Job request: 636

version: "3.0"

expectations:
  population_size: 100000

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


  crmain:
    run: stata-mp:latest analysis/01_eth_cr_analysis_dataset.do
    needs: [generate_cohorts]
    outputs:
      highly_sensitive:
        data: output/analysis_dataset.dta
      moderately_sensitive:
        log: logs/01_eth_cr_analysis_dataset.log

  cr_sgss:
    run: stata-mp:latest analysis/01b_eth_cr_stset_sgss.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stsettested: output/analysis_dataset_STSET_tested.dta
        stsetpositiivetest: output/analysis_dataset_STSET_positivetest.dta
      moderately_sensitive:
        log: logs/01b_eth_cr_stset_sgss.log
  
  cr_hes_covid:
    run: stata-mp:latest analysis/01c_eth_cr_stset_hes.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stsethes: output/analysis_dataset_STSET_hes.dta
        stseticu: output/analysis_dataset_STSET_icu.dta
        stsetonscoviddeath: output/analysis_dataset_STSET_onscoviddeath.dta
      moderately_sensitive:
        log: logs/01c_eth_cr_stset_hes_covid.log

  cr_ons:
    run: stata-mp:latest analysis/01d_eth_cr_stset_death.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stsetons_noncoviddeath: output/analysis_dataset_STSET_ons_noncoviddeath.dta
        stsetonsdeath: output/analysis_dataset_STSET_onsdeath.dta 
      moderately_sensitive:
        log: logs/01d_eth_cr_stset_death.log

  cr_confirmed:
    run: stata-mp:latest analysis/01e_eth_cr_stset_confirmedcovid.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stset_onsconfirmeddeath: output/analysis_dataset_STSET_onsconfirmeddeath.dta 
      moderately_sensitive:
        log: logs/01e_eth_cr_stset_onsconfirmeddeath.log

  cr_underlying:
    run: stata-mp:latest analysis/01f_eth_cr_stset_underlyingcovid.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stset_onsconfirmeddeath: output/analysis_dataset_STSET_onsunderlyingdeath.dta 
      moderately_sensitive:
        log: logs/01e_eth_cr_stset_onsunderlyingdeath.log


  check_region:
    run: stata-mp:latest analysis/02b_eth_region_check.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/02b_region_check.log
        table: output/table0_region.txt

  check_age:
    run: stata-mp:latest analysis/05b_eth_table1_descriptives_eth5_agegroup.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/05b_eth_table1_ages_eth5.log
        table: output/table1_eth5_age.txt

  check_tested:
    run: stata-mp:latest analysis/21_eth_tested_characteristics.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        table: output/table1_tested.txt

  main_carehomes_eth5:
    run: stata-mp:latest analysis/06b_eth_an_multivariable_eth5_carehomesonly.do
    needs: [cr_hes_covid]
    outputs:
      moderately_sensitive:
        log: logs/06b_eth_an_hes_eth5_carehomesonly.log
        table: output/table2_hes_eth5_carehomesonly.txt
        estout: output/estout_table2_hes_eth5_carehomesonly.txt
        graph: output/FP_hes_eth5_carehomesonly.txt
        
  sens_nostp_eth16:
    run: stata-mp:latest analysis/07a_eth_sensanalysis_nostp_eth16.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/07a_eth_sensanalysis_nostp_eth16.log
        table: output/sens_nostp_eth16.txt
        estout: output/estout_sens_nostp_eth16.txt
        graph: output/FP_sens_nostp_eth16.txt

  sens_nostp_eth5:
    run: stata-mp:latest analysis/07b_eth_sensanalysis_nostp_eth5.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/07b_eth_sensanalysis_nostp_eth5.log
        table: output/sens_nostp_eth5.txt
        estout: output/estout_sens_nostp_eth5.txt
        graph: output/FP_sens_nostp_eth5.txt

  sens_ruralurban_eth16:
    run: stata-mp:latest analysis/07c_eth_sensanalysis_ruralurban_eth16.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/07c_eth_sensanalysis_ruralurban_eth16.log
        estout: output/estout_sens_ruralurban_eth16.txt

  sens_confirmed_eth16:
    run: stata-mp:latest analysis/06c_eth_sensanalysis_confirmedcovid_eth16.do
    needs: [cr_confirmed]
    outputs:
      moderately_sensitive:
        log: logs/06c_sens_onsconfirmeddeath_eth16.log
        estout: output/estout_onsconfirmeddeath_eth16.txt
        graph: output/FP_sens_onsconfirmeddeath_eth16.txt

  sens_confirmed_eth5:
    run: stata-mp:latest analysis/06d_eth_sensanalysis_confirmedcovid_eth5.do
    needs: [cr_confirmed]
    outputs:
      moderately_sensitive:
        log: logs/06d_sens_onsconfirmeddeath_eth5.log
        estout: output/estout_onsconfirmeddeath_eth5.txt
        graph: output/FP_sens_onsconfirmeddeath_eth5.txt

  sens_underlying_eth16:
    run: stata-mp:latest analysis/06f_eth_sensanalysis_underlyingcovid_eth16.do
    needs: [cr_underlying]
    outputs:
      moderately_sensitive:
        log: logs/06f_sens_onsunderlyingdeath_eth16.log
        estout: output/estout_onsunderlyingdeath_eth16.txt
        graph: output/FP_sens_onsunderlyingdeath_eth16.txt

  sens_underying_eth5:
    run: stata-mp:latest analysis/06e_eth_sensanalysis_underlyingcovid_eth5.do
    needs: [cr_underlying]
    outputs:
      moderately_sensitive:
        log: logs/06e_sens_onsunderlyingdeath_eth5.log
        estout: output/estout_onsunderlyingdeath_eth5.txt
        graph: output/FP_sens_onsunderlyingdeath_eth5.txt

  main_eth16_testedpop:
    run: stata-mp:latest analysis/11a_eth_an_testedpop_eth16_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/11a_eth_an_testedpop_eth16.log
        table: output/table3_testedpop_eth16_nocarehomes.txt
        estout: output/estout_table3_testedpop_eth16_nocarehomes.txt
        graph: output/FP_testedpop_eth16.txt

  main_eth5_testedpop:
    run: stata-mp:latest analysis/11b_eth_an_testedpop_eth5_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/11b_eth_an_testedpop_eth5.log
        table: output/table3_testedpop_eth5_nocarehomes.txt
        estout: output/estout_table3_testedpop_eth5_nocarehomes.txt
        graph: output/FP_testedpop_eth5.txt

  main_eth16_infectedpop:
    run: stata-mp:latest analysis/11a_eth_an_infectedpop_eth16_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/11a_eth_an_infectedpop_eth16.log
        table: output/table4_infectedpop_eth16_nocarehomes.txt
        estout: output/estout_table4_infectedpop_eth16_nocarehomes.txt
        graph: output/FP_infectedpop_eth16.txt

  main_eth5_infectedpop:
    run: stata-mp:latest analysis/11b_eth_an_infectedpop_eth5_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/11b_eth_an_infectedpop_eth5.log
        table: output/table4_infectedpop_eth5_nocarehomes.txt
        estout: output/estout_table4_infectedpop_eth5_nocarehomes.txt
        graph: output/FP_infectedpop_eth5.txt