_isd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-grp3_isd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-grp3_isd.csv

  make_model_input-cohort_vax-sub_age_80_110-grp4_agi_ibd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-grp4_agi_ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-grp4_agi_ibd.rds

  cox_ipw-cohort_vax-sub_age_80_110-grp4_agi_ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-grp4_agi_ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp4_agi_ibd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-grp4_agi_ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-grp4_agi_ibd.csv

  make_model_input-cohort_vax-sub_age_80_110-grp5_atv:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-grp5_atv
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-grp5_atv.rds

  cox_ipw-cohort_vax-sub_age_80_110-grp5_atv:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-grp5_atv.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp5_atv.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-grp5_atv
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-grp5_atv.csv

  make_model_input-cohort_vax-sub_age_80_110-grp6_trd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-grp6_trd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-grp6_trd.rds

  cox_ipw-cohort_vax-sub_age_80_110-grp6_trd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-grp6_trd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp6_trd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-grp6_trd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-grp6_trd.csv

  make_model_input-cohort_vax-sub_age_80_110-grp7_htd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-grp7_htd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-grp7_htd.rds

  cox_ipw-cohort_vax-sub_age_80_110-grp7_htd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-grp7_htd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp7_htd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-grp7_htd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-grp7_htd.csv

  make_model_input-cohort_vax-sub_age_80_110-grp8_ind:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-grp8_ind
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-grp8_ind.rds

  cox_ipw-cohort_vax-sub_age_80_110-grp8_ind:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-grp8_ind.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-grp8_ind.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-grp8_ind
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-grp8_ind.csv

  make_model_input-cohort_vax-sub_age_80_110-hs:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-hs
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-hs.rds

  cox_ipw-cohort_vax-sub_age_80_110-hs:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-hs.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-hs.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-hs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-hs.csv

  make_model_input-cohort_vax-sub_age_80_110-ibd:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-ibd
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-ibd.rds

  cox_ipw-cohort_vax-sub_age_80_110-ibd:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-ibd.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-ibd.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-ibd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-ibd.csv

  make_model_input-cohort_vax-sub_age_80_110-immune_thromb:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-immune_thromb
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-immune_thromb.rds

  cox_ipw-cohort_vax-sub_age_80_110-immune_thromb:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-immune_thromb.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-immune_thromb.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-immune_thromb
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-immune_thromb.csv

  make_model_input-cohort_vax-sub_age_80_110-ms:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-ms
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-ms.rds

  cox_ipw-cohort_vax-sub_age_80_110-ms:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-ms.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-ms.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-ms
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-ms.csv

  make_model_input-cohort_vax-sub_age_80_110-myasthenia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-myasthenia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-myasthenia.rds

  cox_ipw-cohort_vax-sub_age_80_110-myasthenia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-myasthenia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-myasthenia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-myasthenia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-myasthenia.csv

  make_model_input-cohort_vax-sub_age_80_110-pern_anaemia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-pern_anaemia
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-pern_anaemia.rds

  cox_ipw-cohort_vax-sub_age_80_110-pern_anaemia:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-pern_anaemia.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-pern_anaemia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-pern_anaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-pern_anaemia.csv

  make_model_input-cohort_vax-sub_age_80_110-pmr:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-pmr
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-pmr.rds

  cox_ipw-cohort_vax-sub_age_80_110-pmr:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-pmr.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-pmr.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-pmr
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-pmr.csv

  make_model_input-cohort_vax-sub_age_80_110-psoa:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-psoa
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-psoa.rds

  cox_ipw-cohort_vax-sub_age_80_110-psoa:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-psoa.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-psoa.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-psoa
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-psoa.csv

  make_model_input-cohort_vax-sub_age_80_110-psoriasis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-psoriasis
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-psoriasis.rds

  cox_ipw-cohort_vax-sub_age_80_110-psoriasis:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-psoriasis.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-psoriasis.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-psoriasis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-psoriasis.csv

  make_model_input-cohort_vax-sub_age_80_110-ra:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-ra
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-ra.rds

  cox_ipw-cohort_vax-sub_age_80_110-ra:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-ra.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-ra.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-ra
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-ra.csv

  make_model_input-cohort_vax-sub_age_80_110-uc:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-uc
    needs:
    - preprocess_stage1_history_data_cleaning_prevax
    - preprocess_stage1_history_data_cleaning_vax
    - preprocess_stage1_history_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-uc.rds

  cox_ipw-cohort_vax-sub_age_80_110-uc:
    run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-uc.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_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_80_110-uc.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-uc
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-uc.csv

  ## Table 2 - prevax 

  table2_prevax:
    run: r:latest analysis/descriptives/table2.R prevax
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-addison
    - make_model_input-cohort_prevax-sub_age_18_39-apa
    - make_model_input-cohort_prevax-sub_age_18_39-axial
    - make_model_input-cohort_prevax-sub_age_18_39-celiac
    - make_model_input-cohort_prevax-sub_age_18_39-composite_ai
    - make_model_input-cohort_prevax-sub_age_18_39-crohn
    - make_model_input-cohort_prevax-sub_age_18_39-grave
    - make_model_input-cohort_prevax-sub_age_18_39-grp1_ifa
    - make_model_input-cohort_prevax-sub_age_18_39-grp2_ctd
    - make_model_input-cohort_prevax-sub_age_18_39-grp3_isd
    - make_model_input-cohort_prevax-sub_age_18_39-grp4_agi_ibd
    - make_model_input-cohort_prevax-sub_age_18_39-grp5_atv
    - make_model_input-cohort_prevax-sub_age_18_39-grp6_trd
    - make_model_input-cohort_prevax-sub_age_18_39-grp7_htd
    - make_model_input-cohort_prevax-sub_age_18_39-grp8_ind
    - make_model_input-cohort_prevax-sub_age_18_39-hs
    - make_model_input-cohort_prevax-sub_age_18_39-ibd
    - make_model_input-cohort_prevax-sub_age_18_39-immune_thromb
    - make_model_input-cohort_prevax-sub_age_18_39-ms
    - make_model_input-cohort_prevax-sub_age_18_39-myasthenia
    - make_model_input-cohort_prevax-sub_age_18_39-pern_anaemia
    - make_model_input-cohort_prevax-sub_age_18_39-pmr
    - make_model_input-cohort_prevax-sub_age_18_39-psoa
    - make_model_input-cohort_prevax-sub_age_18_39-psoriasis
    - make_model_input-cohort_prevax-sub_age_18_39-ra
    - make_model_input-cohort_prevax-sub_age_18_39-uc
    - make_model_input-cohort_prevax-sub_age_40_59-addison
    - make_model_input-cohort_prevax-sub_age_40_59-apa
    - make_model_input-cohort_prevax-sub_age_40_59-axial
    - make_model_input-cohort_prevax-sub_age_40_59-celiac
    - make_model_input-cohort_prevax-sub_age_40_59-composite_ai
    - make_model_input-cohort_prevax-sub_age_40_59-crohn
    - make_model_input-cohort_prevax-sub_age_40_59-grave
    - make_model_input-cohort_prevax-sub_age_40_59-grp1_ifa
    - make_model_input-cohort_prevax-sub_age_40_59-grp2_ctd
    - make_model_input-cohort_prevax-sub_age_40_59-grp3_isd
    - make_model_input-cohort_prevax-sub_age_40_59-grp4_agi_ibd
    - make_model_input-cohort_prevax-sub_age_40_59-grp5_atv
    - make_model_input-cohort_prevax-sub_age_40_59-grp6_trd
    - make_model_input-cohort_prevax-sub_age_40_59-grp7_htd
    - make_model_input-cohort_prevax-sub_age_40_59-grp8_ind
    - make_model_input-cohort_prevax-sub_age_40_59-hs
    - make_model_input-cohort_prevax-sub_age_40_59-ibd
    - make_model_input-cohort_prevax-sub_age_40_59-immune_thromb
    - make_model_input-cohort_prevax-sub_age_40_59-ms
    - make_model_input-cohort_prevax-sub_age_40_59-myasthenia
    - make_model_input-cohort_prevax-sub_age_40_59-pern_anaemia
    - make_model_input-cohort_prevax-sub_age_40_59-pmr
    - make_model_input-cohort_prevax-sub_age_40_59-psoa
    - make_model_input-cohort_prevax-sub_age_40_59-psoriasis
    - make_model_input-cohort_prevax-sub_age_40_59-ra
    - make_model_input-cohort_prevax-sub_age_40_59-uc
    - make_model_input-cohort_prevax-sub_age_60_79-addison
    - make_model_input-cohort_prevax-sub_age_60_79-apa
    - make_model_input-cohort_prevax-sub_age_60_79-axial
    - make_model_input-cohort_prevax-sub_age_60_79-celiac
    - make_model_input-cohort_prevax-sub_age_60_79-composite_ai
    - make_model_input-cohort_prevax-sub_age_60_79-crohn
    - make_model_input-cohort_prevax-sub_age_60_79-grave
    - make_model_input-cohort_prevax-sub_age_60_79-grp1_ifa
    - make_model_input-cohort_prevax-sub_age_60_79-grp2_ctd
    - make_model_input-cohort_prevax-sub_age_60_79-grp3_isd
    - make_model_input-cohort_prevax-sub_age_60_79-grp4_agi_ibd
    - make_model_input-cohort_prevax-sub_age_60_79-grp5_atv
    - make_model_input-cohort_prevax-sub_age_60_79-grp6_trd
    - make_model_input-cohort_prevax-sub_age_60_79-grp7_htd
    - make_model_input-cohort_prevax-sub_age_60_79-grp8_ind
    - make_model_input-cohort_prevax-sub_age_60_79-hs
    - make_model_input-cohort_prevax-sub_age_60_79-ibd
    - make_model_input-cohort_prevax-sub_age_60_79-immune_thromb
    - make_model_input-cohort_prevax-sub_age_60_79-ms
    - make_model_input-cohort_prevax-sub_age_60_79-myasthenia
    - make_model_input-cohort_prevax-sub_age_60_79-pern_anaemia
    - make_model_input-cohort_prevax-sub_age_60_79-pmr
    - make_model_input-cohort_prevax-sub_age_60_79-psoa
    - make_model_input-cohort_prevax-sub_age_60_79-psoriasis
    - make_model_input-cohort_prevax-sub_age_60_79-ra
    - make_model_input-cohort_prevax-sub_age_60_79-uc
    - make_model_input-cohort_prevax-sub_age_80_110-addison
    - make_model_input-cohort_prevax-sub_age_80_110-apa
    - make_model_input-cohort_prevax-sub_age_80_110-axial
    - make_model_input-cohort_prevax-sub_age_80_110-celiac
    - make_model_input-cohort_prevax-sub_age_80_110-composite_ai
    - make_model_input-cohort_prevax-sub_age_80_110-crohn
    - make_model_input-cohort_prevax-sub_age_80_110-grave
    - make_model_input-cohort_prevax-sub_age_80_110-grp1_ifa
    - make_model_input-cohort_prevax-sub_age_80_110-grp2_ctd
    - make_model_input-cohort_prevax-sub_age_80_110-grp3_isd
    - make_model_input-cohort_prevax-sub_age_80_110-grp4_agi_ibd
    - make_model_input-cohort_prevax-sub_age_80_110-grp5_atv
    - make_model_input-cohort_prevax-sub_age_80_110-grp6_trd
    - make_model_input-cohort_prevax-sub_age_80_110-grp7_htd
    - make_model_input-cohort_prevax-sub_age_80_110-grp8_ind
    - make_model_input-cohort_prevax-sub_age_80_110-hs
    - make_model_input-cohort_prevax-sub_age_80_110-ibd
    - make_model_input-cohort_prevax-sub_age_80_110-immune_thromb
    - make_model_input-cohort_prevax-sub_age_80_110-ms
    - make_model_input-cohort_prevax-sub_age_80_110-myasthenia
    - make_model_input-cohort_prevax-sub_age_80_110-pern_anaemia
    - make_model_input-cohort_prevax-sub_age_80_110-pmr
    - make_model_input-cohort_prevax-sub_age_80_110-psoa
    - make_model_input-cohort_prevax-sub_age_80_110-psoriasis
    - make_model_input-cohort_prevax-sub_age_80_110-ra
    - make_model_input-cohort_prevax-sub_age_80_110-uc
    outputs:
      moderately_sensitive:
        table2: output/table2_prevax.csv
        table2_midpoint6: output/table2_prevax_midpoint6.csv

  ## Table 2 - unvax 

  table2_unvax:
    run: r:latest analysis/descriptives/table2.R unvax
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-addison
    - make_model_input-cohort_unvax-sub_age_18_39-apa
    - make_model_input-cohort_unvax-sub_age_18_39-axial
    - make_model_input-cohort_unvax-sub_age_18_39-celiac
    - make_model_input-cohort_unvax-sub_age_18_39-composite_ai
    - make_model_input-cohort_unvax-sub_age_18_39-crohn
    - make_model_input-cohort_unvax-sub_age_18_39-grave
    - make_model_input-cohort_unvax-sub_age_18_39-grp1_ifa
    - make_model_input-cohort_unvax-sub_age_18_39-grp2_ctd
    - make_model_input-cohort_unvax-sub_age_18_39-grp3_isd
    - make_model_input-cohort_unvax-sub_age_18_39-grp4_agi_ibd
    - make_model_input-cohort_unvax-sub_age_18_39-grp5_atv
    - make_model_input-cohort_unvax-sub_age_18_39-grp6_trd
    - make_model_input-cohort_unvax-sub_age_18_39-grp7_htd
    - make_model_input-cohort_unvax-sub_age_18_39-grp8_ind
    - make_model_input-cohort_unvax-sub_age_18_39-hs
    - make_model_input-cohort_unvax-sub_age_18_39-ibd
    - make_model_input-cohort_unvax-sub_age_18_39-immune_thromb
    - make_model_input-cohort_unvax-sub_age_18_39-ms
    - make_model_input-cohort_unvax-sub_age_18_39-myasthenia
    - make_model_input-cohort_unvax-sub_age_18_39-pern_anaemia
    - make_model_input-cohort_unvax-sub_age_18_39-pmr
    - make_model_input-cohort_unvax-sub_age_18_39-psoa
    - make_model_input-cohort_unvax-sub_age_18_39-psoriasis
    - make_model_input-cohort_unvax-sub_age_18_39-ra
    - make_model_input-cohort_unvax-sub_age_18_39-uc
    - make_model_input-cohort_unvax-sub_age_40_59-addison
    - make_model_input-cohort_unvax-sub_age_40_59-apa
    - make_model_input-cohort_unvax-sub_age_40_59-axial
    - make_model_input-cohort_unvax-sub_age_40_59-celiac
    - make_model_input-cohort_unvax-sub_age_40_59-composite_ai
    - make_model_input-cohort_unvax-sub_age_40_59-crohn
    - make_model_input-cohort_unvax-sub_age_40_59-grave
    - make_model_input-cohort_unvax-sub_age_40_59-grp1_ifa
    - make_model_input-cohort_unvax-sub_age_40_59-grp2_ctd
    - make_model_input-cohort_unvax-sub_age_40_59-grp3_isd
    - make_model_input-cohort_unvax-sub_age_40_59-grp4_agi_ibd
    - make_model_input-cohort_unvax-sub_age_40_59-grp5_atv
    - make_model_input-cohort_unvax-sub_age_40_59-grp6_trd
    - make_model_input-cohort_unvax-sub_age_40_59-grp7_htd
    - make_model_input-cohort_unvax-sub_age_40_59-grp8_ind
    - make_model_input-cohort_unvax-sub_age_40_59-hs
    - make_model_input-cohort_unvax-sub_age_40_59-ibd
    - make_model_input-cohort_unvax-sub_age_40_59-immune_thromb
    - make_model_input-cohort_unvax-sub_age_40_59-ms
    - make_model_input-cohort_unvax-sub_age_40_59-myasthenia
    - make_model_input-cohort_unvax-sub_age_40_59-pern_anaemia
    - make_model_input-cohort_unvax-sub_age_40_59-pmr
    - make_model_input-cohort_unvax-sub_age_40_59-psoa
    - make_model_input-cohort_unvax-sub_age_40_59-psoriasis
    - make_model_input-cohort_unvax-sub_age_40_59-ra
    - make_model_input-cohort_unvax-sub_age_40_59-uc
    - make_model_input-cohort_unvax-sub_age_60_79-addison
    - make_model_input-cohort_unvax-sub_age_60_79-apa
    - make_model_input-cohort_unvax-sub_age_60_79-axial
    - make_model_input-cohort_unvax-sub_age_60_79-celiac
    - make_model_input-cohort_unvax-sub_age_60_79-composite_ai
    - make_model_input-cohort_unvax-sub_age_60_79-crohn
    - make_model_input-cohort_unvax-sub_age_60_79-grave
    - make_model_input-cohort_unvax-sub_age_60_79-grp1_ifa
    - make_model_input-cohort_unvax-sub_age_60_79-grp2_ctd
    - make_model_input-cohort_unvax-sub_age_60_79-grp3_isd
    - make_model_input-cohort_unvax-sub_age_60_79-grp4_agi_ibd
    - make_model_input-cohort_unvax-sub_age_60_79-grp5_atv
    - make_model_input-cohort_unvax-sub_age_60_79-grp6_trd
    - make_model_input-cohort_unvax-sub_age_60_79-grp7_htd
    - make_model_input-cohort_unvax-sub_age_60_79-grp8_ind
    - make_model_input-cohort_unvax-sub_age_60_79-hs
    - make_model_input-cohort_unvax-sub_age_60_79-ibd
    - make_model_input-cohort_unvax-sub_age_60_79-immune_thromb
    - make_model_input-cohort_unvax-sub_age_60_79-ms
    - make_model_input-cohort_unvax-sub_age_60_79-myasthenia
    - make_model_input-cohort_unvax-sub_age_60_79-pern_anaemia
    - make_model_input-cohort_unvax-sub_age_60_79-pmr
    - make_model_input-cohort_unvax-sub_age_60_79-psoa
    - make_model_input-cohort_unvax-sub_age_60_79-psoriasis
    - make_model_input-cohort_unvax-sub_age_60_79-ra
    - make_model_input-cohort_unvax-sub_age_60_79-uc
    - make_model_input-cohort_unvax-sub_age_80_110-addison
    - make_model_input-cohort_unvax-sub_age_80_110-apa
    - make_model_input-cohort_unvax-sub_age_80_110-axial
    - make_model_input-cohort_unvax-sub_age_80_110-celiac
    - make_model_input-cohort_unvax-sub_age_80_110-composite_ai
    - make_model_input-cohort_unvax-sub_age_80_110-crohn
    - make_model_input-cohort_unvax-sub_age_80_110-grave
    - make_model_input-cohort_unvax-sub_age_80_110-grp1_ifa
    - make_model_input-cohort_unvax-sub_age_80_110-grp2_ctd
    - make_model_input-cohort_unvax-sub_age_80_110-grp3_isd
    - make_model_input-cohort_unvax-sub_age_80_110-grp4_agi_ibd
    - make_model_input-cohort_unvax-sub_age_80_110-grp5_atv
    - make_model_input-cohort_unvax-sub_age_80_110-grp6_trd
    - make_model_input-cohort_unvax-sub_age_80_110-grp7_htd
    - make_model_input-cohort_unvax-sub_age_80_110-grp8_ind
    - make_model_input-cohort_unvax-sub_age_80_110-hs
    - make_model_input-cohort_unvax-sub_age_80_110-ibd
    - make_model_input-cohort_unvax-sub_age_80_110-immune_thromb
    - make_model_input-cohort_unvax-sub_age_80_110-ms
    - make_model_input-cohort_unvax-sub_age_80_110-myasthenia
    - make_model_input-cohort_unvax-sub_age_80_110-pern_anaemia
    - make_model_input-cohort_unvax-sub_age_80_110-pmr
    - make_model_input-cohort_unvax-sub_age_80_110-psoa
    - make_model_input-cohort_unvax-sub_age_80_110-psoriasis
    - make_model_input-cohort_unvax-sub_age_80_110-ra
    - make_model_input-cohort_unvax-sub_age_80_110-uc
    outputs:
      moderately_sensitive:
        table2: output/table2_unvax.csv
        table2_midpoint6: output/table2_unvax_midpoint6.csv

  ## Table 2 - vax 

  table2_vax:
    run: r:latest analysis/descriptives/table2.R vax
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-addison
    - make_model_input-cohort_vax-sub_age_18_39-apa
    - make_model_input-cohort_vax-sub_age_18_39-axial
    - make_model_input-cohort_vax-sub_age_18_39-celiac
    - make_model_input-cohort_vax-sub_age_18_39-composite_ai
    - make_model_input-cohort_vax-sub_age_18_39-crohn
    - make_model_input-cohort_vax-sub_age_18_39-grave
    - make_model_input-cohort_vax-sub_age_18_39-grp1_ifa
    - make_model_input-cohort_vax-sub_age_18_39-grp2_ctd
    - make_model_input-cohort_vax-sub_age_18_39-grp3_isd
    - make_model_input-cohort_vax-sub_age_18_39-grp4_agi_ibd
    - make_model_input-cohort_vax-sub_age_18_39-grp5_atv
    - make_model_input-cohort_vax-sub_age_18_39-grp6_trd
    - make_model_input-cohort_vax-sub_age_18_39-grp7_htd
    - make_model_input-cohort_vax-sub_age_18_39-grp8_ind
    - make_model_input-cohort_vax-sub_age_18_39-hs
    - make_model_input-cohort_vax-sub_age_18_39-ibd
    - make_model_input-cohort_vax-sub_age_18_39-immune_thromb
    - make_model_input-cohort_vax-sub_age_18_39-ms
    - make_model_input-cohort_vax-sub_age_18_39-myasthenia
    - make_model_input-cohort_vax-sub_age_18_39-pern_anaemia
    - make_model_input-cohort_vax-sub_age_18_39-pmr
    - make_model_input-cohort_vax-sub_age_18_39-psoa
    - make_model_input-cohort_vax-sub_age_18_39-psoriasis
    - make_model_input-cohort_vax-sub_age_18_39-ra
    - make_model_input-cohort_vax-sub_age_18_39-uc
    - make_model_input-cohort_vax-sub_age_40_59-addison
    - make_model_input-cohort_vax-sub_age_40_59-apa
    - make_model_input-cohort_vax-sub_age_40_59-axial
    - make_model_input-cohort_vax-sub_age_40_59-celiac
    - make_model_input-cohort_vax-sub_age_40_59-composite_ai
    - make_model_input-cohort_vax-sub_age_40_59-crohn
    - make_model_input-cohort_vax-sub_age_40_59-grave
    - make_model_input-cohort_vax-sub_age_40_59-grp1_ifa
    - make_model_input-cohort_vax-sub_age_40_59-grp2_ctd
    - make_model_input-cohort_vax-sub_age_40_59-grp3_isd
    - make_model_input-cohort_vax-sub_age_40_59-grp4_agi_ibd
    - make_model_input-cohort_vax-sub_age_40_59-grp5_atv
    - make_model_input-cohort_vax-sub_age_40_59-grp6_trd
    - make_model_input-cohort_vax-sub_age_40_59-grp7_htd
    - make_model_input-cohort_vax-sub_age_40_59-grp8_ind
    - make_model_input-cohort_vax-sub_age_40_59-hs
    - make_model_input-cohort_vax-sub_age_40_59-ibd
    - make_model_input-cohort_vax-sub_age_40_59-immune_thromb
    - make_model_input-cohort_vax-sub_age_40_59-ms
    - make_model_input-cohort_vax-sub_age_40_59-myasthenia
    - make_model_input-cohort_vax-sub_age_40_59-pern_anaemia
    - make_model_input-cohort_vax-sub_age_40_59-pmr
    - make_model_input-cohort_vax-sub_age_40_59-psoa
    - make_model_input-cohort_vax-sub_age_40_59-psoriasis
    - make_model_input-cohort_vax-sub_age_40_59-ra
    - make_model_input-cohort_vax-sub_age_40_59-uc
    - make_model_input-cohort_vax-sub_age_60_79-addison
    - make_model_input-cohort_vax-sub_age_60_79-apa
    - make_model_input-cohort_vax-sub_age_60_79-axial
    - make_model_input-cohort_vax-sub_age_60_79-celiac
    - make_model_input-cohort_vax-sub_age_60_79-composite_ai
    - make_model_input-cohort_vax-sub_age_60_79-crohn
    - make_model_input-cohort_vax-sub_age_60_79-grave
    - make_model_input-cohort_vax-sub_age_60_79-grp1_ifa
    - make_model_input-cohort_vax-sub_age_60_79-grp2_ctd
    - make_model_input-cohort_vax-sub_age_60_79-grp3_isd
    - make_model_input-cohort_vax-sub_age_60_79-grp4_agi_ibd
    - make_model_input-cohort_vax-sub_age_60_79-grp5_atv
    - make_model_input-cohort_vax-sub_age_60_79-grp6_trd
    - make_model_input-cohort_vax-sub_age_60_79-grp7_htd
    - make_model_input-cohort_vax-sub_age_60_79-grp8_ind
    - make_model_input-cohort_vax-sub_age_60_79-hs
    - make_model_input-cohort_vax-sub_age_60_79-ibd
    - make_model_input-cohort_vax-sub_age_60_79-immune_thromb
    - make_model_input-cohort_vax-sub_age_60_79-ms
    - make_model_input-cohort_vax-sub_age_60_79-myasthenia
    - make_model_input-cohort_vax-sub_age_60_79-pern_anaemia
    - make_model_input-cohort_vax-sub_age_60_79-pmr
    - make_model_input-cohort_vax-sub_age_60_79-psoa
    - make_model_input-cohort_vax-sub_age_60_79-psoriasis
    - make_model_input-cohort_vax-sub_age_60_79-ra
    - make_model_input-cohort_vax-sub_age_60_79-uc
    - make_model_input-cohort_vax-sub_age_80_110-addison
    - make_model_input-cohort_vax-sub_age_80_110-apa
    - make_model_input-cohort_vax-sub_age_80_110-axial
    - make_model_input-cohort_vax-sub_age_80_110-celiac
    - make_model_input-cohort_vax-sub_age_80_110-composite_ai
    - make_model_input-cohort_vax-sub_age_80_110-crohn
    - make_model_input-cohort_vax-sub_age_80_110-grave
    - make_model_input-cohort_vax-sub_age_80_110-grp1_ifa
    - make_model_input-cohort_vax-sub_age_80_110-grp2_ctd
    - make_model_input-cohort_vax-sub_age_80_110-grp3_isd
    - make_model_input-cohort_vax-sub_age_80_110-grp4_agi_ibd
    - make_model_input-cohort_vax-sub_age_80_110-grp5_atv
    - make_model_input-cohort_vax-sub_age_80_110-grp6_trd
    - make_model_input-cohort_vax-sub_age_80_110-grp7_htd
    - make_model_input-cohort_vax-sub_age_80_110-grp8_ind
    - make_model_input-cohort_vax-sub_age_80_110-hs
    - make_model_input-cohort_vax-sub_age_80_110-ibd
    - make_model_input-cohort_vax-sub_age_80_110-immune_thromb
    - make_model_input-cohort_vax-sub_age_80_110-ms
    - make_model_input-cohort_vax-sub_age_80_110-myasthenia
    - make_model_input-cohort_vax-sub_age_80_110-pern_anaemia
    - make_model_input-cohort_vax-sub_age_80_110-pmr
    - make_model_input-cohort_vax-sub_age_80_110-psoa
    - make_model_input-cohort_vax-sub_age_80_110-psoriasis
    - make_model_input-cohort_vax-sub_age_80_110-ra
    - make_model_input-cohort_vax-sub_age_80_110-uc
    outputs:
      moderately_sensitive:
        table2: output/table2_vax.csv
        table2_midpoint6: output/table2_vax_midpoint6.csv