Job request: 4420

View Repo View project.yaml

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

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

Jobs

ID Status Action
nqwxoj5jytocg2n3 succeeded SCCS_baseline_tables_MOD
x4deb2f6i6uecyr6 succeeded SCCS_first_dose_only_primary_AZ
dlujr7tpcot4dezo succeeded SCCS_vary_risk_windows_AZ
56cgkkrcmoa2jvmz succeeded SCCS_vary_risk_windows_PF

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 5000

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

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 01:02:58

Config

  • Backend:
    TPP
  • Workspace:
    covid-vaccine-neuro-research
  • Branch:
    main
  • Creator:
    annaschultze
  • Force run dependencies:
    False
  • Git Commit Hash:
    9929c73
  • Requested actions:
    • SCCS_first_dose_only_primary_AZ
    • SCCS_baseline_tables_MOD
    • SCCS_vary_risk_windows_AZ
    • SCCS_vary_risk_windows_PF