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Job request: 2079

Organisation:
Bennett Institute
Workspace:
factors-associated-with-covid-19-vaccination
ID:
osldzq4fhz2s4ed5
View repo View project.yaml

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

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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 
######################################

# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.

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

version: '3.0'

expectations:
  population_size: 1000000

actions:

  # Extract data for study population flow chart
  generate_study_population_flow_chart_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart.csv

  # Calculate numbers for study population flow chart
  flow_chart:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Study_definition_flow_chart.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population_flow_chart_data]
    outputs:
      moderately_sensitive:
        html: output/Study_definition_flow_chart.html
        
  # Extract study data
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  # Process data
  data_process:
    run: r:latest analysis/R/Scripts/00_process_data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        data2: output/data/data_modelling.rds
        
  # Summarise data
  data_properties:
    run: r:latest analysis/R/Scripts/01_data_properties.R output/data/data_all.rds output/data_properties
    needs: [generate_study_population, data_process]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_all*.txt
        
  # # More data summaries
  # data_summaries:
  #   run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Data_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/Data_summaries.html

  # # Coxph models
  # cox_models:
  #   run: r:latest analysis/R/Scripts/02a_models_coxph.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/testing/mod*.rds
        
  # # Coxme model
  # coxme_model:
  #   run: r:latest analysis/R/Scripts/02b_models_coxme.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/testing/mod_test*.rds
  
  # # Model summaries
  # cox_models_summaries:
  #   run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Model_comparisons.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
  #   needs: [generate_study_population, data_process, cox_models, coxme_model]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/Model_comparisons.html
  
  # # AFT vs Cox models feasibility
  # aft_vs_cox_poc:
  #   run: r:latest analysis/R/Scripts/02c_models_cox_vs_aft_poc.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/testing/cox_vs_aft/mod*.rds
  #     moderately_sensitive:
  #       tables: output/models/testing/cox_vs_aft/table*.csv
  #       plots: output/models/testing/cox_vs_aft/plot*.svg

  # # AFT models
  # aft_vs_cox_models:
  #   run: r:latest analysis/R/Scripts/02d_models_cox_vs_aft.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/cox_vs_aft/mod*.rds
        
  # # Model comparison
  # aft_vs_cox_comparison:
  #   run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Cox_vs_aft_model_comparison.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
  #   needs: [generate_study_population, data_process, aft_vs_cox_models]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/Cox_vs_aft_model_comparison.html
        
  # Final (stratified cox) model
  model_final:
    run: r:latest analysis/R/Scripts/03_model_final.R
    needs: [generate_study_population, data_process]
    outputs:
      highly_sensitive :
        models: output/models/final/mod*.rds
 
  # Strata summaries
  strata_summary:
    run: r:latest analysis/R/Scripts/04_strata_summary.R
    needs: [data_process, model_final]
    outputs:
      moderately_sensitive:
        plots: output/models/final/plot_strata*.svg
        csv: output/models/final/cmlhaz_quantiles.csv
  
  # # Results summary
  # results_summary:
  #   run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Results_summary.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
  #   needs: [data_process, model_final]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/Results_summary.html
        
  # Table and figure
  table_and_figure:
    run: r:latest analysis/R/Scripts/05_table_and_figure.R
    needs: [generate_study_population, data_process, model_final]
    outputs:
      moderately_sensitive:
        tables: output/models/final/tab*.csv
        plots: output/models/final/plot*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:21:32

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

Job information

Status
Succeeded
Backend
TPP
Workspace
factors-associated-with-covid-19-vaccination
Requested by
Will Hulme
Branch
master
Force run dependencies
No
Git commit hash
f347569
Requested actions
  • table_and_figure

Code comparison

Compare the code used in this Job Request