Skip to content

Job request: 4651

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-vaccine-neuro-research
ID:
j7sllml4qxoqtryt
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Anna Schultze requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:

  # extract relevant cohorts 
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sccs_and_historical_cohort
    outputs:
      highly_sensitive:
        cohort: output/input_sccs_and_historical_cohort.csv

  apply_exclusion_criteria:
    run: stata-mp:latest analysis/apply_exclusion_criteria.do 
    needs: [generate_cohort] 
    outputs:
      moderately_sensitive: 
        log: output/logs/apply_exclusion_criteria.log
        denominators: output/tables/denominators*
      highly_sensitive:
        cohort_controls: output/input_historical_controls.csv
        cohort_az_cases: output/input_AZ_cases.csv
        cohort_pfizer_cases: output/input_PF_cases.csv 
        cohort_moderna_cases: output/input_MOD_cases.csv 

  # main analyses 
  SCCS_first_dose_only_primary_AZ:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do AZ
    needs: [apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_AZ.log
        results: output/tables/results_summary_primary_AZ* 
      highly_sensitive:
        sccs_pop_BP: output/temp_data/sccs_popn_BP_AZ*
        sccs_pop_TM: output/temp_data/sccs_popn_TM_AZ*
        sccs_pop_GBS: output/temp_data/sccs_popn_GBS_AZ*
        sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_AZ*
        sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_AZ*
        sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_AZ*

  SCCS_first_dose_only_primary_PF:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do PF 
    needs: [apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_PF.log
        results: output/tables/results_summary_primary_PF*
      highly_sensitive:
        sccs_pop_BP: output/temp_data/sccs_popn_BP_PF*
        sccs_pop_TM: output/temp_data/sccs_popn_TM_PF*
        sccs_pop_GBS: output/temp_data/sccs_popn_GBS_PF*
        sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_PF*
        sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_PF*
        sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_PF*

  SCCS_first_dose_only_primary_MOD:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do MOD 
    needs: [apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_MOD.log
        results: output/tables/results_summary_primary_MOD*
      highly_sensitive:
        sccs_pop_BP: output/temp_data/sccs_popn_BP_MOD*
        sccs_pop_TM: output/temp_data/sccs_popn_TM_MOD*
        sccs_pop_GBS: output/temp_data/sccs_popn_GBS_MOD*
        sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_MOD*
        sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_MOD*
        sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_MOD*

  # baseline tables (AZ and PF only due to small MOD numbers)
  SCCS_baseline_tables_AZ:
    run: stata-mp:latest analysis/SCCS_baseline_tables.do AZ
    needs: [SCCS_first_dose_only_primary_AZ] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_baseline_tables_AZ.log
        tables: output/tables/baseline_AZ/*

  SCCS_baseline_tables_PF:
    run: stata-mp:latest analysis/SCCS_baseline_tables.do PF
    needs: [SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_baseline_tables_PF.log
        tables: output/tables/baseline_PF/*

  SCCS_baseline_tables_MOD:
    run: stata-mp:latest analysis/SCCS_baseline_tables.do MOD
    needs: [SCCS_first_dose_only_primary_MOD] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_baseline_tables_MOD.log
        tables: output/tables/baseline_MOD/*

  # check assumptions 
  SCCS_assumption_checking_AZ:
    run: stata-mp:latest analysis/SCCS_assumption_checking.do AZ
    needs: [SCCS_first_dose_only_primary_AZ] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_assumption_checking_AZ.log
        plots_S1: output/plots/S1_exposure_centered_interval_AZ*
        plots_S2: output/plots/S2_censored_futime_AZ*

  SCCS_assumption_checking_PF:
    run: stata-mp:latest analysis/SCCS_assumption_checking.do PF
    needs: [SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_assumption_checking_PF.log
        plots_S1: output/plots/S1_exposure_centered_interval_PF*
        plots_S2: output/plots/S2_censored_futime_PF*

  # sensitivity analyses 
  ## stratified analyses 
  SCCS_stratified_analyses_AZ:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_stratified.do AZ
    needs: [SCCS_first_dose_only_primary_AZ] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_stratified_AZ.log
        results: output/tables/results_summary_stratified_AZ.csv

  SCCS_stratified_analyses_PF:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_stratified.do PF
    needs: [SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_stratified_PF.log
        results: output/tables/results_summary_stratified_PF.csv

  ## changing risk windows 
  SCCS_vary_risk_windows_AZ:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_risk.do AZ
    needs: [SCCS_first_dose_only_primary_AZ] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_risk_AZ.log
        results: output/tables/results_summary_sens_risk_AZ.csv

  SCCS_vary_risk_windows_PF:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_risk.do PF
    needs: [SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_risk_PF.log
        results: output/tables/results_summary_sens_risk_PF.csv

  ## second doses 
  SCCS_second_dose_AZ:
    run: stata-mp:latest analysis/SCCS_first_second_dose_analyses_neuro.do AZ
    needs: [SCCS_first_dose_only_primary_AZ, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_second_dose_analyses_neuro_AZ.log
        results: output/tables/results_summary_second_doses_AZ.csv

  SCCS_second_dose_PF:
    run: stata-mp:latest analysis/SCCS_first_second_dose_analyses_neuro.do PF
    needs: [SCCS_first_dose_only_primary_PF, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_second_dose_analyses_neuro_PF.log
        results: output/tables/results_summary_second_doses_PF*

  ## AZ vs Pfizer 
  SCCS_comparative_AZ_Pfizer:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_sens_AZ_vs_PF.do 
    needs: [SCCS_first_dose_only_primary_AZ, SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_sens_AZ_vs_PF.log
        results: output/tables/results_summary_sens_AZ_vs_PF.csv

  ## Check for overlap 
  SCCS_overlap_check_AZ:
    run: stata-mp:latest analysis/SCCS_check_all_outcome_overlaps_and_distn_source_BP.do AZ
    needs: [SCCS_first_dose_only_primary_AZ, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_check_all_outcome_overlaps_and_distn_source_BP_AZ.log

  SCCS_overlap_check_PF:
    run: stata-mp:latest analysis/SCCS_check_all_outcome_overlaps_and_distn_source_BP.do PF
    needs: [SCCS_first_dose_only_primary_PF, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_check_all_outcome_overlaps_and_distn_source_BP_PF.log

  SCCS_overlap_check_MOD:
    run: stata-mp:latest analysis/SCCS_check_all_outcome_overlaps_and_distn_source_BP.do MOD
    needs: [SCCS_first_dose_only_primary_MOD, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_check_all_outcome_overlaps_and_distn_source_BP_MOD.log

  ## Sensitivity - censoring and second dose 
  SCCS_censor_2dose_AZ:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_censor_at2nd_dose.do AZ
    needs: [SCCS_first_dose_only_primary_AZ, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_sens_censor_at2nd_dose_AZ.log
        results: output/tables/results_summary_sens_censor_at2nd_dose_AZ.csv

  SCCS_censor_2dose_PF:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_censor_at2nd_dose.do PF
    needs: [SCCS_first_dose_only_primary_PF, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_sens_censor_at2nd_dose_PF.log
        results: output/tables/results_summary_sens_censor_at2nd_dose_PF.csv

  SCCS_postvacc2dose_AZ:
    run: stata-mp:latest analysis/SCCS_sens_2nd_dose_only_postvaccbase.do AZ
    needs: [SCCS_first_dose_only_primary_AZ, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_sens_2nd_dose_only_postvaccbase_AZ.log
        results: output/tables/results_summary_sens_2nd_dose_only_postvaccbase_AZ.csv

  SCCS_postvacc2dose_PF:
    run: stata-mp:latest analysis/SCCS_sens_2nd_dose_only_postvaccbase.do PF
    needs: [SCCS_first_dose_only_primary_PF, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_sens_2nd_dose_only_postvaccbase_PF.log
        results: output/tables/results_summary_sens_2nd_dose_only_postvaccbase_PF.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:33:13

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

Job request

Status
Succeeded
Backend
TPP
Workspace
covid-vaccine-neuro-research
Requested by
Anna Schultze
Branch
main
Force run dependencies
No
Git commit hash
1495da2
Requested actions
  • SCCS_second_dose_AZ
  • SCCS_second_dose_PF
  • SCCS_censor_2dose_AZ
  • SCCS_censor_2dose_PF
  • SCCS_postvacc2dose_AZ
  • SCCS_postvacc2dose_PF

Code comparison

Compare the code used in this job request