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Job request: 6123

Organisation:
The UK Renal Registry
Workspace:
ckd-coverage-ve
ID:
k5bqykput4bg5gsk
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ed Parker 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 
######################################
# Script defines project pipeline via series of actions
######################################

version: '3.0'

expectations:
  population_size: 300000

actions:

  # Extract data ----
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data
    outputs:
      highly_sensitive:
        cohort: output/data/input.csv
  
# Process data ----
  data_process:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data: output/data/data_processed.rds
        csv: output/data/data_processed.csv
        
# Select cohort ----
  data_selection_coverage:
    run: r:latest analysis/coverage/data_selection_coverage.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/data/data_cohort_coverage.rds
        csv: output/data/data_cohort_coverage.csv
      moderately_sensitive:
        csv: output/tables/flowchart_coverage.csv

 # Data properties ----      
  data_properties:
    run: r:latest analysis/data_properties.R output/data/data_cohort_coverage.rds output/data_properties
    needs: [data_selection_coverage]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/data_cohort*.txt
        
  # Table 1 ----
  table_1_coverage:
    run: r:latest analysis/coverage/table_1_coverage.R
    needs: [data_selection_coverage]
    outputs:
      highly_sensitive:
        data: output/tables/table1_coverage_redacted.rds
      moderately_sensitive:
        table: output/tables/table1_coverage_redacted.html
        
  # Cox models - dose-2 coverage ----
  cox_model:
    run: r:latest analysis/coverage/cox_model.R
    needs: [data_selection_coverage]
    outputs:
      highly_sensitive:
        data1: output/data/data_cox.rds
        data2: output/model/mod_strat_coxph_redacted.rds
        csv: output/data/data_cox.csv
      moderately_sensitive:
        csv: output/model/mod_strat_coxph_redacted.csv
        
  # Logistic models - dose-2 coverage ----
  logistic_model:
    run: r:latest analysis/coverage/logistic_model.R
    needs: [cox_model]
    outputs:
      highly_sensitive:
        data: output/model/mod_strat_logistic_redacted.rds
      moderately_sensitive:
        csv: output/model/mod_strat_logistic_redacted.csv

  # Coverage summaries ----
  vaccine_coverage:
    run: r:latest -e 'rmarkdown::render("analysis/coverage/vaccine_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
    needs: [data_selection_coverage, table_1_coverage, cox_model, logistic_model]
    outputs:
      moderately_sensitive:
        html: output/markdown/vaccine_coverage.html
        csv: output/tables/coverage_over_time_rounded.csv

  # Coverage summaries ----
#  cox_model_check:
#    run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
#    needs: [data_selection_coverage, cox_model]
#    outputs:
#      moderately_sensitive:
#        html: output/markdown/cox_model_check.html

# Select cohort (VE) ----
  data_selection_VE:
    run: r:latest analysis/VE/data_selection_VE.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/data/data_cohort_VE.rds
        csv: output/data/data_cohort_VE.csv
      moderately_sensitive:
        csv: output/tables/flowchart_VE.csv

  # Table 1 (VE) ----
  table_1_VE:
    run: r:latest analysis/VE/table_1_VE.R
    needs: [data_selection_VE]
    outputs:
      highly_sensitive:
        data: output/tables/table1_VE_redacted.rds
      moderately_sensitive:
        table: output/tables/table1_VE_redacted.html

  # Table IRR
  table_irr:
    run: r:latest analysis/VE/table_irr.R
    needs: [data_selection_VE]
    outputs:
      highly_sensitive:
        data: output/tables/table_irr_redacted.rds
      moderately_sensitive:
        csv: output/tables/table_irr_redacted.csv
        
  # Table IRR - verification (adapted from prior scripts)
  table_irr_verification:
    run: r:latest analysis/VE/table_irr_verification.R
    needs: [data_selection_VE]
    outputs:
      moderately_sensitive:
        csv: output/tables/table_irr_redacted_verification.csv
  
  # Cox models - comparative VE ----
  cox_model_VE:
    run: r:latest analysis/VE/cox_model_VE.R
    needs: [data_selection_VE, table_irr]
    outputs:
      highly_sensitive:
        data: output/model/VE/modelcox*.rds
      moderately_sensitive:
        csv: output/model/VE/modelcox*.csv
        txt: output/model/VE/modelcox*.txt
   
  # Cox VE summaries ----
  cox_VE_summary:
    run: r:latest -e 'rmarkdown::render("analysis/VE/cox_VE_summary.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
    needs: [data_selection_VE, table_1_VE, table_irr, cox_model_VE]
    outputs:
      moderately_sensitive:
        html: output/markdown/cox_VE_summary.html
        
# Select cohort (VE matched) ----
  data_selection_VE_matched:
    run: r:latest analysis/VE_matched/data_selection_VE_matched.R
    needs: [data_selection_VE]
    outputs:
      highly_sensitive:
        data: output/data/data_cohort_VE_matched.rds
        csv: output/data/data_cohort_VE_matched.csv
      moderately_sensitive:
        csv: output/tables/flowchart_VE_matched.csv

  # Table 1 (VE) ----
  table_1_VE_matched:
    run: r:latest analysis/VE_matched/table_1_VE.R
    needs: [data_selection_VE_matched]
    outputs:
      highly_sensitive:
        data: output/tables/table1_VE_matched_redacted.rds
      moderately_sensitive:
        table: output/tables/table1_VE_matched_redacted.html

  # Table IRR
  table_irr_matched:
    run: r:latest analysis/VE_matched/table_irr.R
    needs: [data_selection_VE_matched]
    outputs:
      highly_sensitive:
        data: output/tables/table_irr_matched_redacted.rds
      moderately_sensitive:
        csv: output/tables/table_irr_matched_redacted.csv

  # Cox models - comparative VE ----
  cox_model_VE_matched:
    run: r:latest analysis/VE_matched/cox_model_VE.R
    needs: [data_selection_VE_matched, table_irr_matched]
    outputs:
      highly_sensitive:
        data: output/model/VE_matched/modelcox*.rds
      moderately_sensitive:
        csv: output/model/VE_matched/modelcox*.csv
        txt: output/model/VE_matched/modelcox*.txt
   
  # Cox VE summaries ----
  cox_VE_summary_matched:
    run: r:latest -e 'rmarkdown::render("analysis/VE_matched/cox_VE_summary_matched.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
    needs: [data_selection_VE_matched, table_1_VE_matched, table_irr_matched, cox_model_VE_matched]
    outputs:
      moderately_sensitive:
        html: output/markdown/cox_VE_summary_matched.html
        
        
  # Check session info for set of packages ----
  #session:
  #  run: r:latest -e 'rmarkdown::render("analysis/session.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
  #  needs: [data_selection]
  #  outputs:
  #    moderately_sensitive:
  #      html: output/markdown/session.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:38:28

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

Job information

Status
Succeeded
Backend
TPP
Workspace
ckd-coverage-ve
Requested by
Ed Parker
Branch
main
Force run dependencies
No
Git commit hash
4733c6e
Requested actions
  • data_selection_VE_matched
  • table_1_VE_matched

Code comparison

Compare the code used in this Job Request