project.yaml

version: "3.0"

expectations:
  population_size: 100000

actions:
  generate_cohortMAIN:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_cohort2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019
    outputs:
      highly_sensitive:
        cohort: output/input_2019.csv
  
  generate_cohortSEPT2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sept2020
    outputs:
      highly_sensitive:
        cohort: output/input_sept2020.csv
        
  generate_flowchartdata:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart.csv

  crMAIN:
    run: stata-mp:latest analysis/cr_create_analysis_dataset_GENERAL.do MAIN
    needs: [generate_cohortMAIN]
    outputs:
      highly_sensitive:
        data: analysis/cr_create_analysis_dataset_MAIN_STSET.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_datasetMAIN.log
  
  crSEPT2020:
    run: stata-mp:latest analysis/cr_create_analysis_dataset_GENERAL.do SEPT2020
    needs: [generate_cohortSEPT2020]
    outputs:
      highly_sensitive:
        data: analysis/cr_create_analysis_dataset_SEPT2020_STSET.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_datasetSEPT2020.log
  
  cr2019:
    run: stata-mp:latest analysis/cr_create_analysis_dataset_GENERAL.do 2019
    needs: [generate_cohort2019]
    outputs:
      highly_sensitive:
        data: analysis/cr_create_analysis_dataset_2019_STSET.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset2019.log
  
  imputedataMAIN:
    run: stata-mp:latest analysis/an_impute_GENERAL.do MAIN
    needs: [crMAIN]
    outputs:
      highly_sensitive:
        data: analysis/an_impute_imputeddata_MAIN.dta
      moderately_sensitive:
        log: analysis/output/an_impute_MAIN.log

  imputedataSEPT2020:
    run: stata-mp:latest analysis/an_impute_GENERAL.do SEPT2020
    needs: [crSEPT2020]
    outputs:
      highly_sensitive:
        data: analysis/an_impute_imputeddata_SEPT2020.dta
      moderately_sensitive:
        log: analysis/output/an_impute_SEPT2020.log
  
  imputedata2019:
    run: stata-mp:latest analysis/an_impute_GENERAL.do 2019
    needs: [cr2019]
    outputs:
      highly_sensitive:
        data: analysis/an_impute_imputeddata_2019.dta
      moderately_sensitive:
        log: analysis/output/an_impute_2019.log
    
  descriptive_table1:
    run: stata-mp:latest analysis/an_tablecontent_PublicationDescriptivesTable.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_tablecontent_PublicationDescriptivesTable.txt
  
  absoluterisksbycause:
    run: stata-mp:latest analysis/an_covid_vs_othercauses_abs_AGE.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covid_vs_othercauses_abs_AGE.log
        graph: analysis/output/an_covid_vs_othercauses_abs_AGE_GRAPH.svg
        estimates: analysis/output/an_covid_vs_othercauses_abs_AGE_ESTIMATES.dta

  agesexmodelsMAIN:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do MAIN
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex_MAIN.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_MAIN*.ster

  agesexmodelsSEPT2020:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do SEPT2020
    needs: [crSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex_SEPT2020.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_SEPT2020*.ster
 
  agesexmodels2019:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do 2019
    needs: [cr2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex_2019.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_2019*.ster
 
  agesexmodelsSA_anyonDC:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do MAIN SA_anywhereonDC
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex_MAINSA_anywhereonDC.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_MAINSA_anywhereonDC*.ster

  agesexmodelsSA_u071only:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do MAIN SA_u071only
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex_MAINSA_u071only.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_MAINSA_u071only*.ster

  fullmodelsMAIN:
    run: stata-mp:latest analysis/an_covidvsnoncovid_full_GENERAL.do MAIN
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_full_MAIN.log
        models: analysis/output/models/an_covidvsnoncovid_full_MAIN*.ster

  fullmodelsSEPT2020:
    run: stata-mp:latest analysis/an_covidvsnoncovid_full_GENERAL.do SEPT2020
    needs: [crSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_full_SEPT2020.log
        models: analysis/output/models/an_covidvsnoncovid_full_SEPT2020*.ster

  fullmodels2019:
    run: stata-mp:latest analysis/an_covidvsnoncovid_full_GENERAL.do 2019
    needs: [cr2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_full_2019.log
        models: analysis/output/models/an_covidvsnoncovid_full_2019*.ster
  
  ethnicity_model_and_graph:
    run: stata-mp:latest analysis/an_ethnicitybycod_logisticversion.do
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_ethnicitybycod_logisticversion.log
        graph: analysis/output/an_ethnicitybycod_logisticversion.svg
 
  deathsonly_models:
    run: stata-mp:latest analysis/an_deathsonlyanalysis.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_deathsonlyanalysis.log
        models: analysis/output/models/an_deathsonlyanalysis_*.ster  

  imp_modelMAIN_C_AGESEX:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN coviddeath agesex agespl
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed_MAIN_coviddeath_agesex_agespl.log
        models: analysis/output/models/an_imputed_agesex_MAIN_coviddeath.ster  
         
  imp_modelMAIN_NC_AGESEX:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN noncoviddeath agesex agespl
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed_MAIN_noncoviddeath_agesex_agespl.log
        models: analysis/output/models/an_imputed_agesex_MAIN_noncoviddeath.ster  
         
  imp_modelMAIN_C_FULLspl:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN coviddeath full agespl
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
         
  imp_modelMAIN_C_FULLgrp:    
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN coviddeath full agegrp
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelMAIN_NC_FULLspl:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN noncoviddeath full agespl
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelMAIN_NC_FULLgrp:    
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN noncoviddeath full agegrp
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_C_AGESEX:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 coviddeath agesex agespl
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_NC_AGESEX:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 noncoviddeath agesex agespl
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_C_FULLspl:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 coviddeath full agespl
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_C_FULLgrp:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 coviddeath full agegrp
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_NC_FULLspl:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 noncoviddeath full agespl
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_NC_FULLgrp:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 noncoviddeath full agegrp
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_model2019_AGESEX:
    run: stata-mp:latest analysis/an_imputed_GENERAL 2019 primarycaredeath agesex agespl
    needs: [imputedata2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_model2019_FULLspl: 
    run: stata-mp:latest analysis/an_imputed_GENERAL 2019 primarycaredeath full agespl
    needs: [imputedata2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_model2019_FULLgrp:
    run: stata-mp:latest analysis/an_imputed_GENERAL 2019 primarycaredeath full agegrp
    needs: [imputedata2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelMAIN_C_SAanywhereonDC:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN coviddeath agesex agespl SA_anywhereonDC
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
        
  imp_modelMAIN_NC_SAanywhereonDC:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN noncoviddeath agesex agespl SA_anywhereonDC
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
        
  imp_modelMAIN_C_SAu071only:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN coviddeath agesex agespl SA_u071only
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
        
  imp_modelMAIN_C_SAu071only:   
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN noncoviddeath agesex agespl SA_u071only
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelMAIN_DEATHSONLY:     
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN deathsonlyCvN agesex agespl
    needs: [imputedataMAIN]  
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
        
  covnoncov_forestplot:
    run: stata-mp:latest analysis/an_processout_agesex_covvsnon_forestplots.do
    needs: 
      - agesexmodelsMAIN 
      - imp_modelMAIN_C_AGESEX 
      - imp_modelMAIN_NC_AGESEX
    outputs:
      moderately_sensitive:
        log: analysis/output/an_processout_agesex_covvsnon_forestplots_TABLE.txt
        graph: analysis/output/an_processout_agesex_covvsnon_forestplots_GRAPH.svg
 
  covnoncov_appxestimatestable:
    run: stata-mp:latest analysis/an_processout_agesex_covvsnon_table.do
    needs: 
      - agesexmodelsMAIN 
      - agesexmodels2019
      - imp_modelMAIN_C_AGESEX
      - imp_modelMAIN_NC_AGESEX
      - imp_model2019_AGESEX
      - imp_modelMAIN_C_FULLspl
      - imp_modelMAIN_C_FULLgrp
      - imp_modelMAIN_NC_FULLspl
      - imp_modelMAIN_NC_FULLgrp
      - imp_model2019_FULLspl
      - imp_model2019_FULLgrp
    outputs:
      moderately_sensitive:
        log: analysis/output/an_processout_agesex_covvsnon_table.txt
 
  deathsonly_ORfigure:
    run: stata-mp:latest analysis/an_processout_deathsonlyanalysis.do
    needs: 
      - deathsonly_models 
      - imp_modelMAIN_DEATHSONLY
    outputs:
      moderately_sensitive:
        log: analysis/output/an_processout_deathsonlyanalysis_TABLE.txt
        graph: analysis/output/an_processout_deathsonlyanalysis_GRAPH.svg 


  run_model:
    run: stata-mp:latest analysis/model.do
    needs: [generate_cohorts]
    outputs:
      moderately_sensitive:
        log: logs/model.log

  run_all:
    needs:
      - run_model
    # In order to be valid this action needs to define a run commmand and some
    # output. We don't really care what these are but the below does the trick.
    # In a future release of the platform, this special action won't need to be
    # defined at all.
    run: cohortextractor:latest --version
    outputs:
      moderately_sensitive:
        whatever: project.yaml