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Job request: 4018

Organisation:
Bennett Institute
Workspace:
aimpaper-analysis
ID:
xiw4466orm3jnt62
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Elsie Horne 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: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project.R 
  ## Edit and run create_project.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Metadata for study design 
  ## # # # # # # # # # # # # # # # # # # # 

  design:
    run: r:latest analysis/00_design.R
    outputs:
      highly_sensitive:
        dates_json: analysis/lib/dates.json
        dates_rds: analysis/lib/dates.rds

  ## # # # # # # # # # # # # # # # # # # # 
  ## Study definition 
  ## # # # # # # # # # # # # # # # # # # # 

  study_definition:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    needs:
    - design
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Process the data 
  ## # # # # # # # # # # # # # # # # # # # 

  process_data:
    run: r:latest analysis/01_data_process.R
    needs:
    - design
    - study_definition
    outputs:
      highly_sensitive:
        data: output/data/data_processed_*.rds
        variables: analysis/lib/all_variables.rds
      moderately_sensitive:
        elig_dates: output/tables/elig_dates_tibble.csv
        death_counts: output/tables/death_count_*.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Summary tables for each jcvi_group 
  ## # # # # # # # # # # # # # # # # # # # 

  summary_table_02:
    run: r:latest analysis/02_summary_tables.R 02
    needs:
    - process_data
    outputs:
      moderately_sensitive:
        table: output/tables/summary_table_02.csv

  summary_table_09:
    run: r:latest analysis/02_summary_tables.R 09
    needs:
    - process_data
    outputs:
      moderately_sensitive:
        table: output/tables/summary_table_09.csv

  summary_table_11:
    run: r:latest analysis/02_summary_tables.R 11
    needs:
    - process_data
    outputs:
      moderately_sensitive:
        table: output/tables/summary_table_11.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Models for each jcvi_group and model_type 
  ## # # # # # # # # # # # # # # # # # # # 

  model_02_unadj:
    run: r:latest analysis/03_model.R 02 unadj
    needs:
    - process_data
    outputs:
      highly_sensitive:
        model: output/models/model_02_unadj_*.rds
      moderately_sensitive:
        table: output/tables/table_02_unadj.csv

  model_09_unadj:
    run: r:latest analysis/03_model.R 09 unadj
    needs:
    - process_data
    outputs:
      highly_sensitive:
        model: output/models/model_09_unadj_*.rds
      moderately_sensitive:
        table: output/tables/table_09_unadj.csv

  model_11_unadj:
    run: r:latest analysis/03_model.R 11 unadj
    needs:
    - process_data
    outputs:
      highly_sensitive:
        model: output/models/model_11_unadj_*.rds
      moderately_sensitive:
        table: output/tables/table_11_unadj.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Cumulative incidence analysis 
  ## # # # # # # # # # # # # # # # # # # # 

  cml_inc_model_jcvi_group:
    run: r:latest analysis/04_cumulative_incidence.R jcvi_group
    needs:
    - design
    - study_definition
    - process_data
    outputs:
      highly_sensitive:
        model: output/models/surv_model_jcvi_group.rds
      moderately_sensitive:
        cml_inc_plot: output/figures/cml_inc_plot_jcvi_group.png
        survtable: output/tables/survtable_jcvi_group.csv

  cml_inc_model_elig_date:
    run: r:latest analysis/04_cumulative_incidence.R elig_date
    needs:
    - design
    - study_definition
    - process_data
    outputs:
      highly_sensitive:
        model: output/models/surv_model_elig_date.rds
      moderately_sensitive:
        cml_inc_plot: output/figures/cml_inc_plot_elig_date.png
        survtable: output/tables/survtable_elig_date.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:17:14

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

Job information

Status
Succeeded
Backend
TPP
Workspace
aimpaper-analysis
Requested by
Elsie Horne
Branch
main
Force run dependencies
Yes
Git commit hash
44524c3
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request