Job request: 168

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher George Hickman requested one or more actions to be run against real patient data in the School Age Children project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

ID Status Action
wx27ra4bje2ra4ai-manually-set Succeeded 12_an_tablecontent_HRtable_SENSE_covid_death

Pipeline

Show Hide project.yaml
version: "3.0"
expectations:
  population_size: 20000

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

  worms_generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_worms
    outputs:
      highly_sensitive:
        cohort: output/input_worms.csv

  01_cr_analysis_dataset:
    needs: [generate_cohort]
    run: stata-mp:latest analysis/01_cr_analysis_dataset.do
    outputs:
      moderately_sensitive:
        log: log/01_cr_analysis_dataset.log
      highly_sensitive:
        check_data: "tempdata/analysis_dataset.dta"
        data: "tempdata/cr_create_analysis_dataset_STSET_*_ageband_*.dta"
        ageband_data: "tempdata/analysis_dataset_ageband_*.dta"

  WORMS_01_cr_analysis_dataset:
    needs: [worms_generate_cohort]
    run: stata-mp:latest analysis/WORMS_01_cr_analysis_dataset.do
    outputs:
      moderately_sensitive:
        log: log/WORMS_01_cr_analysis_dataset.log
      highly_sensitive:
        check_data: "tempdata/analysis_dataset_worms.dta"
        data: "tempdata/cr_create_analysis_dataset_STSET_worms_ageband_*.dta"
        ageband_data: "tempdata/analysis_dataset_worms_ageband_*.dta"

  02_an_data_checks:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/02_an_data_checks.do
    outputs:
      moderately_sensitive:
        log: log/02_an_data_checks.log
        histogram: "output/01_histogram_outcomes.svg"

  WORMS_02_an_data_checks:
    needs: [WORMS_01_cr_analysis_dataset]
    run: stata-mp:latest analysis/WORMS_02_an_data_checks.do
    outputs:
      moderately_sensitive:
        log: log/WORMS_02_an_data_checks.log

  03a_an_descriptive_tables:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/03a_an_descriptive_tables.do
    outputs:
      moderately_sensitive:
        log: log/03a_an_descriptive_tables.log

  03b_an_descriptive_table_1:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/03b_an_descriptive_table_1.do
    outputs:
      moderately_sensitive:
        log: log/03b_an_descriptive_table_1.log
        data: "output/03b_an_descriptive_table_1_kids_cat3_ageband*.txt"

  04a_an_descriptive_tables:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04a_an_descriptive_tables.do
    outputs:
      moderately_sensitive:
        log: log/04a_an_descriptive_tables.log

  04b_an_descriptive_table_2_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do non_covid_death
    outputs:
      moderately_sensitive:
        log: 04b_an_descriptive_table_2_non_covid_death.log
        data: "output/04b_an_descriptive_table_2_non_covid_death_ageband*.txt"

  04b_an_descriptive_table_2_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: 04b_an_descriptive_table_2_covid_tpp_prob.log
        data: "output/04b_an_descriptive_table_2_covid_tpp_prob_ageband*.txt"

  04b_an_descriptive_table_2_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do covid_death
    outputs:
      moderately_sensitive:
        log: 04b_an_descriptive_table_2_covid_death.log
        data: "output/04b_an_descriptive_table_2_covid_death_ageband*.txt"

  04b_an_descriptive_table_2_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do covid_icu
    outputs:
      moderately_sensitive:
        log: 04b_an_descriptive_table_2_covid_icu.log
        data: "output/04b_an_descriptive_table_2_covid_icu_ageband*.txt"

  04b_an_descriptive_table_2_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/04b_an_descriptive_table_2.do covidadmission
    outputs:
      moderately_sensitive:
        log: 04b_an_descriptive_table_2_covidadmission.log
        data: "output/04b_an_descriptive_table_2_covidadmission_ageband*.txt"

  06_univariate_analysis_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do non_covid_death kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_non_covid_death.log
        data: "output/an_univariable_cox_models_non_covid_death_AGESEX_*_ageband_*.ster"

  07a_an_multivariable_cox_models_demogADJ_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_non_covid_death.log
        data: "output/an_multivariate_cox_models_non_covid_death_*_DEMOGADJ_ageband_*.ster"

  07b_an_multivariable_cox_models_FULL_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_non_covid_death.log
        data: "output/an_multivariate_cox_models_non_covid_death_*_MAINFULLYADJMODEL_ageband_*.ster"
        other_data: "output/an_sense_non_covid_death_plus_eth_12mo_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_non_covid_death.log
        data: "output/an_sense_non_covid_death_CCeth_bmi_smok_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_non_covid_death_Sense4_*.log
        data: "output/an_sense_non_covid_death_age_underlying_timescale_ageband_*.ster"

  10_an_interaction_cox_models_shield_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_non_covid_death.log
        data: "output/an_interaction_cox_models_non_covid_death_kids_cat3_shield_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_time_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_time.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_time_non_covid_death.log
        data: "output/an_interaction_cox_models_non_covid_death_kids_cat3_cat_time_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_weeks_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_weeks.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_weeks_non_covid_death.log
        data: "output/an_interaction_cox_models_non_covid_death_week0_ageband_*.ster"

  10_an_interaction_cox_models_sex_non_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_non_covid_death.log
        data: "output/an_interaction_cox_models_non_covid_death_kids_cat3_male_MAINFULLYADJMODEL_*.ster"

  06_univariate_analysis_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do covid_tpp_prob kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_covid_tpp_prob.log
        data: "output/an_univariable_cox_models_covid_tpp_prob_AGESEX_*_ageband_*.ster"

  07a_an_multivariable_cox_models_demogADJ_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_covid_tpp_prob.log
        data: "output/an_multivariate_cox_models_covid_tpp_prob_*_DEMOGADJ_ageband_*.ster"

  07b_an_multivariable_cox_models_FULL_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_tpp_prob.log
        data: "output/an_multivariate_cox_models_covid_tpp_prob_*_MAINFULLYADJMODEL_ageband_*.ster"
        other_data: "output/an_sense_covid_tpp_prob_plus_eth_12mo_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_tpp_prob.log
        data: "output/an_sense_covid_tpp_prob_CCeth_bmi_smok_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_tpp_prob_Sense4_*.log
        data: "output/an_sense_covid_tpp_prob_age_underlying_timescale_ageband_*.ster"

  10_an_interaction_cox_models_shield_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_tpp_prob.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_kids_cat3_shield_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_time_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_time.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_time_covid_tpp_prob.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_kids_cat3_cat_time_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_weeks_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_weeks.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_weeks_covid_tpp_prob.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_week0_ageband_*.ster"

  10_an_interaction_cox_models_sex_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_tpp_prob.log
        data: "output/an_interaction_cox_models_covid_tpp_prob_kids_cat3_male_MAINFULLYADJMODEL_*.ster"

  06_univariate_analysis_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do covid_death kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_covid_death.log
        data: "output/an_univariable_cox_models_covid_death_AGESEX_*_ageband_*.ster"

  07a_an_multivariable_cox_models_demogADJ_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do covid_death
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_covid_death.log
        data: "output/an_multivariate_cox_models_covid_death_*_DEMOGADJ_ageband_*.ster"

  07b_an_multivariable_cox_models_FULL_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covid_death
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_death.log
        data: "output/an_multivariate_cox_models_covid_death_*_MAINFULLYADJMODEL_ageband_*.ster"
        other_data: "output/an_sense_covid_death_plus_eth_12mo_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covid_death
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_death.log
        data: "output/an_sense_covid_death_CCeth_bmi_smok_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covid_death
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_death_Sense4_*.log
        data: "output/an_sense_covid_death_age_underlying_timescale_ageband_*.ster"

  10_an_interaction_cox_models_shield_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_death.log
        data: "output/an_interaction_cox_models_covid_death_kids_cat3_shield_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_time_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_time.do covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_time_covid_death.log
        data: "output/an_interaction_cox_models_covid_death_kids_cat3_cat_time_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_weeks_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_weeks.do covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_weeks_covid_death.log
        data: "output/an_interaction_cox_models_covid_death_week0_ageband_*.ster"

  10_an_interaction_cox_models_sex_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covid_death
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_death.log
        data: "output/an_interaction_cox_models_covid_death_kids_cat3_male_MAINFULLYADJMODEL_*.ster"

  06_univariate_analysis_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do covid_icu kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_covid_icu.log
        data: "output/an_univariable_cox_models_covid_icu_AGESEX_*_ageband_*.ster"

  07a_an_multivariable_cox_models_demogADJ_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_covid_icu.log
        data: "output/an_multivariate_cox_models_covid_icu_*_DEMOGADJ_ageband_*.ster"

  07b_an_multivariable_cox_models_FULL_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covid_icu.log
        data: "output/an_multivariate_cox_models_covid_icu_*_MAINFULLYADJMODEL_ageband_*.ster"
        other_data: "output/an_sense_covid_icu_plus_eth_12mo_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covid_icu.log
        data: "output/an_sense_covid_icu_CCeth_bmi_smok_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_icu_Sense4_*.log
        data: "output/an_sense_covid_icu_age_underlying_timescale_ageband_*.ster"
        
  07d_an_multivariable_cox_models_FULL_Sense5_covid_tpp_prob:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_tpp_prob_Sense5_time_ints.log
        data: "output/an_sense_covid_tpp_prob_time_int_ageband_*.ster"       
 
  07d_an_multivariable_cox_models_FULL_Sense5_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense5_time_ints.log
        data: "output/an_sense_covidadmission_time_int_ageband_*.ster" 
        
  07d_an_multivariable_cox_models_FULL_Sense5_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_icu_Sense5_time_ints.log
        data: "output/an_sense_covid_icu_time_int_ageband_*.ster" 
        
  07d_an_multivariable_cox_models_FULL_Sense5_covid_death:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense5.do covid_death
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covid_death_Sense5_time_ints.log
        data: "output/an_sense_covid_death_time_int_ageband_*.ster"     

  10_an_interaction_cox_models_shield_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covid_icu.log
        data: "output/an_interaction_cox_models_covid_icu_kids_cat3_shield_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_time_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_time.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_time_covid_icu.log
        data: "output/an_interaction_cox_models_covid_icu_kids_cat3_cat_time_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_weeks_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_weeks.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_weeks_covid_icu.log
        data: "output/an_interaction_cox_models_covid_icu_week0_ageband_*.ster"

  10_an_interaction_cox_models_sex_covid_icu:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covid_icu.log
        data: "output/an_interaction_cox_models_covid_icu_kids_cat3_male_MAINFULLYADJMODEL_*.ster"

  06_univariate_analysis_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_univariate_analysis.do covidadmission kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/06_univariate_analysis_covidadmission.log
        data: "output/an_univariable_cox_models_covidadmission_AGESEX_*_ageband_*.ster"

  07a_an_multivariable_cox_models_demogADJ_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07a_an_multivariable_cox_models_demogADJ.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/07a_an_multivariable_cox_models_covidadmission.log
        data: "output/an_multivariate_cox_models_covidadmission_*_DEMOGADJ_ageband_*.ster"

  07b_an_multivariable_cox_models_FULL_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07b_an_multivariable_cox_models_FULL.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/07b_an_multivariable_cox_models_covidadmission.log
        data: "output/an_multivariate_cox_models_covidadmission_*_MAINFULLYADJMODEL_ageband_*.ster"
        other_data: "output/an_sense_covidadmission_plus_eth_12mo_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense3_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense3.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_FULL_Sense3_covidadmission.log
        data: "output/an_sense_covidadmission_CCeth_bmi_smok_ageband_*.ster"

  07d_an_multivariable_cox_models_FULL_Sense4_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/07d_an_multivariable_cox_models_FULL_Sense4.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/07d_an_multivariable_cox_models_covidadmission_Sense4_*.log
        data: "output/an_sense_covidadmission_age_underlying_timescale_ageband_*.ster"

  10_an_interaction_cox_models_shield_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_shield.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_shield_covidadmission.log
        data: "output/an_interaction_cox_models_covidadmission_kids_cat3_shield_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_time_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_time.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_time_covidadmission.log
        data: "output/an_interaction_cox_models_covidadmission_kids_cat3_cat_time_MAINFULLYADJMODEL_*.ster"

  10_an_interaction_cox_models_weeks_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10a_an_interaction_cox_models_weeks_covidad.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_weeks_covidadmission.log
        data: "output/an_interaction_cox_models_covidadmission_week*_ageband_*.ster"

  10_an_interaction_cox_models_sex_covidadmission:
    needs: [01_cr_analysis_dataset]
    run: stata-mp:latest analysis/10_an_interaction_cox_models_sex.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/10_an_interaction_cox_models_sex_covidadmission.log
        data: "output/an_interaction_cox_models_covidadmission_kids_cat3_male_MAINFULLYADJMODEL_*.ster"

  WORMS_06_univariate_analysis:
    needs: [WORMS_01_cr_analysis_dataset]
    run: stata-mp:latest analysis/WORMS_06_univariate_analysis.do worms kids_cat3 gp_number_kids
    outputs:
      moderately_sensitive:
        log: log/WORMS_06_univariate_analysis.log
        data: "output/an_univariable_cox_models_worms_AGESEX_*_ageband_*.ster"

  WORMS_07a_an_multivariable_cox_models_demogADJ:
    needs: [WORMS_01_cr_analysis_dataset]
    run: stata-mp:latest analysis/WORMS_07a_an_multivariable_cox_models_demogADJ.do worms
    outputs:
      moderately_sensitive:
        log: log/WORMS_07a_an_multivariable_cox_models_demogADJ.log
        data: "output/an_multivariate_cox_models_worms_*_DEMOGADJ_noeth_ageband_*.ster"

  WORMS_07b_an_multivariable_cox_models_FULL:
    needs: [WORMS_01_cr_analysis_dataset]
    run: stata-mp:latest analysis/WORMS_07b_an_multivariable_cox_models_FULL.do worms
    outputs:
      moderately_sensitive:
        log: log/WORMS_07b_an_multivariable_cox_models_FULL.log
        data: "output/an_multivariate_cox_models_worms_*_MAINFULLYADJMODEL_noeth_ageband_*.ster"

  08_an_tablecontent_HRtable_non_covid_death:
    needs:
      - 01_cr_analysis_dataset
      - 06_univariate_analysis_non_covid_death
      - 07a_an_multivariable_cox_models_demogADJ_non_covid_death
      - 07b_an_multivariable_cox_models_FULL_non_covid_death
    run: stata-mp:latest analysis/08_an_tablecontent_HRtable.do non_covid_death
    outputs:
      moderately_sensitive:
        log: log/08_an_tablecontent_HRtable_non_covid_death.log
        data: "output/an_tablecontents_HRtable_non_covid_death.txt"

  08_an_tablecontent_HRtable_covid_tpp_prob:
    needs:
      - 01_cr_analysis_dataset
      - 06_univariate_analysis_covid_tpp_prob
      - 07a_an_multivariable_cox_models_demogADJ_covid_tpp_prob
      - 07b_an_multivariable_cox_models_FULL_covid_tpp_prob
    run: stata-mp:latest analysis/08_an_tablecontent_HRtable.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: log/08_an_tablecontent_HRtable_covid_tpp_prob.log
        data: "output/an_tablecontents_HRtable_covid_tpp_prob.txt"

  08_an_tablecontent_HRtable_covid_death:
    needs:
      - 01_cr_analysis_dataset
      - 06_univariate_analysis_covid_death
      - 07a_an_multivariable_cox_models_demogADJ_covid_death
      - 07b_an_multivariable_cox_models_FULL_covid_death
    run: stata-mp:latest analysis/08_an_tablecontent_HRtable.do covid_death
    outputs:
      moderately_sensitive:
        log: log/08_an_tablecontent_HRtable_covid_death.log
        data: "output/an_tablecontents_HRtable_covid_death.txt"

  08_an_tablecontent_HRtable_covid_icu:
    needs:
      - 01_cr_analysis_dataset
      - 06_univariate_analysis_covid_icu
      - 07a_an_multivariable_cox_models_demogADJ_covid_icu
      - 07b_an_multivariable_cox_models_FULL_covid_icu
    run: stata-mp:latest analysis/08_an_tablecontent_HRtable.do covid_icu
    outputs:
      moderately_sensitive:
        log: log/08_an_tablecontent_HRtable_covid_icu.log
        data: "output/an_tablecontents_HRtable_covid_icu.txt"

  08_an_tablecontent_HRtable_covidadmission:
    needs:
      - 01_cr_analysis_dataset
      - 06_univariate_analysis_covidadmission
      - 07a_an_multivariable_cox_models_demogADJ_covidadmission
      - 07b_an_multivariable_cox_models_FULL_covidadmission
    run: stata-mp:latest analysis/08_an_tablecontent_HRtable.do covidadmission
    outputs:
      moderately_sensitive:
        log: log/08_an_tablecontent_HRtable_covidadmission.log
        data: "output/an_tablecontents_HRtable_covidadmission.txt"

  WORMS_08_an_tablecontent_HRtable:
    needs:
      - WORMS_01_cr_analysis_dataset
      - WORMS_06_univariate_analysis
      - WORMS_07a_an_multivariable_cox_models_demogADJ
      - WORMS_07b_an_multivariable_cox_models_FULL
    run: stata-mp:latest analysis/WORMS_08_an_tablecontent_HRtable.do worms
    outputs:
      moderately_sensitive:
        log: log/WORMS_08_an_tablecontent_HRtable.log
        data: "output/an_tablecontents_HRtable_worms.txt"

  15_anHRfigure_all_outcomes_covidadmission:
    needs:
      - 07b_an_multivariable_cox_models_FULL_non_covid_death
      - 07b_an_multivariable_cox_models_FULL_covid_tpp_prob
      - 07b_an_multivariable_cox_models_FULL_covid_death
      - 07b_an_multivariable_cox_models_FULL_covid_icu
      - 07b_an_multivariable_cox_models_FULL_covidadmission
    run: stata-mp:latest analysis/15_anHRfigure_all_outcomes.do covidadmission
    outputs:
      moderately_sensitive:
        log: 15_anHRfigure_all_outcomes.log
        data: "output/15_an_tablecontents_HRtable_all_outcomes_ANALYSES.txt"
        figure: "output/15_an_HRforest_all_outcomes_ageband_*.svg"

  11_an_interaction_HR_tables_forest_non_covid_death:
    needs:
      - 10_an_interaction_cox_models_shield_non_covid_death
      - 10_an_interaction_cox_models_time_non_covid_death
      - 10_an_interaction_cox_models_weeks_non_covid_death
      - 10_an_interaction_cox_models_sex_non_covid_death
    run: stata-mp:latest analysis/11_an_interaction_HR_tables_forest.do non_covid_death
    outputs:
      moderately_sensitive:
        log: 11_an_interaction_HR_tables_forest_non_covid_death.log
        data: "output/11_an_int_tab_contents_HRtable_non_covid_death.txt"

  11_an_interaction_HR_tables_forest_covid_tpp_prob:
    needs:
      - 10_an_interaction_cox_models_shield_covid_tpp_prob
      - 10_an_interaction_cox_models_time_covid_tpp_prob
      - 10_an_interaction_cox_models_weeks_covid_tpp_prob
      - 10_an_interaction_cox_models_sex_covid_tpp_prob
    run: stata-mp:latest analysis/11_an_interaction_HR_tables_forest.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: 11_an_interaction_HR_tables_forest_covid_tpp_prob.log
        data: "output/11_an_int_tab_contents_HRtable_covid_tpp_prob.txt"

  11_an_interaction_HR_tables_forest_covid_death:
    needs:
      - 10_an_interaction_cox_models_shield_covid_death
      - 10_an_interaction_cox_models_time_covid_death
      - 10_an_interaction_cox_models_weeks_covid_death
      - 10_an_interaction_cox_models_sex_covid_death
    run: stata-mp:latest analysis/11_an_interaction_HR_tables_forest.do covid_death
    outputs:
      moderately_sensitive:
        log: 11_an_interaction_HR_tables_forest_covid_death.log
        data: "output/11_an_int_tab_contents_HRtable_covid_death.txt"

  11_an_interaction_HR_tables_forest_covid_icu:
    needs:
      - 10_an_interaction_cox_models_shield_covid_icu
      - 10_an_interaction_cox_models_time_covid_icu
      - 10_an_interaction_cox_models_weeks_covid_icu
      - 10_an_interaction_cox_models_sex_covid_icu
    run: stata-mp:latest analysis/11_an_interaction_HR_tables_forest.do covid_icu
    outputs:
      moderately_sensitive:
        log: 11_an_interaction_HR_tables_forest_covid_icu.log
        data: "output/11_an_int_tab_contents_HRtable_covid_icu.txt"

  11_an_interaction_HR_tables_forest_covidadmission:
    needs:
      - 10_an_interaction_cox_models_shield_covidadmission
      - 10_an_interaction_cox_models_time_covidadmission
      - 10_an_interaction_cox_models_weeks_covidadmission
      - 10_an_interaction_cox_models_sex_covidadmission
    run: stata-mp:latest analysis/11_an_interaction_HR_tables_forest.do covidadmission
    outputs:
      moderately_sensitive:
        log: 11_an_interaction_HR_tables_forest_covidadmission.log
        data: "output/11_an_int_tab_contents_HRtable_covidadmission.txt"

  11a_an_interaction_HR_tables_forest_WEEKS_covidadmission:
    needs:
      - 10_an_interaction_cox_models_shield_non_covid_death
      - 10_an_interaction_cox_models_shield_covid_tpp_prob
      - 10_an_interaction_cox_models_shield_covid_death
      - 10_an_interaction_cox_models_shield_covid_icu
      - 10_an_interaction_cox_models_shield_covidadmission
      - 10_an_interaction_cox_models_time_non_covid_death
      - 10_an_interaction_cox_models_time_covid_tpp_prob
      - 10_an_interaction_cox_models_time_covid_death
      - 10_an_interaction_cox_models_time_covid_icu
      - 10_an_interaction_cox_models_time_covidadmission
      - 10_an_interaction_cox_models_weeks_non_covid_death
      - 10_an_interaction_cox_models_weeks_covid_tpp_prob
      - 10_an_interaction_cox_models_weeks_covid_death
      - 10_an_interaction_cox_models_weeks_covid_icu
      - 10_an_interaction_cox_models_weeks_covidadmission
      - 10_an_interaction_cox_models_sex_non_covid_death
      - 10_an_interaction_cox_models_sex_covid_tpp_prob
      - 10_an_interaction_cox_models_sex_covid_death
      - 10_an_interaction_cox_models_sex_covid_icu
      - 10_an_interaction_cox_models_sex_covidadmission
    run: stata-mp:latest analysis/11a_an_interaction_HR_tables_forest_WEEKS.do covidadmission
    outputs:
      moderately_sensitive:
        log: 11a_an_interaction_HR_tables_forest_WEEKS.log
        data: "output/an_int_tab_contents_HRtable_WEEKS.txt"

  12_an_tablecontent_HRtable_SENSE_non_covid_death:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense3_non_covid_death
      - 07d_an_multivariable_cox_models_FULL_Sense4_non_covid_death
      - 07b_an_multivariable_cox_models_FULL_non_covid_death
    run: stata-mp:latest analysis/12_an_tablecontent_HRtable_SENSE.do non_covid_death
    outputs:
      moderately_sensitive:
        log: 12_an_tablecontent_HRtable_SENSE_non_covid_death.log
        data: "output/12_an_sense_HRtable_non_covid_death_SENSE_ANALYSES.txt"
        figure: "output/12_an_HRforest_SENSE_non_covid_death_ageband_*.svg"

  12_an_tablecontent_HRtable_SENSE_covid_tpp_prob:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense3_covid_tpp_prob
      - 07d_an_multivariable_cox_models_FULL_Sense4_covid_tpp_prob
      - 07d_an_multivariable_cox_models_FULL_Sense5_covid_tpp_prob
      - 07b_an_multivariable_cox_models_FULL_covid_tpp_prob
    run: stata-mp:latest analysis/12_an_tablecontent_HRtable_SENSE.do covid_tpp_prob
    outputs:
      moderately_sensitive:
        log: 12_an_tablecontent_HRtable_SENSE_covid_tpp_prob.log
        data: "output/12_an_sense_HRtable_covid_tpp_prob_SENSE_ANALYSES.txt"
        figure: "output/12_an_HRforest_SENSE_covid_tpp_prob_ageband_*.svg"

  12_an_tablecontent_HRtable_SENSE_covid_death:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense3_covid_death
      - 07d_an_multivariable_cox_models_FULL_Sense4_covid_death
      - 07d_an_multivariable_cox_models_FULL_Sense5_covid_death
      - 07b_an_multivariable_cox_models_FULL_covid_death
    run: stata-mp:latest analysis/12_an_tablecontent_HRtable_SENSE.do covid_death
    outputs:
      moderately_sensitive:
        log: 12_an_tablecontent_HRtable_SENSE_covid_death.log
        data: "output/12_an_sense_HRtable_covid_death_SENSE_ANALYSES.txt"
        figure: "output/12_an_HRforest_SENSE_covid_death_ageband_*.svg"

  12_an_tablecontent_HRtable_SENSE_covid_icu:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense3_covid_icu
      - 07d_an_multivariable_cox_models_FULL_Sense4_covid_icu
      - 07d_an_multivariable_cox_models_FULL_Sense5_covid_icu
      - 07b_an_multivariable_cox_models_FULL_covid_icu
    run: stata-mp:latest analysis/12_an_tablecontent_HRtable_SENSE.do covid_icu
    outputs:
      moderately_sensitive:
        log: 12_an_tablecontent_HRtable_SENSE_covid_icu.log
        data: "output/12_an_sense_HRtable_covid_icu_SENSE_ANALYSES.txt"
        figure: "output/12_an_HRforest_SENSE_covid_icu_ageband_*.svg"

  12_an_tablecontent_HRtable_SENSE_covidadmission:
    needs:
      - 07d_an_multivariable_cox_models_FULL_Sense3_covidadmission
      - 07d_an_multivariable_cox_models_FULL_Sense4_covidadmission
      - 07d_an_multivariable_cox_models_FULL_Sense5_covidadmission
      - 07b_an_multivariable_cox_models_FULL_covidadmission
    run: stata-mp:latest analysis/12_an_tablecontent_HRtable_SENSE.do covidadmission
    outputs:
      moderately_sensitive:
        log: 12_an_tablecontent_HRtable_SENSE_covidadmission.log
        data: "output/12_an_sense_HRtable_covidadmission_SENSE_ANALYSES.txt"
        figure: "output/12_an_HRforest_SENSE_covidadmission_ageband_*.svg"

  run_all:
    needs:
      - 02_an_data_checks
      - 03a_an_descriptive_tables
      - 03b_an_descriptive_table_1
      - 04a_an_descriptive_tables
      - 04b_an_descriptive_table_2_covid_death
      - 04b_an_descriptive_table_2_covid_icu
      - 04b_an_descriptive_table_2_covid_tpp_prob
      - 04b_an_descriptive_table_2_covidadmission
      - 04b_an_descriptive_table_2_non_covid_death
      - 08_an_tablecontent_HRtable_covid_death
      - 08_an_tablecontent_HRtable_covid_icu
      - 08_an_tablecontent_HRtable_covid_tpp_prob
      - 08_an_tablecontent_HRtable_covidadmission
      - 08_an_tablecontent_HRtable_non_covid_death
      - 11_an_interaction_HR_tables_forest_covid_death
      - 11_an_interaction_HR_tables_forest_covid_icu
      - 11_an_interaction_HR_tables_forest_covid_tpp_prob
      - 11_an_interaction_HR_tables_forest_covidadmission
      - 11_an_interaction_HR_tables_forest_non_covid_death
      - 11a_an_interaction_HR_tables_forest_WEEKS_covidadmission
      - 12_an_tablecontent_HRtable_SENSE_covid_death
      - 12_an_tablecontent_HRtable_SENSE_covid_icu
      - 12_an_tablecontent_HRtable_SENSE_covid_tpp_prob
      - 12_an_tablecontent_HRtable_SENSE_covidadmission
      - 12_an_tablecontent_HRtable_SENSE_non_covid_death
      - 15_anHRfigure_all_outcomes_covidadmission
      - WORMS_02_an_data_checks
      - WORMS_08_an_tablecontent_HRtable
    # 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 seems to
    # do the trick.
    run: cohortextractor:latest --version
    outputs:
      moderately_sensitive:
        whatever: project.yaml

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:00:00

Config

  • Backend:
    TPP
  • Workspace:
    school-age-children
  • Branch:
    master
  • Creator:
    ghickman
  • Force run dependencies:
    False
  • Git Commit Hash:
    c2536cf
  • Requested actions:
    • 12_an_tablecontent_HRtable_SENSE_covid_death