Job request: 708

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
        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_icu:
    run: stata-mp:latest analysis/01e_eth_cr_stset_icu.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stsetons_icu: output/analysis_dataset_STSET_icu.dta
      moderately_sensitive:
        log: logs/01e_eth_cr_stset_icu.log

  check_eth16:
    run: stata-mp:latest analysis/02a_eth_outcomes_checks_eth16.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/02a_outcomes_checks_eth16.log
        table: output/table0_outcomes_eth16.txt

  check_eth5:
    run: stata-mp:latest analysis/02b_eth_outcomes_checks_eth5.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/02b_outcomes_checks_eth5.log
        table: output/table0_outcomes_eth5.txt

  check_tested:
    run: stata-mp:latest analysis/06_eth_tested_characteristics.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        table: output/table1_tested.txt
        
  table1_eth16:
    run: stata-mp:latest analysis/03a_eth_table1_descriptives_eth16_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/03a_eth_table1_eth16_nocarehomes.log
        table: output/table1_eth16.txt

  table1_eth5:
    run: stata-mp:latest analysis/03b_eth_table1_descriptives_eth5_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/03b_eth_table1_eth5.log
        table: output/table1_eth5.txt

  table1_eth5_carehomes:
    run: stata-mp:latest analysis/03d_eth_table1_descriptives_eth5_carehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/03d_eth_table1_eth5_carehomes.log
        table: output/table1_eth5_carehomes.txt

  main_eth16:
    run: stata-mp:latest analysis/04a_eth_an_multivariable_eth16_nocarehomes.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/04a_eth_an_multivariable_eth16.log
        table: output/table2_eth16.txt
        estout: output/estout_table2_eth16.txt
        graph: output/FP_multivariable_eth16.txt

  icu_eth16:
    run: stata-mp:latest analysis/04a_eth_an_icu_eth16_nocarehomes.do
    needs: [cr_icu]
    outputs:
      moderately_sensitive:
        log: logs/04a_eth_an_icu_eth16.log
        table: output/table2_icu_eth16.txt
        estout: output/estout_icu_eth16.txt
        graph: output/FP_icu_eth16.txt


  main_eth5:
    run: stata-mp:latest analysis/04b_eth_an_multivariable_eth5_nocarehomes.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/04b_eth_an_multivariable_eth5.log
        table: output/table2_eth5.txt
        estout: output/estout_table2_eth5.txt
        graph: output/FP_multivariable_eth5.txt

  icu_eth5:
    run: stata-mp:latest analysis/04b_eth_an_icu_eth5_nocarehomes.do
    needs: [cr_icu]
    outputs:
      moderately_sensitive:
        log: logs/04b_eth_an_icu_eth5.log
        table: output/table2_icu_eth5.txt
        estout: output/estout_icu_eth5.txt
        graph: output/FP_icu_eth5.txt

  main_eth5_carehomes:
    run: stata-mp:latest analysis/04d_eth_an_multivariable_eth5_carehomes.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/04d_eth_an_multivariable_eth5_carehomes.log
        table: output/table2_eth5_carehomes.txt
        estout: output/estout_table2_eth5_carehomes.txt
        graph: output/FP_multivariable_eth5_carehomes.txt

  main_eth16_testedpop:
    run: stata-mp:latest analysis/07a_eth_an_testedpop_eth16_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/07a_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/07b_eth_an_testedpop_eth5_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/07b_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/08a_eth_an_infectedpop_eth16_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/08a_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/08b_eth_an_infectedpop_eth5_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/08b_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

  icu_eth5_carehomes:
    run: stata-mp:latest analysis/04d_eth_an_icu_eth5_carehomes.do
    needs: [cr_icu]
    outputs:
      moderately_sensitive:
        log: logs/04d_eth_an_icu_eth5_carehomes.log
        table: output/table2_icu_eth5_carehomes.txt
        estout: output/estout_icu_eth5_carehomes.txt
        graph: output/FP_icu_eth5_carehomes.txt