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Job request: 20000

Organisation:
University of Liverpool
Workspace:
flucats
ID:
cwyntu2ecnwbq2r7

This page shows the technical details of what happened when authorised researcher Louis Fisher 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: 1000

actions:

  generate_study_population_conscious_level_blood_pressure:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-03-01 to 2020-04-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blood_pressure*.csv

  generate_study_population_clinical_concern_dehydration:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-03-01 to 2020-04-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_dehydration*.csv

  generate_study_population_heart_rate_resp_rate:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-03-01 to 2020-04-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate_resp_rate*.csv

  generate_study_population_ox_temp:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-03-01 to 2020-04-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_temperature*.csv

  generate_study_population_who_dem:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-03-01 to 2020-04-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic_variables*.csv

  generate_study_population_com_presc:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-03-01 to 2020-04-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_prescription*.csv

  generate_study_population_resp:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-03-01 to 2020-04-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_exhaustion*.csv

  generate_study_population_cov_testing:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-03-01 to 2020-04-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_cov_testing*.csv

  ############

  generate_study_population_conscious_level_blood_pressure_2:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-05-01 to 2020-06-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blood_pressur*.csv

  generate_study_population_clinical_concern_dehydration_2:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-05-01 to 2020-06-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_dehydratio*.csv

  generate_study_population_heart_rate_resp_rate_2:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-05-01 to 2020-06-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate_resp_rat*.csv

  generate_study_population_ox_temp_2:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-05-01 to 2020-06-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_temperatur*.csv

  generate_study_population_who_dem_2:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-05-01 to 2020-06-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic_variable*.csv

  generate_study_population_com_presc_2:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-05-01 to 2020-06-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_prescriptio*.csv

  generate_study_population_resp_2:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-05-01 to 2020-06-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_exhaustio*.csv

  generate_study_population_cov_testing_2:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-05-01 to 2020-06-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_cov_testin*.csv

  ##############

  generate_study_population_conscious_level_blood_pressure_3:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-07-01 to 2020-08-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blood_pressu*.csv

  generate_study_population_clinical_concern_dehydration_3:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-07-01 to 2020-08-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_dehydrati*.csv

  generate_study_population_heart_rate_resp_rate_3:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-07-01 to 2020-08-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate_resp_ra*.csv

  generate_study_population_ox_temp_3:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-07-01 to 2020-08-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_temperatu*.csv

  generate_study_population_who_dem_3:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-07-01 to 2020-08-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic_variabl*.csv

  generate_study_population_com_presc_3:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-07-01 to 2020-08-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_prescripti*.csv

  generate_study_population_resp_3:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-07-01 to 2020-08-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_exhausti*.csv

  generate_study_population_cov_testing_3:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-07-01 to 2020-08-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_cov_testi*.csv

  #######################

  generate_study_population_conscious_level_blood_pressure_4:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-09-01 to 2020-10-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blood_press*.csv

  generate_study_population_clinical_concern_dehydration_4:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-09-01 to 2020-10-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_dehydrat*.csv

  generate_study_population_heart_rate_resp_rate_4:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-09-01 to 2020-10-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate_resp_r*.csv

  generate_study_population_ox_temp_4:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-09-01 to 2020-10-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_temperat*.csv

  generate_study_population_who_dem_4:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-09-01 to 2020-10-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic_variab*.csv

  generate_study_population_com_presc_4:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-09-01 to 2020-10-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_prescript*.csv

  generate_study_population_resp_4:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-09-01 to 2020-10-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_exhaust*.csv

  generate_study_population_cov_testing_4:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-09-01 to 2020-10-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_cov_test*.csv

  ############################

  generate_study_population_conscious_level_blood_pressure_5:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-11-01 to 2020-12-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
      
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blood_pres*.csv

  generate_study_population_clinical_concern_dehydration_5:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-11-01 to 2020-12-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_dehydra*.csv

  generate_study_population_heart_rate_resp_rate_5:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-11-01 to 2020-12-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate_resp_*.csv

  generate_study_population_ox_temp_5:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-11-01 to 2020-12-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_tempera*.csv

  generate_study_population_who_dem_5:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-11-01 to 2020-12-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic_varia*.csv

  generate_study_population_com_presc_5:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-11-01 to 2020-12-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_prescrip*.csv

  generate_study_population_resp_5:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-11-01 to 2020-12-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_exhaus*.csv

  generate_study_population_cov_testing_5:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2020-11-01 to 2020-12-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_cov_tes*.csv

  ####################

  generate_study_population_conscious_level_blood_pressure_6:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-01-01 to 2021-02-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blood_pre*.csv

  generate_study_population_clinical_concern_dehydration_6:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-01-01 to 2021-02-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_dehydr*.csv

  generate_study_population_heart_rate_resp_rate_6:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-01-01 to 2021-02-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate_resp*.csv

  generate_study_population_ox_temp_6:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-01-01 to 2021-02-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_temper*.csv

  generate_study_population_who_dem_6:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-01-01 to 2021-02-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic_vari*.csv

  generate_study_population_com_presc_6:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-01-01 to 2021-02-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_prescri*.csv

  generate_study_population_resp_6:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-01-01 to 2021-02-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_exhau*.csv

  generate_study_population_cov_testing_6:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-01-01 to 2021-02-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_cov_te*.csv

  ###################


  generate_study_population_conscious_level_blood_pressure_7:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-03-01 to 2021-04-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blood_pr*.csv

  generate_study_population_clinical_concern_dehydration_7:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-03-01 to 2021-04-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_dehyd*.csv

  generate_study_population_heart_rate_resp_rate_7:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-03-01 to 2021-04-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate_res*.csv

  generate_study_population_ox_temp_7:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-03-01 to 2021-04-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_tempe*.csv

  generate_study_population_who_dem_7:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-03-01 to 2021-04-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic_var*.csv

  generate_study_population_com_presc_7:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-03-01 to 2021-04-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_presc*.csv

  generate_study_population_resp_7:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-03-01 to 2021-04-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_exha*.csv

  generate_study_population_cov_testing_7:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-03-01 to 2021-04-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_cov_t*.csv

  ###################

  generate_study_population_conscious_level_blood_pressure_8:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-05-01 to 2021-06-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blood_p*.csv

  generate_study_population_clinical_concern_dehydration_8:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-05-01 to 2021-06-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_dehy*.csv

  generate_study_population_heart_rate_resp_rate_8:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-05-01 to 2021-06-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate_re*.csv

  generate_study_population_ox_temp_8:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-05-01 to 2021-06-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_temp*.csv

  generate_study_population_who_dem_8:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-05-01 to 2021-06-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic_va*.csv

  generate_study_population_com_presc_8:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-05-01 to 2021-06-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_pres*.csv

  generate_study_population_resp_8:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-05-01 to 2021-06-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_exh*.csv

  generate_study_population_cov_testing_8:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-05-01 to 2021-06-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_cov_*.csv

  ###################

  generate_study_population_conscious_level_blood_pressure_9:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-07-01 to 2021-08-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blood_*.csv

  generate_study_population_clinical_concern_dehydration_9:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-07-01 to 2021-08-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_deh*.csv

  generate_study_population_heart_rate_resp_rate_9:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-07-01 to 2021-08-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate_r*.csv

  generate_study_population_ox_temp_9:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-07-01 to 2021-08-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_tem*.csv

  generate_study_population_who_dem_9:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-07-01 to 2021-08-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic_v*.csv

  generate_study_population_com_presc_9:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-07-01 to 2021-08-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_pre*.csv

  generate_study_population_resp_9:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-07-01 to 2021-08-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_ex*.csv

  generate_study_population_cov_testing_9:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-07-01 to 2021-08-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_cov*.csv

  ##############

  generate_study_population_conscious_level_blood_pressure_10:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-09-01 to 2021-11-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blood*.csv

  generate_study_population_clinical_concern_dehydration_10:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-09-01 to 2021-11-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_de*.csv

  generate_study_population_heart_rate_resp_rate_10:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-09-01 to 2021-11-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate_*.csv

  generate_study_population_ox_temp_10:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-09-01 to 2021-11-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_te*.csv

  generate_study_population_who_dem_10:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-09-01 to 2021-11-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic_*.csv

  generate_study_population_com_presc_10:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-09-01 to 2021-11-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_pr*.csv

  generate_study_population_resp_10:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-09-01 to 2021-11-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_e*.csv

  generate_study_population_cov_testing_10:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-09-01 to 2021-11-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_co*.csv

  ##############

  generate_study_population_conscious_level_blood_pressure_11:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-12-01 to 2022-02-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_bloo*.csv

  generate_study_population_clinical_concern_dehydration_11:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-12-01 to 2022-02-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_d*.csv

  generate_study_population_heart_rate_resp_rate_11:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-12-01 to 2022-02-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rate*.csv

  generate_study_population_ox_temp_11:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-12-01 to 2022-02-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_t*.csv

  generate_study_population_who_dem_11:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-12-01 to 2022-02-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographic*.csv

  generate_study_population_com_presc_11:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-12-01 to 2022-02-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_p*.csv

  generate_study_population_resp_11:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-12-01 to 2022-02-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory_*.csv

  generate_study_population_cov_testing_11:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-12-01 to 2022-02-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_c*.csv

  ##############

  generate_study_population_conscious_level_blood_pressure_12:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2022-03-01 to 2022-06-01 by month"
      --output-file=output/input_conscious_level_blood_pressure.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
      --param include_hospital_admissions=True
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_conscious_level_blo*.csv

  generate_study_population_clinical_concern_dehydration_12:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2022-03-01 to 2022-06-01 by month"
      --output-file=output/input_clinical_concern_dehydration.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=causing_clinical_concern,clinical_concern_note,dehydration_or_shock
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_clinical_concern_*.csv

  generate_study_population_heart_rate_resp_rate_12:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2022-03-01 to 2022-06-01 by month"
      --output-file=output/input_heart_rate_resp_rate.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate,inspired_oxygen
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_heart_rat*.csv

  generate_study_population_ox_temp_12:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2022-03-01 to 2022-06-01 by month"
      --output-file=output/input_oxygen_saturation_temperature.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
      --param include_hospital_admissions=False
      --param include_numeric_variables=True
    outputs:
      highly_sensitive:
        cohort: output/input_oxygen_saturation_*.csv

  generate_study_population_who_dem_12:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2022-03-01 to 2022-06-01 by month"
      --output-file=output/input_who_performance_score_demographic_variables.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_who_performance_score_demographi*.csv

  generate_study_population_com_presc_12:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2022-03-01 to 2022-06-01 by month"
      --output-file=output/input_comorbidity_prescription.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=comorbidity_variables,prescription_variables
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_comorbidity_*.csv

  generate_study_population_resp_12:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2022-03-01 to 2022-06-01 by month"
      --output-file=output/input_severe_respiratory_distress_respiratory_exhaustion.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_severe_respiratory_distress_respiratory*.csv

  generate_study_population_cov_testing_12:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2022-03-01 to 2022-06-01 by month"
      --output-file=output/input_cov_testing.csv
      --output-format=csv
      --with-end-date-fix
      --param varset=suspected_covid,probable_covid
      --param include_hospital_admissions=False
      --param include_numeric_variables=False
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  ##############

  generate_study_population_test:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_test --output-format=csv --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_test.csv

  generate_study_population_end:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_end --output-format=csv --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_end.csv

  generate_study_population_eth:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format=csv --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv

  join_cohorts:
    run: python:latest python analysis/analysis/join_cohorts.py --input-dir=output --output-dir=output/joined
    needs: [
      generate_study_population_conscious_level_blood_pressure,
      generate_study_population_clinical_concern_dehydration,
      generate_study_population_heart_rate_resp_rate,
      generate_study_population_ox_temp,
      generate_study_population_who_dem,
      generate_study_population_com_presc,
      generate_study_population_resp,
      generate_study_population_cov_testing,
      generate_study_population_conscious_level_blood_pressure_2,
      generate_study_population_clinical_concern_dehydration_2,
      generate_study_population_heart_rate_resp_rate_2,
      generate_study_population_ox_temp_2,
      generate_study_population_who_dem_2,
      generate_study_population_com_presc_2,
      generate_study_population_resp_2,
      generate_study_population_cov_testing_2,
      generate_study_population_conscious_level_blood_pressure_3,
      generate_study_population_clinical_concern_dehydration_3,
      generate_study_population_heart_rate_resp_rate_3,
      generate_study_population_ox_temp_3,
      generate_study_population_who_dem_3,
      generate_study_population_com_presc_3,
      generate_study_population_resp_3,
      generate_study_population_cov_testing_3,
      generate_study_population_conscious_level_blood_pressure_4,
      generate_study_population_clinical_concern_dehydration_4,
      generate_study_population_heart_rate_resp_rate_4,
      generate_study_population_ox_temp_4,
      generate_study_population_who_dem_4,
      generate_study_population_com_presc_4,
      generate_study_population_resp_4,
      generate_study_population_cov_testing_4,
      generate_study_population_conscious_level_blood_pressure_5,
      generate_study_population_clinical_concern_dehydration_5,
      generate_study_population_heart_rate_resp_rate_5,
      generate_study_population_ox_temp_5,
      generate_study_population_who_dem_5,
      generate_study_population_com_presc_5,
      generate_study_population_resp_5,
      generate_study_population_cov_testing_5,
      generate_study_population_conscious_level_blood_pressure_6,
      generate_study_population_clinical_concern_dehydration_6,
      generate_study_population_heart_rate_resp_rate_6,
      generate_study_population_ox_temp_6,
      generate_study_population_who_dem_6,
      generate_study_population_com_presc_6,
      generate_study_population_resp_6,
      generate_study_population_cov_testing_6,
      generate_study_population_conscious_level_blood_pressure_7,
      generate_study_population_clinical_concern_dehydration_7,
      generate_study_population_heart_rate_resp_rate_7,
      generate_study_population_ox_temp_7,
      generate_study_population_who_dem_7,
      generate_study_population_com_presc_7,
      generate_study_population_resp_7,
      generate_study_population_cov_testing_7,
      generate_study_population_conscious_level_blood_pressure_8,
      generate_study_population_clinical_concern_dehydration_8,
      generate_study_population_heart_rate_resp_rate_8,
      generate_study_population_ox_temp_8,
      generate_study_population_who_dem_8,
      generate_study_population_com_presc_8,
      generate_study_population_resp_8,
      generate_study_population_cov_testing_8,
      generate_study_population_conscious_level_blood_pressure_9,
      generate_study_population_clinical_concern_dehydration_9,
      generate_study_population_heart_rate_resp_rate_9,
      generate_study_population_ox_temp_9,
      generate_study_population_who_dem_9,
      generate_study_population_com_presc_9,
      generate_study_population_resp_9,
      generate_study_population_cov_testing_9,
      generate_study_population_conscious_level_blood_pressure_10,
      generate_study_population_clinical_concern_dehydration_10,
      generate_study_population_heart_rate_resp_rate_10,
      generate_study_population_ox_temp_10,
      generate_study_population_who_dem_10,
      generate_study_population_com_presc_10,
      generate_study_population_resp_10,
      generate_study_population_cov_testing_10,
      generate_study_population_conscious_level_blood_pressure_11,
      generate_study_population_clinical_concern_dehydration_11,
      generate_study_population_heart_rate_resp_rate_11,
      generate_study_population_ox_temp_11,
      generate_study_population_who_dem_11,
      generate_study_population_com_presc_11,
      generate_study_population_resp_11,
      generate_study_population_cov_testing_11,
      generate_study_population_conscious_level_blood_pressure_12,
      generate_study_population_clinical_concern_dehydration_12,
      generate_study_population_heart_rate_resp_rate_12,
      generate_study_population_ox_temp_12,
      generate_study_population_who_dem_12,
      generate_study_population_com_presc_12,
      generate_study_population_resp_12,
      generate_study_population_cov_testing_12,
      ]
    outputs:
      highly_sensitive:
        counts: output/joined/input_*.csv

  join_cohorts_end:
    run: >
      cohort-joiner:v0.0.44
        --lhs output/joined/input_*.csv
        --rhs output/input_end.csv
        --output-dir output/joined/full
    needs: [
      join_cohorts,
      generate_study_population_end
      ]
    outputs:
      highly_sensitive:
        cohort: output/joined/full/input*.csv

  join_cohorts_eth:
    run: >
      cohort-joiner:v0.0.44
        --lhs output/joined/full/input_*.csv
        --rhs output/input_ethnicity.csv
        --output-dir output/joined/full/eth
    needs: [
      join_cohorts_end,
      generate_study_population_eth
      ]
    outputs:
      highly_sensitive:
        cohort: output/joined/full/eth/inpu*.csv

  cohort_description:
    run: >
      python:latest python analysis/analysis/cohort_description.py
        --study_def_paths "output/joined/full/eth/input_*.csv"
        --demographics "sex" "imdQ5" "ethnicity" "age_band" "homeless" "residential_care" "region" "asthma" "addisons_hypoadrenalism" "chronic_heart_disease" "chronic_respiratory_disease" "ckd_primis_stage" "renal_disease" "ckd35_or_renal_disease" "ckd_os" "liver_disease" "pregnant" "diabetes" "gestational_diabetes" "obesity" "mental_illness" "neurological_disorder" "hypertension" "pneumonia" "immunosuppression_disorder" "immunosuppression_chemo" "immunosuppression_medication" "splenic_disease" "statins" "hospital_admission" "icu_admission" "died_any" "covid_related_death" "covid_death" "type_of_residence" "first_vaccination" "has_second_dose" "has_booster_dose" "shield" "nonshield" "covadm1" "covadm2" "pfd1rx" "pfd2rx" "azd1rx" "azd2rx" "covrx1" "covrx2"
    needs: [join_cohorts_eth]
    outputs:
      moderately_sensitive:
        counts: output/cohort_description.csv
        counts_redacted: output/cohort_description_redacted.csv

  combined_input_files:
    run: python:latest python analysis/analysis/combine_input_files.py
    needs: [join_cohorts_eth]
    outputs:
      highly_sensitive:
        attrition: output/joined/full/input_all.csv

  population_count:
    run: python:latest python analysis/analysis/population_count.py
    needs: [combined_input_files]
    outputs:
      moderately_sensitive:
        count: output/joined/full/population_count.csv

  column_counts:
    run: python:latest python analysis/analysis/column_counts.py
    needs: [combined_input_files]
    outputs:
      moderately_sensitive:
        attrition: output/column_counts*

  numeric_values_check:
    run: python:latest python analysis/analysis/check_numeric_values.py
    needs: [combined_input_files]
    outputs:
      moderately_sensitive:
        table: output/joined/full/proportions_numeric.csv
        raw: output/joined/full/proportions_numeric_raw.csv
        dist: output/joined/full/dist*.csv

  template_frequency:
    run: python:latest python analysis/analysis/template_frequency.py
    needs: [combined_input_files]
    outputs:
      moderately_sensitive:
        attrition: output/joined/full/template_frequency.csv
  
  check_deaths:
    run: python:latest python analysis/analysis/check_deaths.py
    needs: [generate_study_population_end, generate_study_population_test]
    outputs:
      moderately_sensitive:
        attrition: output/died_any_counts.csv
        test: output/*_test_counts.csv
        
  # generate_first_outputs:
  #   run: r:latest analysis/flucats_descriptive_basic.R
  #   needs: [combined_input_files]
  #   outputs:
  #     moderately_sensitive:
  #       attrition: output/attrition.csv
  #       histogram_age: output/age_hist.png
  #       date_plot: output/weekly_template.png
  #       flucat_tables: output/flucat*.csv
  #       sex_table: output/sex_table.csv
  #       region_table: output/region_table.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 07:52:50

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

Job information

Status
Failed
Backend
EMIS
Workspace
flucats
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
0015ddc
Requested actions
  • generate_study_population_com_presc_2
  • generate_study_population_com_presc_3
  • generate_study_population_com_presc_4
  • generate_study_population_com_presc_5
  • generate_study_population_com_presc_6
  • generate_study_population_com_presc_7
  • generate_study_population_com_presc_8
  • generate_study_population_com_presc_9
  • generate_study_population_com_presc_10
  • generate_study_population_com_presc_11
  • generate_study_population_com_presc_12
  • join_cohorts
  • join_cohorts_end
  • join_cohorts_eth
  • cohort_description