project.yaml

version: '3.0'

expectations:
  population_size: 30000

actions:

### study cohort ###
  generate_study_population_case:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case
    outputs:
      highly_sensitive:
        cohort: output/input_case.csv

  generate_study_population_case_test:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_test
    outputs:
      highly_sensitive:
        cohort: output/input_case_test.csv

  generate_study_population_control_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1
    outputs:
      highly_sensitive:
        cohort: output/input_control_1.csv

  generate_study_population_control_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2
    outputs:
      highly_sensitive:
        cohort: output/input_control_2.csv

  generate_study_population_control_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_3
    outputs:
      highly_sensitive:
        cohort: output/input_control_3.csv

  generate_study_population_control_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_4
    outputs:
      highly_sensitive:
        cohort: output/input_control_4.csv

  generate_study_population_control_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_5
    outputs:
      highly_sensitive:
        cohort: output/input_control_5.csv

  generate_study_population_control_6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_6
    outputs:
      highly_sensitive:
        cohort: output/input_control_6.csv

  generate_study_population_control_7:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_7
    outputs:
      highly_sensitive:
        cohort: output/input_control_7.csv

  generate_study_population_control_8:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_8
    outputs:
      highly_sensitive:
        cohort: output/input_control_8.csv

  case_check:  
    run: r:latest analysis/case_check.R
    needs: [generate_study_population_case]
    outputs:
      highly_sensitive:
        cohort: output/case_ch.csv
      moderately_sensitive:
        table1: output/case_check.csv
        table2: output/case_frequency_check.csv

  sepsis_trend:  
    run: r:latest analysis/sepsis_trend.R
    needs: [case_check]
    outputs:
      moderately_sensitive:
        plot1: output/figure_2.1.jpeg
        plot2: output/figure_2.2.jpeg
        plot3: output/figure_2.3.jpeg
        table1: output/figure_2.3_table.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2022-12-31 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  sepsis_trend_rate:  
    run: r:latest analysis/sepsis_trend_rate.R
    needs: [case_check,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_rate.jpeg
        table1: output/figure_rate_table.csv

  sepsis_trend_rate_com:  
    run: r:latest analysis/sepsis_trend_rate_com.R
    needs: [case_check,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_rate_com.jpeg

  sepsis_trend_rate_hos:  
    run: r:latest analysis/sepsis_trend_rate_hos.R
    needs: [case_check,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_rate_hos.jpeg

  process1:  
    run: r:latest analysis/process1.R
    needs: [case_check,generate_study_population_control_1,generate_study_population_control_2,
    generate_study_population_control_3,generate_study_population_control_4,generate_study_population_control_5,
    generate_study_population_control_6,generate_study_population_control_7,generate_study_population_control_8]
    outputs:
      highly_sensitive:
        cohort1: output/case_191.csv
        cohort2: output/case_192.csv
        cohort3: output/case_201.csv
        cohort4: output/case_202.csv
        cohort5: output/case_211.csv
        cohort6: output/case_212.csv
        cohort7: output/case_221.csv
        cohort8: output/case_222.csv
        cohort9: output/control_191.csv
        cohort10: output/control_192.csv
        cohort11: output/control_201.csv
        cohort12: output/control_202.csv
        cohort13: output/control_211.csv
        cohort14: output/control_212.csv
        cohort15: output/control_221.csv
        cohort16: output/control_222.csv

  matching1:
    run: python:latest python analysis/matching1.py
    needs: [process1]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_191.csv
        table2: output/matched_matches_191.csv
        table3: output/matched_combined_191.csv
        table4: output/matched_cases_192.csv
        table5: output/matched_matches_192.csv
        table6: output/matched_combined_192.csv
      moderately_sensitive: 
        report1: output/matching_report_191.txt
        report2: output/matching_report_192.txt

  matching2:
    run: python:latest python analysis/matching2.py
    needs: [process1]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_201.csv
        table2: output/matched_matches_201.csv
        table3: output/matched_combined_201.csv
        table4: output/matched_cases_202.csv
        table5: output/matched_matches_202.csv
        table6: output/matched_combined_202.csv
      moderately_sensitive: 
        report1: output/matching_report_201.txt
        report2: output/matching_report_202.txt

  matching3:
    run: python:latest python analysis/matching3.py
    needs: [process1]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_211.csv
        table2: output/matched_matches_211.csv
        table3: output/matched_combined_211.csv
        table4: output/matched_cases_212.csv
        table5: output/matched_matches_212.csv
        table6: output/matched_combined_212.csv
      moderately_sensitive: 
        report1: output/matching_report_211.txt
        report2: output/matching_report_212.txt

  matching4:
    run: python:latest python analysis/matching4.py
    needs: [process1]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_221.csv
        table2: output/matched_matches_221.csv
        table3: output/matched_combined_221.csv
      moderately_sensitive: 
        report1: output/matching_report_221.txt


  process_covidinclude:  
    run: r:latest analysis/process_covidinclude.R
    needs: [generate_study_population_case]
    outputs:
      highly_sensitive:
        cohort: output/case_covidinclude.csv
      moderately_sensitive:
        table1: output/case_frequency_check1.csv
        table2: output/case_frequency_check2.csv

  sepsis_trend_rate_covidinclude:  
    run: r:latest analysis/sepsis_trend_rate_covidinclude.R
    needs: [process_covidinclude,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_rate_covidinclude.jpeg
        table1: output/figure_rate_covidinclude_table.csv
        plot2: output/figure_rate_covidinclude_com.jpeg
        plot3: output/figure_rate_covidinclude_hos.jpeg

  process_noexclude:  
    run: r:latest analysis/process_noexclude.R
    needs: [generate_study_population_case]
    outputs:
      moderately_sensitive:
        plot1: output/figure_noexclude.jpeg
        table1: output/figure_noexclude_table.csv

  process2_idextraction:  
    run: r:latest analysis/process2_idextraction.R
    needs: [matching1,matching2,matching3,matching4]
    outputs:
      highly_sensitive:
        cohort: output/case_id.csv

  generate_study_population_variables:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_variables
    needs: [process2_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_variables.csv

  process3_idextraction:  
    run: r:latest analysis/process3_idextraction.R
    needs: [matching1,matching2,matching3,matching4]
    outputs:
      highly_sensitive:
        cohort1: output/control_id_191.csv
        cohort2: output/control_id_192.csv
        cohort3: output/control_id_201.csv
        cohort4: output/control_id_202.csv
        cohort5: output/control_id_211.csv
        cohort6: output/control_id_212.csv
        cohort7: output/control_id_221.csv

  generate_study_population_control_var_191:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_191
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_191.csv

  generate_study_population_control_var_192:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_192
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_192.csv

  generate_study_population_control_var_201:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_201
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_201.csv

  generate_study_population_control_var_202:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_202
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_202.csv

  generate_study_population_control_var_211:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_211
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_211.csv

  generate_study_population_control_var_212:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_212
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_212.csv

  generate_study_population_control_var_221:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_221
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_221.csv

  process_data:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population_variables]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_case_data.rds

  process_data_control:
    run: r:latest analysis/data_process_control.R
    needs: [generate_study_population_control_var_191,generate_study_population_control_var_192,
    generate_study_population_control_var_201,generate_study_population_control_var_202,
    generate_study_population_control_var_211,generate_study_population_control_var_212,
    generate_study_population_control_var_221]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_control_data.rds

# Skim data
  skim_data_case:
    run: r:latest analysis/data_skim.R output/processed/input_case_data.rds output/data_properties
    needs: [process_data]
    outputs: 
      moderately_sensitive:
        txt1: output/data_properties/input_case_data_skim.txt
        txt2: output/data_properties/input_case_data_coltypes.txt
        txt3: output/data_properties/input_case_data_tabulate.txt

  skim_data_control:
    run: r:latest analysis/data_skim.R output/processed/input_control_data.rds output/data_properties
    needs: [process_data_control]
    outputs: 
      moderately_sensitive:
        txt1: output/data_properties/input_control_data_skim.txt
        txt2: output/data_properties/input_control_data_coltypes.txt
        txt3: output/data_properties/input_control_data_tabulate.txt

  extract_case_ab_6w: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_ab
    needs: [process2_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_case_ab.csv

  extract_control_ab_6w_191: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_191
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_191.csv

  extract_control_ab_6w_192: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_192
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_192.csv

  extract_control_ab_6w_201: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_201
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_201.csv

  extract_control_ab_6w_202: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_202
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_202.csv

  extract_control_ab_6w_211: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_211
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_211.csv

  extract_control_ab_6w_212: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_212
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_212.csv

  extract_control_ab_6w_221: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_221
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_221.csv

  process_ab_case:
    run: r:latest analysis/process_ab_case.R
    needs: [extract_case_ab_6w]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_case_ab.rds

  process_ab_control:
    run: r:latest analysis/process_ab_control.R
    needs: [extract_control_ab_6w_191,extract_control_ab_6w_192,extract_control_ab_6w_201,
    extract_control_ab_6w_202,extract_control_ab_6w_211,extract_control_ab_6w_212,extract_control_ab_6w_221]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_control_ab.rds

  check_age_dist:  
    run: r:latest analysis/check_age_dist.R
    needs: [matching1,matching2,matching3,matching4]
    outputs:
      moderately_sensitive:
        plot1: output/case_18.jpeg

  extract_case_var_add:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_var_add
    needs: [process2_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_case_var_add.csv

  extract_case_var_add_191: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_191
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_191.csv

  extract_case_var_add_192: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_192
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_192.csv

  extract_case_var_add_201: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_201
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_201.csv

  extract_case_var_add_202: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_202
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_202.csv

  extract_case_var_add_211: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_211
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_211.csv

  extract_case_var_add_212: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_212
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_212.csv

  extract_case_var_add_221: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_221
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_221.csv

  process_model_var:
    run: r:latest analysis/process_model_var.R
    needs: [matching1,matching2,matching3,matching4,
    process_data,process_data_control,
    process_ab_case,process_ab_control,
    process_ab_case_6w,process_ab_control_6w,
    extract_case_var_add,extract_case_var_add_191,
    extract_case_var_add_192,extract_case_var_add_201,
    extract_case_var_add_202,extract_case_var_add_211,
    extract_case_var_add_212,extract_case_var_add_221]
    outputs:
      highly_sensitive: 
        rds1: output/processed/input_model_c_h.rds
        rds2: output/processed/input_model_c.rds
        rds3: output/processed/input_model_h.rds

  process_table_1:
    run: r:latest analysis/Table1.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/table_1_case.csv
        table2: output/table_1_control.csv

  process_table_1_separate:
    run: r:latest analysis/Table1_separate.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/table_1_case_com.csv
        table2: output/table_1_control_com.csv
        table3: output/table_1_case_hos.csv
        table4: output/table_1_control_hos.csv

  process_table_1_byimd:
    run: r:latest analysis/Table1_byimd.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/table_1_imd1_case.csv
        table2: output/table_1_imd2_case.csv
        table3: output/table_1_imd3_case.csv
        table4: output/table_1_imd4_case.csv
        table5: output/table_1_imd5_case.csv
        table6: output/table_1_imd1_control.csv
        table7: output/table_1_imd2_control.csv
        table8: output/table_1_imd3_control.csv
        table9: output/table_1_imd4_control.csv
        table10: output/table_1_imd5_control.csv

  model_crude_ch:
    run: r:latest analysis/model_crude_ch.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_ch.rds

  model_crude_c:
    run: r:latest analysis/model_crude_c.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_c.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_c.rds

  model_crude_h:
    run: r:latest analysis/model_crude_h.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_h.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_h.rds

  model_crude_plot:
    run: r:latest analysis/model_crude_plot.R
    needs: [model_crude_h,model_crude_c,model_crude_ch]
    outputs:
      moderately_sensitive:
        table1: output/crude_plota.csv
        table2: output/crude_plotb.csv

  Figure_2A_crude:  
    run: r:latest analysis/Figure_2A_crude.R
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_2A_crude_1.jpeg
        plot2: output/Figure_2A_crude_2.jpeg

  Figure_2B_crude:  
    run: r:latest analysis/Figure_2B_crude.R
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2B_crude.jpeg

  Figure_2C_crude:  
    run: r:latest analysis/Figure_2C_crude.R
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2C_crude.jpeg

  Figure_2D_crude:  
    run: r:latest analysis/Figure_2D_crude.R
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2D_crude.jpeg

  Figure_2E_crude:  
    run: r:latest analysis/Figure_2E_crude.R
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2E_crude.jpeg

  model_adjusted_plot:
    run: r:latest analysis/model_adjusted_plot.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_plotimd.csv
        table1: output/adjusted_plota.csv
        table2: output/adjusted_plotb.csv
        table3: output/adjusted_plotc.csv
        table4: output/adjusted_plotd.csv
        table5: output/adjusted_plote.csv

  Figure_2A:  
    run: r:latest analysis/Figure_2A.R
    needs: [model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_2A_adjusted_1.jpeg
        plot2: output/Figure_2A_adjusted_2.jpeg

  Figure_2B:  
    run: r:latest analysis/Figure_2B.R
    needs: [model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2B_adjusted.jpeg

  Figure_2C:  
    run: r:latest analysis/Figure_2C.R
    needs: [model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2C_adjusted.jpeg

  Figure_2D:  
    run: r:latest analysis/Figure_2D.R
    needs: [model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2D_adjusted.jpeg

  Figure_2E:  
    run: r:latest analysis/Figure_2E.R
    needs: [model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2E_adjusted.jpeg

  model_adjusted_plot_type:
    run: r:latest analysis/model_adjusted_plot_type.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_type_plotimd.csv
        table1: output/adjusted_type_plota.csv
        table2: output/adjusted_type_plotb.csv
        table3: output/adjusted_type_plotc.csv
        table4: output/adjusted_type_plotd.csv
        table5: output/adjusted_type_plote.csv

  Figure_2E_type:  
    run: r:latest analysis/Figure_2E_type.R
    needs: [model_adjusted_plot_type]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2E_adjusted_type.jpeg

  model_imd:
    run: r:latest analysis/model_imd.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/imd_model.csv
        table2: output/imd_model_covid.csv
        table3: output/imd_model_cardiometabolic.csv
        
  Figure_2_IMD:  
    run: r:latest analysis/Figure_2_IMD.R
    needs: [model_imd]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_2_IMD.jpeg

  Figure_2_IMD_crude:  
    run: r:latest analysis/Figure_2_IMD_crude.R
    needs: [model_imd]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_2_IMD_crude.jpeg

  Figure_2_IMD_combine:  
    run: r:latest analysis/Figure_2_IMD_combine.R
    needs: [model_imd,model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_2_IMD_combine.jpeg

  mortality_rate:
    run: r:latest analysis/mortality_rate.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/model_mortality.csv

  mortality_model_time:
    run: r:latest analysis/mortality_model_time.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/model_mortality_1.csv
        table2: output/model_mortality_2.csv
        table3: output/model_mortality_3.csv
        table4: output/model_mortality_all.csv

  plot_mortality_model:
    run: r:latest -e 'rmarkdown::render("analysis/mortality_model_plot.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [mortality_model_time]
    outputs:
      moderately_sensitive:
        csv: output/mortality_model_plot.html

  mortality_table:
    run: r:latest analysis/mortality_table.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/mortality_table_all.csv
        table2: output/mortality_table_c.csv
        table3: output/mortality_table_h.csv

  age_check:
    run: r:latest analysis/age_check.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        plot1: output/age_check_1.jpeg
        plot2: output/age_check_2.jpeg

  model_adjusted_clinical:
    run: r:latest analysis/model_adjusted_clinical.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_clinical_1.csv
        table1: output/adjusted_clinical_2.csv
        table2: output/adjusted_clinical_3.csv

  Figure_adjusted_clinical:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_adjusted_clinical]
    outputs:
      moderately_sensitive:
        csv: output/Figure_adjusted_clinical.html

  Figure_crude_demo:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_demo.html

  Figure_crude_clinical:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_clinical.html

### adjusted model in period 1/2/3 ###
  model_adjusted_clinical_period_1:
    run: r:latest analysis/model_adjusted_clinical_period_1.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_clinical_1_period_1.csv
        table1: output/adjusted_clinical_2_period_1.csv
        table2: output/adjusted_clinical_3_period_1.csv

  model_adjusted_clinical_period_2:
    run: r:latest analysis/model_adjusted_clinical_period_2.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_clinical_1_period_2.csv
        table1: output/adjusted_clinical_2_period_2.csv
        table2: output/adjusted_clinical_3_period_2.csv

  model_adjusted_clinical_period_3:
    run: r:latest analysis/model_adjusted_clinical_period_3.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_clinical_1_period_3.csv
        table1: output/adjusted_clinical_2_period_3.csv
        table2: output/adjusted_clinical_3_period_3.csv

  Figure_adjusted_clinical_period_1:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical_period_1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_adjusted_clinical_period_1]
    outputs:
      moderately_sensitive:
        csv: output/Figure_adjusted_clinical_period_1.html

  Figure_adjusted_clinical_period_2:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical_period_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_adjusted_clinical_period_2]
    outputs:
      moderately_sensitive:
        csv: output/Figure_adjusted_clinical_period_2.html

  Figure_adjusted_clinical_period_3:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical_period_3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_adjusted_clinical_period_3]
    outputs:
      moderately_sensitive:
        csv: output/Figure_adjusted_clinical_period_3.html

### crude model in period 1/2/3 ###
  model_crude_ch_period_1:
    run: r:latest analysis/model_crude_ch_period_1.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_period_1.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_ch_period_1.rds

  model_crude_ch_period_2:
    run: r:latest analysis/model_crude_ch_period_2.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_period_2.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_ch_period_2.rds

  model_crude_ch_period_3:
    run: r:latest analysis/model_crude_ch_period_3.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_period_3.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_ch_period_3.rds

  model_crude_c_period_1:
    run: r:latest analysis/model_crude_c_period_1.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_c_period_1.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_c_period_1.rds

  model_crude_c_period_2:
    run: r:latest analysis/model_crude_c_period_2.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_c_period_2.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_c_period_2.rds

  model_crude_c_period_3:
    run: r:latest analysis/model_crude_c_period_3.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_c_period_3.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_c_period_3.rds

  model_crude_h_period_1:
    run: r:latest analysis/model_crude_h_period_1.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_h_period_1.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_h_period_1.rds

  model_crude_h_period_2:
    run: r:latest analysis/model_crude_h_period_2.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_h_period_2.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_h_period_2.rds

  model_crude_h_period_3:
    run: r:latest analysis/model_crude_h_period_3.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_h_period_3.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_h_period_3.rds

  model_crude_plot_period_1:
    run: r:latest analysis/model_crude_plot_period_1.R
    needs: [model_crude_h_period_1,model_crude_c_period_1,model_crude_ch_period_1]
    outputs:
      moderately_sensitive:
        table1: output/crude_plota_period_1.csv
        table2: output/crude_plotb_period_1.csv

  model_crude_plot_period_2:
    run: r:latest analysis/model_crude_plot_period_2.R
    needs: [model_crude_h_period_2,model_crude_c_period_2,model_crude_ch_period_2]
    outputs:
      moderately_sensitive:
        table1: output/crude_plota_period_2.csv
        table2: output/crude_plotb_period_2.csv

  model_crude_plot_period_3:
    run: r:latest analysis/model_crude_plot_period_3.R
    needs: [model_crude_h_period_3,model_crude_c_period_3,model_crude_ch_period_3]
    outputs:
      moderately_sensitive:
        table1: output/crude_plota_period_3.csv
        table2: output/crude_plotb_period_3.csv

  Figure_crude_clinical_period_1:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical_period_1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_1]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_clinical_period_1.html

  Figure_crude_clinical_period_2:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical_period_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_2]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_clinical_period_2.html

  Figure_crude_clinical_period_3:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical_period_3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_3]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_clinical_period_3.html

  Figure_crude_demo_period_1:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo_period_1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_1]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_demo_period_1.html

  Figure_crude_demo_period_2:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo_period_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_2]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_demo_period_2.html

  Figure_crude_demo_period_3:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo_period_3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_3]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_demo_period_3.html
### extract ab from -42days to index date
  extract_case_ab_in6w: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_ab_6w
    needs: [process2_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_case_ab_6w.csv

  extract_control_ab_in6w_191: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_191
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_191.csv

  extract_control_ab_in6w_192: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_192
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_192.csv

  extract_control_ab_in6w_201: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_201
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_201.csv

  extract_control_ab_in6w_202: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_202
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_202.csv

  extract_control_ab_in6w_211: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_211
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_211.csv

  extract_control_ab_in6w_212: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_212
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_212.csv

  extract_control_ab_in6w_221: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_221
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_221.csv

  process_ab_case_6w:
    run: r:latest analysis/process_ab_case_6w.R
    needs: [extract_case_ab_in6w]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_case_ab_6w.rds

  process_ab_control_6w:
    run: r:latest analysis/process_ab_control_6w.R
    needs: [extract_control_ab_in6w_191,extract_control_ab_in6w_192,extract_control_ab_in6w_201,
    extract_control_ab_in6w_202,extract_control_ab_in6w_211,extract_control_ab_in6w_212,extract_control_ab_in6w_221]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_control_ab_6w.rds

  Figure_age_community:  
    run: r:latest analysis/Figure_age_community.R
    needs: [process_model_var,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_age_1.jpeg
        plot2: output/figure_age_2.jpeg
        plot3: output/figure_age_3.jpeg

  Figure_age_hospital:  
    run: r:latest analysis/Figure_age_hospital.R
    needs: [process_model_var,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_age_hos_1.jpeg
        plot2: output/figure_age_hos_2.jpeg
        plot3: output/figure_age_hos_3.jpeg

##### sensitivity #####

##### antibiotic use within six weeks #####
  sen_adjusted_clinical_ab_6w:
    run: r:latest analysis/sensitivity/sen_adjusted_clinical_ab_6w.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/sen_adjusted_clinical_ab_6w_1.csv
        table1: output/sen_adjusted_clinical_ab_6w_2.csv
        table2: output/sen_adjusted_clinical_ab_6w_3.csv

  Figure_sen_adjusted_clinical_ab_6w:
    run: r:latest -e 'rmarkdown::render("analysis/sensitivity/Figure_sen_adjusted_clinical_ab_6w.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [sen_adjusted_clinical_ab_6w]
    outputs:
      moderately_sensitive:
        csv: output/Figure_sen_adjusted_clinical_ab_6w.html

  sen_crude_ab_6w:
    run: r:latest analysis/sensitivity/sen_crude_ab_6w.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/sen_crude_ab_6w_plot.csv

  Figure_sen_crude_ab_6w:
    run: r:latest -e 'rmarkdown::render("analysis/sensitivity/Figure_sen_crude_ab_6w.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [sen_crude_ab_6w]
    outputs:
      moderately_sensitive:
        csv: output/Figure_sen_crude_ab_6w.html

##### including 18+ only #####
  model_adjusted_clinical_18:
    run: r:latest analysis/sensitivity/model_adjusted_clinical_18.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_clinical_18_1.csv
        table1: output/adjusted_clinical_18_2.csv
        table2: output/adjusted_clinical_18_3.csv

  Figure_adjusted_clinical_18:
    run: r:latest -e 'rmarkdown::render("analysis/sensitivity/Figure_adjusted_clinical_18.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_adjusted_clinical_18]
    outputs:
      moderately_sensitive:
        csv: output/Figure_adjusted_clinical_18.html

  model_crude_c_18:
    run: r:latest analysis/sensitivity/model_crude_c_18.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_c_18.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_c_18.rds

  model_crude_ch_18:
    run: r:latest analysis/sensitivity/model_crude_ch_18.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_ch_18.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_ch_18.rds

  model_crude_h_18:
    run: r:latest analysis/sensitivity/model_crude_h_18.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_h_18.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_h_18.rds

  model_crude_plot_18:
    run: r:latest analysis/sensitivity/model_crude_plot_18.R
    needs: [model_crude_h_18,model_crude_c_18,model_crude_ch_18]
    outputs:
      moderately_sensitive:
        table1: output/crude_plota_18.csv
        table2: output/crude_plotb_18.csv

  Figure_crude_demo_18:
    run: r:latest -e 'rmarkdown::render("analysis/sensitivity/Figure_crude_demo_18.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_18]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_demo_18.html

  Figure_crude_clinical_18:
    run: r:latest -e 'rmarkdown::render("analysis/sensitivity/Figure_crude_clinical_18.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_18]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_clinical_18.html

  model_imd_18:
    run: r:latest analysis/sensitivity/model_imd_18.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/imd_model_18.csv
        table2: output/imd_model_covid_18.csv
        table3: output/imd_model_cardiometabolic_18.csv

  model_imd_fully_18:
    run: r:latest analysis/sensitivity/model_imd_fully_18.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/model_imd_fully_18.csv

  Figure_IMD_18:  
    run: r:latest analysis/sensitivity/Figure_IMD_18.R
    needs: [model_imd_18,model_imd_fully_18]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_IMD_18.jpeg

##### mortality study #####

  sen_mortality_model_community:
    run: r:latest analysis/sensitivity/sen_mortality_model_community.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/sen_model_mortality_community_1.csv
        table2: output/sen_model_mortality_community_2.csv
        table3: output/sen_model_mortality_community_3.csv
        table4: output/sen_model_mortality_community_all.csv

  Figure_mortality_community:
    run: r:latest -e 'rmarkdown::render("analysis/sensitivity/Figure_mortality_community.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [sen_mortality_model_community]
    outputs:
      moderately_sensitive:
        csv: output/Figure_mortality_community.html

  sen_mortality_model_community_test:
    run: r:latest analysis/sensitivity/sen_mortality_model_community_test.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/sen_model_mortality_community_test.csv