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Job request: 17779

Organisation:
DataLab
Workspace:
long-covid-sick-notes
ID:
s67syc7mp5kp65d7
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Andrea Schaffer requested one or more actions to be run against real patient data in the 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population_covid_2020:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_covid_2020
      --output-dir=output/cohorts
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_covid_2020.csv.gz

  generate_study_population_covid_2021:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_covid_2021
      --output-dir=output/cohorts
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_covid_2021.csv.gz

  generate_study_population_general_match_vars_2019:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_general_match_vars
      --output-dir=output/cohorts
      --output-format=csv.gz
      --index-date-range="2019-02-01"
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_general_match_vars_2019-02-01.csv.gz

  generate_study_population_general_match_vars_2020:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_general_match_vars
      --output-dir=output/cohorts
      --output-format=csv.gz
      --index-date-range="2020-02-01"
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_general_match_vars_2020-02-01.csv.gz

  generate_study_population_general_match_vars_2021:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_general_match_vars
      --output-dir=output/cohorts
      --output-format=csv.gz
      --index-date-range="2021-02-01"
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_general_match_vars_2021-02-01.csv.gz

  generate_study_population_pneumonia_2019:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_pneumonia_2019
      --output-dir=output/cohorts
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_pneumonia_2019.csv.gz

  matching_2019:
    run: python:latest python analysis/match_running.py "2019" --output-dir=output/cohorts
    needs: [generate_study_population_covid_2020, generate_study_population_general_match_vars_2019]
    outputs:
      moderately_sensitive:
        matching_report: output/cohorts/matching_report_general_2019.txt
      highly_sensitive:
        matched_cohort: output/cohorts/matched_matches_general_2019.csv

  matching_2020:
    run: python:latest python analysis/match_running.py "2020" --output-dir=output/cohorts
    needs: [generate_study_population_covid_2020, generate_study_population_general_match_vars_2020]
    outputs:
      moderately_sensitive:
        matching_report: output/cohorts/matching_report_general_2020.txt
      highly_sensitive:
        matched_cohort: output/cohorts/matched_matches_general_2020.csv

  matching_2021:
    run: python:latest python analysis/match_running.py "2021" --output-dir=output/cohorts
    needs: [generate_study_population_covid_2021, generate_study_population_general_match_vars_2021]
    outputs:
      moderately_sensitive:
        matching_report: output/cohorts/matching_report_general_2021.txt
      highly_sensitive:
        matched_cohort: output/cohorts/matched_matches_general_2021.csv

  generate_study_population_matched_2019:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_matched_2019
      --output-dir=output/cohorts
      --output-format=csv.gz
    needs: [matching_2019]
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_matched_2019.csv.gz

  generate_study_population_matched_2020:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_matched_2020
      --output-dir=output/cohorts
      --output-format=csv.gz
    needs: [matching_2020]
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_matched_2020.csv.gz

  generate_study_population_matched_2021:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_matched_2021
      --output-dir=output/cohorts
      --output-format=csv.gz
    needs: [matching_2021]
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_matched_2021.csv.gz

  reconcile_sick_note_spells_covid_2020:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_covid_2020"
    needs: [generate_study_population_covid_2020]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_covid_2020_with_duration.csv

  reconcile_sick_note_spells_covid_2021:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_covid_2021"
    needs: [generate_study_population_covid_2021]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_covid_2021_with_duration.csv

  reconcile_sick_note_spells_general_2019:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_matched_2019"
    needs: [generate_study_population_matched_2019]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_matched_2019_with_duration.csv

  reconcile_sick_note_spells_general_2020:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_matched_2020"
    needs: [generate_study_population_matched_2020]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_matched_2020_with_duration.csv

  reconcile_sick_note_spells_general_2021:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_matched_2021"
    needs: [generate_study_population_matched_2021]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_matched_2021_with_duration.csv

  reconcile_sick_note_spells_pneumonia_2019:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_pneumonia_2019"
    needs: [generate_study_population_pneumonia_2019]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_pneumonia_2019_with_duration.csv

  covid_2020_rates_cohort:
    run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "covid_2020" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_covid_2020]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_*.dta
  
  covid_2021_rates_cohort:
    run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "covid_2021" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_covid_2021]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates*.dta

  general_2019_rates_cohort:
    run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "matched_2019" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_general_2019]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_matched_2019.dta

  general_2020_rates_cohort:
    run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "matched_2020" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_general_2020]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_matched_2020.dta

  general_2021_rates_cohort:
    run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "matched_2021" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_general_2021]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_matched_2021.dta

  pneumonia_2019_rates_cohort:
    run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "pneumonia_2019" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_pneumonia_2019]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_pneumonia_2019.dta

  covid_2020_rates:
    run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "covid_2020" --output-dir=output/tabfig
    needs: [covid_2020_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid_2020.csv

  covid_2021_rates:
    run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "covid_2021" --output-dir=output/tabfig
    needs: [covid_2021_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid_2021.csv

  general_2019_rates:
    run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "matched_2019" --output-dir=output/tabfig
    needs: [general_2019_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_matched_2019.csv

  general_2020_rates:
    run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "matched_2020" --output-dir=output/tabfig
    needs: [general_2020_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_matched_2020.csv

  general_2021_rates:
    run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "matched_2021" --output-dir=output/tabfig
    needs: [general_2021_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_matched_2021.csv
        
  pneumonia_2019_rates:
    run: stata-mp:latest analysis/rates/100_cr_simple_rates_hosp.do "pneumonia_2019" --output-dir=output/tabfig
    needs: [pneumonia_2019_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_hosp_pneumonia_2019.csv

  covid_hosp_2020_rates:
    run: stata-mp:latest analysis/rates/100_cr_simple_rates_hosp.do "covid_2020" --output-dir=output/tabfig
    needs: [covid_2020_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_hosp_covid_2020.csv

  covid_hosp_2021_rates:
    run: stata-mp:latest analysis/rates/100_cr_simple_rates_hosp.do "covid_2021" --output-dir=output/tabfig
    needs: [covid_2021_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_hosp_covid_2021.csv

  append_cohorts:
    run: stata-mp:latest analysis/cox_models/200_cr_data_management_matching.do --output-dir=output/cohorts
    needs: [covid_2021_rates_cohort, covid_2020_rates_cohort, pneumonia_2019_rates_cohort, general_2021_rates_cohort, general_2020_rates_cohort, general_2019_rates_cohort]
    outputs:
      moderately_sensitive:
        log: output/cohorts/append_cohorts.txt
      highly_sensitive: 
        dataset: output/cohorts/combined_covid_2020_pneumonia.dta
        dataset2: output/cohorts/combined_covid_2021_pneumonia.dta
        dataset3: output/cohorts/combined_covid_2020_general_2019.dta
        dataset4: output/cohorts/combined_covid_2021_general_2019.dta
        dataset5: output/cohorts/combined_covid_general_2020.dta
        dataset6: output/cohorts/combined_covid_general_2021.dta

  cox_models:
    run: stata-mp:latest analysis/cox_models/201_cox_models.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models.txt
        dataset: output/tabfig/cox_model_summary.csv

  # Cox model overall stratified by age
  cox_models_age:
    run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "age_group" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_summary_age_group.txt
        dataset: output/tabfig/cox_model_summary_age_group*.csv

  # Cox model overall stratified by ethnicity
  cox_models_ethnicity:
    run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "ethnicity" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_summary_ethnicity.txt
        dataset: output/tabfig/cox_model_summary_ethnicity.csv

   # Cox model overall stratified by IMD
  cox_models_imd:
    run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "imd" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_summary_imd.txt
        dataset: output/tabfig/cox_model_summary_imd.csv

  # Cox model overall stratified by region
  cox_models_region:
    run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "region_9" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_summary_region_9.txt
        dataset: output/tabfig/cox_model_summary_region_9.csv

  # Cox model overall stratified by sex
  cox_models_sex:
    run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "male" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_summary_male.txt
        dataset: output/tabfig/cox_model_summary_male.csv

  # Cox modes split by follow-up time
  cox_models_split_2020_pneumo:
    run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2020_pneumonia"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_pneumonia.txt
        dataset: output/tabfig/cox_model_split_summary_2020_pneumonia.csv

  cox_models_split_2021_pneumo:
    run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2021_pneumonia"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_pneumonia.txt
        dataset: output/tabfig/cox_model_split_summary_2021_pneumonia.csv
  
  cox_models_split_2020_gen_2019:
    run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2020_general_2019"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_general_2019.txt
        dataset: output/tabfig/cox_model_split_summary_2020_general_2019.csv
        
  cox_models_split_2021_gen_2019:
    run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2021_general_2019"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_general_2019.txt
        dataset: output/tabfig/cox_model_split_summary_2021_general_2019.csv

  cox_models_split_gen_2020:
    run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "general_2020"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2020.txt
        dataset: output/tabfig/cox_model_split_summary_general_2020.csv
        
  cox_models_split_gen_2021:
    run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "general_2021"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2021.txt
        dataset: output/tabfig/cox_model_split_summary_general_2021.csv

  #  Cox modes split by follow-up time - stratified by age
  cox_models_split_2020_pneumo_age:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2020_pneumonia" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_pneumonia_age_group.txt
        dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_age_group.csv

  cox_models_split_2021_pneumo_age:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2021_pneumonia"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_pneumonia_age_group.txt
        dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_age_group.csv
  
  cox_models_split_2020_gen_2019_age:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2020_general_2019"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_general_2019_age_group.txt
        dataset: output/tabfig/cox_model_split_summary_2020_general_2019_age_group.csv
        
  cox_models_split_2021_gen_2019_age:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2021_general_2019" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_general_2019_age_group.txt
        dataset: output/tabfig/cox_model_split_summary_2021_general_2019_age_group.csv

  cox_models_split_gen_2020_age:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "general_2020"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2020_age_group.txt
        dataset: output/tabfig/cox_model_split_summary_general_2020_age_group.csv
        
  cox_models_split_gen_2021_age:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "general_2021" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2021_age_group.txt
        dataset: output/tabfig/cox_model_split_summary_general_2021_age_group.csv

  #  Cox models split by follow-up time - stratified by ethnicity
  cox_models_split_2020_pneumo_ethnicity:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2020_pneumonia" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_pneumonia_ethnicity.txt
        dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_ethnicity.csv

  cox_models_split_2021_pneumo_ethnicity:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2021_pneumonia" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_pneumonia_ethnicity.txt
        dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_ethnicity.csv
  
  cox_models_split_2020_gen_2019_ethnicity:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2020_general_2019" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_general_2019_ethnicity.txt
        dataset: output/tabfig/cox_model_split_summary_2020_general_2019_ethnicity.csv
        
  cox_models_split_2021_gen_2019_ethnicity:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2021_general_2019"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_general_2019_ethnicity.txt
        dataset: output/tabfig/cox_model_split_summary_2021_general_2019_ethnicity.csv

  cox_models_split_gen_2020_ethnicity:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "general_2020" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2020_ethnicity.txt
        dataset: output/tabfig/cox_model_split_summary_general_2020_ethnicity.csv
        
  cox_models_split_gen_2021_ethnicity:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "general_2021" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2021_ethnicity.txt
        dataset: output/tabfig/cox_model_split_summary_general_2021_ethnicity.csv

  #  Cox models split by follow-up time - stratified by IMD
  cox_models_split_2020_pneumo_imd:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2020_pneumonia" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_pneumonia_imd.txt
        dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_imd.csv

  cox_models_split_2021_pneumo_imd:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2021_pneumonia" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_pneumonia_imd.txt
        dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_imd.csv
  
  cox_models_split_2020_gen_2019_imd:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2020_general_2019"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_general_2019_imd.txt
        dataset: output/tabfig/cox_model_split_summary_2020_general_2019_imd.csv
        
  cox_models_split_2021_gen_2019_imd:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2021_general_2019"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_general_2019_imd.txt
        dataset: output/tabfig/cox_model_split_summary_2021_general_2019_imd.csv

  cox_models_split_gen_2020_imd:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "general_2020" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2020_imd.txt
        dataset: output/tabfig/cox_model_split_summary_general_2020_imd.csv
        
  cox_models_split_gen_2021_imd:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "general_2021" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2021_imd.txt
        dataset: output/tabfig/cox_model_split_summary_general_2021_imd.csv

  # Cox models split by follow-up time - stratified by region
  cox_models_split_2020_pneumo_region:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2020_pneumonia"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_pneumonia_region.txt
        dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_region.csv

  cox_models_split_2021_pneumo_region:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2021_pneumonia" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_pneumonia_region.txt
        dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_region.csv
  
  cox_models_split_2020_gen_2019_region:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2020_general_2019"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_general_2019_region.txt
        dataset: output/tabfig/cox_model_split_summary_2020_general_2019_region.csv
        
  cox_models_split_2021_gen_2019_region:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2021_general_2019"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_general_2019_region.txt
        dataset: output/tabfig/cox_model_split_summary_2021_general_2019_region.csv

  cox_models_split_gen_2020_region:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "general_2020"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2020_region.txt
        dataset: output/tabfig/cox_model_split_summary_general_2020_region.csv
        
  cox_models_split_gen_2021_region:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "general_2021" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2021_region.txt
        dataset: output/tabfig/cox_model_split_summary_general_2021_region.csv
  
  #  Cox models split by follow-up time - stratified by sex
  cox_models_split_2020_pneumo_sex:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2020_pneumonia" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_pneumonia_sex.txt
        dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_sex.csv

  cox_models_split_2021_pneumo_sex:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2021_pneumonia" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_pneumonia_sex.txt
        dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_sex.csv
  
  cox_models_split_2020_gen_2019_sex:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2020_general_2019" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2020_general_2019_sex.txt
        dataset: output/tabfig/cox_model_split_summary_2020_general_2019_sex.csv
        
  cox_models_split_2021_gen_2019_sex:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2021_general_2019"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_2021_general_2019_sex.txt
        dataset: output/tabfig/cox_model_split_summary_2021_general_2019_sex.csv

  cox_models_split_gen_2020_sex:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "general_2020"
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2020_sex.txt
        dataset: output/tabfig/cox_model_split_summary_general_2020_sex.csv
        
  cox_models_split_gen_2021_sex:
    run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "general_2021" 
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models_split_general_2021_sex.txt
        dataset: output/tabfig/cox_model_split_summary_general_2021_sex.csv

  # describe_duration_diagnoses:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/describe_duration_diagnoses.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [covid_2021_rates_cohort, covid_2020_rates_cohort, general_2019_rates_cohort, general_2020_rates_cohort, general_2021_rates_cohort, pneumonia_2019_rates_cohort]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/describe_duration_diagnoses.html
  #       table: output/tabfig/med_mean_overall.csv
  #       table2: output/tabfig/med_mean_age_group.csv
  #       table3: output/tabfig/med_mean_sex.csv
  #       table4: output/tabfig/med_mean_ethnicity.csv
  #       table5: output/tabfig/med_mean_imd.csv
  #       table6: output/tabfig/med_mean_region.csv
  #       subplots: output/tabfig/diag_*.png 

  table1:
    run: r:latest analysis/descriptive/1_table1_demo_clinical.R
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        table: output/tabfig/table1_*.csv

  visualise_diagnoses:
    run: r:latest analysis/descriptive/2_visualise_diagnoses.R
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        table: output/tabfig/diag_by_cohort.csv
        plot: output/tabfig/diag_all.png        

  check_died:
    run: r:latest analysis/descriptive/3_check_died.R
    needs: [covid_2020_rates_cohort, covid_2021_rates_cohort, general_2019_rates_cohort,
            general_2020_rates_cohort, general_2021_rates_cohort, pneumonia_2019_rates_cohort,
            reconcile_sick_note_spells_general_2020, reconcile_sick_note_spells_general_2019,
            reconcile_sick_note_spells_general_2021]
    outputs:
      moderately_sensitive:
        table1: output/tabfig/check_died_*.csv        
#        table3: output/tabfig/check_ons*.csv
        table4: output/tabfig/check_index*.csv
        table5: output/tabfig/check_deregister*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:26:10

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Succeeded
Backend
TPP
Workspace
long-covid-sick-notes
Requested by
Andrea Schaffer
Branch
master
Force run dependencies
No
Git commit hash
794b685
Requested actions
  • general_2019_rates_cohort
  • general_2020_rates_cohort
  • general_2021_rates_cohort
  • check_died