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Job request: 12225

Workspace:
vaccine-effectiveness-in-children
ID:
kypvlb6nuubb3bfs

This page shows the technical details of what happened when authorised researcher Colm Andrews 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

  • Action:
    vax2_over12
    Status:
    Status: Failed
    Job identifier:
    hh7pxyuqmg765om3
  • Action:
    vax2_under12
    Status:
    Status: Succeeded
    Job identifier:
    4mlgbf44tf5kcn3m

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 
  ## # # # # # # # # # # # # # # # # # # # 
  ##   
  ## # # # # # # # # # # # # # # # # # # # 
  ## Over 12s cohort 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Extract and match 

  extract_treated_over12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_treated
      --output-file output/over12/extract/input_treated.feather --param cohort=over12
    outputs:
      highly_sensitive:
        extract: output/over12/extract/input_treated.feather

  process_treated_over12:
    run: r:latest analysis/treated/process_treated.R over12
    needs:
    - extract_treated_over12
    outputs:
      highly_sensitive:
        rds: output/over12/treated/*.rds

  vax2_over12:
    run: r:latest analysis/treated/second_vax.R over12
    needs:
    - extract_treated_under12
    outputs:
      moderately_sensitive:
         csv: output/over12/treated/*.csv


  extract_controlpotential_over12_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/over12/matchround1/extract/input_controlpotential.feather
      --param cohort=over12 --param matching_round=1 --param index_date=2021-09-20
    needs: []
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround1/extract/input_controlpotential.feather

  process_controlpotential_over12_1:
    run: r:latest analysis/matching/process_controlpotential.R over12 1
    needs:
    - extract_controlpotential_over12_1
    outputs:
      highly_sensitive:
        rds: output/over12/matchround1/process/*.rds

  match_potential_over12_1:
    run: r:latest analysis/matching/match_potential.R over12 1
    needs:
    - process_treated_over12
    - process_controlpotential_over12_1
    outputs:
      highly_sensitive:
        rds: output/over12/matchround1/potential/*.rds
        csv: output/over12/matchround1/potential/*.csv.gz

  extract_controlactual_over12_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/over12/matchround1/extract/input_controlactual.feather
      --param cohort=over12 --param matching_round=1
    needs:
    - match_potential_over12_1
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround1/extract/input_controlactual.feather

  process_controlactual_over12_1:
    run: r:latest analysis/matching/process_controlactual.R over12 1
    needs:
    - process_treated_over12
    - match_potential_over12_1
    - extract_controlpotential_over12_1
    - extract_controlactual_over12_1
    outputs:
      highly_sensitive:
        rds: output/over12/matchround1/actual/*.rds
        csv: output/over12/matchround1/actual/*.csv.gz

  extract_controlpotential_over12_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/over12/matchround2/extract/input_controlpotential.feather
      --param cohort=over12 --param matching_round=2 --param index_date=2021-10-11
    needs:
    - process_controlactual_over12_1
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround2/extract/input_controlpotential.feather

  process_controlpotential_over12_2:
    run: r:latest analysis/matching/process_controlpotential.R over12 2
    needs:
    - extract_controlpotential_over12_2
    outputs:
      highly_sensitive:
        rds: output/over12/matchround2/process/*.rds

  match_potential_over12_2:
    run: r:latest analysis/matching/match_potential.R over12 2
    needs:
    - process_treated_over12
    - process_controlpotential_over12_2
    - process_controlactual_over12_1
    outputs:
      highly_sensitive:
        rds: output/over12/matchround2/potential/*.rds
        csv: output/over12/matchround2/potential/*.csv.gz

  extract_controlactual_over12_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/over12/matchround2/extract/input_controlactual.feather
      --param cohort=over12 --param matching_round=2
    needs:
    - match_potential_over12_2
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround2/extract/input_controlactual.feather

  process_controlactual_over12_2:
    run: r:latest analysis/matching/process_controlactual.R over12 2
    needs:
    - process_treated_over12
    - match_potential_over12_2
    - extract_controlpotential_over12_2
    - extract_controlactual_over12_2
    - process_controlactual_over12_1
    outputs:
      highly_sensitive:
        rds: output/over12/matchround2/actual/*.rds
        csv: output/over12/matchround2/actual/*.csv.gz

  extract_controlpotential_over12_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/over12/matchround3/extract/input_controlpotential.feather
      --param cohort=over12 --param matching_round=3 --param index_date=2021-11-01
    needs:
    - process_controlactual_over12_2
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround3/extract/input_controlpotential.feather

  process_controlpotential_over12_3:
    run: r:latest analysis/matching/process_controlpotential.R over12 3
    needs:
    - extract_controlpotential_over12_3
    outputs:
      highly_sensitive:
        rds: output/over12/matchround3/process/*.rds

  match_potential_over12_3:
    run: r:latest analysis/matching/match_potential.R over12 3
    needs:
    - process_treated_over12
    - process_controlpotential_over12_3
    - process_controlactual_over12_2
    outputs:
      highly_sensitive:
        rds: output/over12/matchround3/potential/*.rds
        csv: output/over12/matchround3/potential/*.csv.gz

  extract_controlactual_over12_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/over12/matchround3/extract/input_controlactual.feather
      --param cohort=over12 --param matching_round=3
    needs:
    - match_potential_over12_3
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround3/extract/input_controlactual.feather

  process_controlactual_over12_3:
    run: r:latest analysis/matching/process_controlactual.R over12 3
    needs:
    - process_treated_over12
    - match_potential_over12_3
    - extract_controlpotential_over12_3
    - extract_controlactual_over12_3
    - process_controlactual_over12_2
    outputs:
      highly_sensitive:
        rds: output/over12/matchround3/actual/*.rds
        csv: output/over12/matchround3/actual/*.csv.gz

  extract_controlpotential_over12_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/over12/matchround4/extract/input_controlpotential.feather
      --param cohort=over12 --param matching_round=4 --param index_date=2021-11-22
    needs:
    - process_controlactual_over12_3
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround4/extract/input_controlpotential.feather

  process_controlpotential_over12_4:
    run: r:latest analysis/matching/process_controlpotential.R over12 4
    needs:
    - extract_controlpotential_over12_4
    outputs:
      highly_sensitive:
        rds: output/over12/matchround4/process/*.rds

  match_potential_over12_4:
    run: r:latest analysis/matching/match_potential.R over12 4
    needs:
    - process_treated_over12
    - process_controlpotential_over12_4
    - process_controlactual_over12_3
    outputs:
      highly_sensitive:
        rds: output/over12/matchround4/potential/*.rds
        csv: output/over12/matchround4/potential/*.csv.gz

  extract_controlactual_over12_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/over12/matchround4/extract/input_controlactual.feather
      --param cohort=over12 --param matching_round=4
    needs:
    - match_potential_over12_4
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround4/extract/input_controlactual.feather

  process_controlactual_over12_4:
    run: r:latest analysis/matching/process_controlactual.R over12 4
    needs:
    - process_treated_over12
    - match_potential_over12_4
    - extract_controlpotential_over12_4
    - extract_controlactual_over12_4
    - process_controlactual_over12_3
    outputs:
      highly_sensitive:
        rds: output/over12/matchround4/actual/*.rds
        csv: output/over12/matchround4/actual/*.csv.gz

  extract_controlfinal_over12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlfinal
      --output-file output/over12/extract/input_controlfinal.feather --param cohort=over12
      --param n_matching_rounds=4
    needs:
    - process_controlactual_over12_4
    outputs:
      highly_sensitive:
        extract: output/over12/extract/input_controlfinal.feather

  process_controlfinal_over12:
    run: r:latest analysis/matching/process_controlfinal.R over12
    needs:
    - process_controlactual_over12_1
    - process_controlactual_over12_2
    - process_controlactual_over12_3
    - process_controlactual_over12_4
    - extract_controlfinal_over12
    - process_treated_over12
    outputs:
      highly_sensitive:
        extract: output/over12/match/*.rds

  table1_over12:
    run: r:latest analysis/matching/table1.R over12
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        csv: output/over12/table1/*.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Model 

  km_over12_all_postest:
    run: r:latest analysis/model/km.R over12 all postest
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/all/postest/*.rds
        png: output/over12/models/km/all/postest/*.png

  km_over12_all_emergency:
    run: r:latest analysis/model/km.R over12 all emergency
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/all/emergency/*.rds
        png: output/over12/models/km/all/emergency/*.png

  km_over12_all_covidemergency:
    run: r:latest analysis/model/km.R over12 all covidemergency
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/all/covidemergency/*.rds
        png: output/over12/models/km/all/covidemergency/*.png

  km_over12_all_covidadmitted:
    run: r:latest analysis/model/km.R over12 all covidadmitted
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/all/covidadmitted/*.rds
        png: output/over12/models/km/all/covidadmitted/*.png

  km_over12_all_covidcritcare:
    run: r:latest analysis/model/km.R over12 all covidcritcare
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/all/covidcritcare/*.rds
        png: output/over12/models/km/all/covidcritcare/*.png

  km_over12_all_coviddeath:
    run: r:latest analysis/model/km.R over12 all coviddeath
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/all/coviddeath/*.rds
        png: output/over12/models/km/all/coviddeath/*.png

  km_over12_all_noncoviddeath:
    run: r:latest analysis/model/km.R over12 all noncoviddeath
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/all/noncoviddeath/*.rds
        png: output/over12/models/km/all/noncoviddeath/*.png

  km_over12_prior_covid_infection_postest:
    run: r:latest analysis/model/km.R over12 prior_covid_infection postest
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/prior_covid_infection/postest/*.rds
        png: output/over12/models/km/prior_covid_infection/postest/*.png

  km_over12_prior_covid_infection_emergency:
    run: r:latest analysis/model/km.R over12 prior_covid_infection emergency
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/prior_covid_infection/emergency/*.rds
        png: output/over12/models/km/prior_covid_infection/emergency/*.png

  km_over12_prior_covid_infection_covidemergency:
    run: r:latest analysis/model/km.R over12 prior_covid_infection covidemergency
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/prior_covid_infection/covidemergency/*.rds
        png: output/over12/models/km/prior_covid_infection/covidemergency/*.png

  km_over12_prior_covid_infection_covidadmitted:
    run: r:latest analysis/model/km.R over12 prior_covid_infection covidadmitted
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/prior_covid_infection/covidadmitted/*.rds
        png: output/over12/models/km/prior_covid_infection/covidadmitted/*.png

  km_over12_prior_covid_infection_covidcritcare:
    run: r:latest analysis/model/km.R over12 prior_covid_infection covidcritcare
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/prior_covid_infection/covidcritcare/*.rds
        png: output/over12/models/km/prior_covid_infection/covidcritcare/*.png

  km_over12_prior_covid_infection_coviddeath:
    run: r:latest analysis/model/km.R over12 prior_covid_infection coviddeath
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/prior_covid_infection/coviddeath/*.rds
        png: output/over12/models/km/prior_covid_infection/coviddeath/*.png

  km_over12_prior_covid_infection_noncoviddeath:
    run: r:latest analysis/model/km.R over12 prior_covid_infection noncoviddeath
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/prior_covid_infection/noncoviddeath/*.rds
        png: output/over12/models/km/prior_covid_infection/noncoviddeath/*.png

  combine_km_over12:
    run: r:latest analysis/model/km_combine.R over12
    needs:
    - km_over12_all_postest
    - km_over12_all_emergency
    - km_over12_all_covidemergency
    - km_over12_all_covidadmitted
    - km_over12_all_covidcritcare
    - km_over12_all_coviddeath
    - km_over12_all_noncoviddeath
    - km_over12_prior_covid_infection_postest
    - km_over12_prior_covid_infection_emergency
    - km_over12_prior_covid_infection_covidemergency
    - km_over12_prior_covid_infection_covidadmitted
    - km_over12_prior_covid_infection_covidcritcare
    - km_over12_prior_covid_infection_coviddeath
    - km_over12_prior_covid_infection_noncoviddeath
    outputs:
      moderately_sensitive:
        rds: output/over12/models/km/combined/*.csv
        png: output/over12/models/km/combined/*.png

  ## # # # # # # # # # # # # # # # # # # # 
  ## Under 12s cohort 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Extract and match 

  extract_treated_under12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_treated
      --output-file output/under12/extract/input_treated.feather --param cohort=under12
    outputs:
      highly_sensitive:
        extract: output/under12/extract/input_treated.feather

  process_treated_under12:
    run: r:latest analysis/treated/process_treated.R under12
    needs:
    - extract_treated_under12
    outputs:
      highly_sensitive:
        rds: output/under12/treated/*.rds
  
  vax2_under12:
    run: r:latest analysis/treated/second_vax.R under12
    needs:
    - extract_treated_under12
    outputs:
      moderately_sensitive:
         csv: output/under12/treated/*.csv

  extract_controlpotential_under12_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/under12/matchround1/extract/input_controlpotential.feather
      --param cohort=under12 --param matching_round=1 --param index_date=2022-04-04
    needs: []
    outputs:
      highly_sensitive:
        cohort: output/under12/matchround1/extract/input_controlpotential.feather

  process_controlpotential_under12_1:
    run: r:latest analysis/matching/process_controlpotential.R under12 1
    needs:
    - extract_controlpotential_under12_1
    outputs:
      highly_sensitive:
        rds: output/under12/matchround1/process/*.rds

  match_potential_under12_1:
    run: r:latest analysis/matching/match_potential.R under12 1
    needs:
    - process_treated_under12
    - process_controlpotential_under12_1
    outputs:
      highly_sensitive:
        rds: output/under12/matchround1/potential/*.rds
        csv: output/under12/matchround1/potential/*.csv.gz

  extract_controlactual_under12_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/under12/matchround1/extract/input_controlactual.feather
      --param cohort=under12 --param matching_round=1
    needs:
    - match_potential_under12_1
    outputs:
      highly_sensitive:
        cohort: output/under12/matchround1/extract/input_controlactual.feather

  process_controlactual_under12_1:
    run: r:latest analysis/matching/process_controlactual.R under12 1
    needs:
    - process_treated_under12
    - match_potential_under12_1
    - extract_controlpotential_under12_1
    - extract_controlactual_under12_1
    outputs:
      highly_sensitive:
        rds: output/under12/matchround1/actual/*.rds
        csv: output/under12/matchround1/actual/*.csv.gz

  extract_controlpotential_under12_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/under12/matchround2/extract/input_controlpotential.feather
      --param cohort=under12 --param matching_round=2 --param index_date=2022-04-25
    needs:
    - process_controlactual_under12_1
    outputs:
      highly_sensitive:
        cohort: output/under12/matchround2/extract/input_controlpotential.feather

  process_controlpotential_under12_2:
    run: r:latest analysis/matching/process_controlpotential.R under12 2
    needs:
    - extract_controlpotential_under12_2
    outputs:
      highly_sensitive:
        rds: output/under12/matchround2/process/*.rds

  match_potential_under12_2:
    run: r:latest analysis/matching/match_potential.R under12 2
    needs:
    - process_treated_under12
    - process_controlpotential_under12_2
    - process_controlactual_under12_1
    outputs:
      highly_sensitive:
        rds: output/under12/matchround2/potential/*.rds
        csv: output/under12/matchround2/potential/*.csv.gz

  extract_controlactual_under12_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/under12/matchround2/extract/input_controlactual.feather
      --param cohort=under12 --param matching_round=2
    needs:
    - match_potential_under12_2
    outputs:
      highly_sensitive:
        cohort: output/under12/matchround2/extract/input_controlactual.feather

  process_controlactual_under12_2:
    run: r:latest analysis/matching/process_controlactual.R under12 2
    needs:
    - process_treated_under12
    - match_potential_under12_2
    - extract_controlpotential_under12_2
    - extract_controlactual_under12_2
    - process_controlactual_under12_1
    outputs:
      highly_sensitive:
        rds: output/under12/matchround2/actual/*.rds
        csv: output/under12/matchround2/actual/*.csv.gz

  extract_controlpotential_under12_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/under12/matchround3/extract/input_controlpotential.feather
      --param cohort=under12 --param matching_round=3 --param index_date=2022-05-16
    needs:
    - process_controlactual_under12_2
    outputs:
      highly_sensitive:
        cohort: output/under12/matchround3/extract/input_controlpotential.feather

  process_controlpotential_under12_3:
    run: r:latest analysis/matching/process_controlpotential.R under12 3
    needs:
    - extract_controlpotential_under12_3
    outputs:
      highly_sensitive:
        rds: output/under12/matchround3/process/*.rds

  match_potential_under12_3:
    run: r:latest analysis/matching/match_potential.R under12 3
    needs:
    - process_treated_under12
    - process_controlpotential_under12_3
    - process_controlactual_under12_2
    outputs:
      highly_sensitive:
        rds: output/under12/matchround3/potential/*.rds
        csv: output/under12/matchround3/potential/*.csv.gz

  extract_controlactual_under12_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/under12/matchround3/extract/input_controlactual.feather
      --param cohort=under12 --param matching_round=3
    needs:
    - match_potential_under12_3
    outputs:
      highly_sensitive:
        cohort: output/under12/matchround3/extract/input_controlactual.feather

  process_controlactual_under12_3:
    run: r:latest analysis/matching/process_controlactual.R under12 3
    needs:
    - process_treated_under12
    - match_potential_under12_3
    - extract_controlpotential_under12_3
    - extract_controlactual_under12_3
    - process_controlactual_under12_2
    outputs:
      highly_sensitive:
        rds: output/under12/matchround3/actual/*.rds
        csv: output/under12/matchround3/actual/*.csv.gz

  extract_controlpotential_under12_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/under12/matchround4/extract/input_controlpotential.feather
      --param cohort=under12 --param matching_round=4 --param index_date=2022-06-06
    needs:
    - process_controlactual_under12_3
    outputs:
      highly_sensitive:
        cohort: output/under12/matchround4/extract/input_controlpotential.feather

  process_controlpotential_under12_4:
    run: r:latest analysis/matching/process_controlpotential.R under12 4
    needs:
    - extract_controlpotential_under12_4
    outputs:
      highly_sensitive:
        rds: output/under12/matchround4/process/*.rds

  match_potential_under12_4:
    run: r:latest analysis/matching/match_potential.R under12 4
    needs:
    - process_treated_under12
    - process_controlpotential_under12_4
    - process_controlactual_under12_3
    outputs:
      highly_sensitive:
        rds: output/under12/matchround4/potential/*.rds
        csv: output/under12/matchround4/potential/*.csv.gz

  extract_controlactual_under12_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/under12/matchround4/extract/input_controlactual.feather
      --param cohort=under12 --param matching_round=4
    needs:
    - match_potential_under12_4
    outputs:
      highly_sensitive:
        cohort: output/under12/matchround4/extract/input_controlactual.feather

  process_controlactual_under12_4:
    run: r:latest analysis/matching/process_controlactual.R under12 4
    needs:
    - process_treated_under12
    - match_potential_under12_4
    - extract_controlpotential_under12_4
    - extract_controlactual_under12_4
    - process_controlactual_under12_3
    outputs:
      highly_sensitive:
        rds: output/under12/matchround4/actual/*.rds
        csv: output/under12/matchround4/actual/*.csv.gz

  extract_controlfinal_under12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlfinal
      --output-file output/under12/extract/input_controlfinal.feather --param cohort=under12
      --param n_matching_rounds=4
    needs:
    - process_controlactual_under12_4
    outputs:
      highly_sensitive:
        extract: output/under12/extract/input_controlfinal.feather

  process_controlfinal_under12:
    run: r:latest analysis/matching/process_controlfinal.R under12
    needs:
    - process_controlactual_under12_1
    - process_controlactual_under12_2
    - process_controlactual_under12_3
    - process_controlactual_under12_4
    - extract_controlfinal_under12
    - process_treated_under12
    outputs:
      highly_sensitive:
        extract: output/under12/match/*.rds

  table1_under12:
    run: r:latest analysis/matching/table1.R under12
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        csv: output/under12/table1/*.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Model 

  km_under12_all_postest:
    run: r:latest analysis/model/km.R under12 all postest
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/all/postest/*.rds
        png: output/under12/models/km/all/postest/*.png

  km_under12_all_emergency:
    run: r:latest analysis/model/km.R under12 all emergency
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/all/emergency/*.rds
        png: output/under12/models/km/all/emergency/*.png

  km_under12_all_covidemergency:
    run: r:latest analysis/model/km.R under12 all covidemergency
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/all/covidemergency/*.rds
        png: output/under12/models/km/all/covidemergency/*.png

  km_under12_all_covidadmitted:
    run: r:latest analysis/model/km.R under12 all covidadmitted
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/all/covidadmitted/*.rds
        png: output/under12/models/km/all/covidadmitted/*.png

  km_under12_all_covidcritcare:
    run: r:latest analysis/model/km.R under12 all covidcritcare
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/all/covidcritcare/*.rds
        png: output/under12/models/km/all/covidcritcare/*.png

  km_under12_all_coviddeath:
    run: r:latest analysis/model/km.R under12 all coviddeath
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/all/coviddeath/*.rds
        png: output/under12/models/km/all/coviddeath/*.png

  km_under12_all_noncoviddeath:
    run: r:latest analysis/model/km.R under12 all noncoviddeath
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/all/noncoviddeath/*.rds
        png: output/under12/models/km/all/noncoviddeath/*.png

  km_under12_prior_covid_infection_postest:
    run: r:latest analysis/model/km.R under12 prior_covid_infection postest
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/prior_covid_infection/postest/*.rds
        png: output/under12/models/km/prior_covid_infection/postest/*.png

  km_under12_prior_covid_infection_emergency:
    run: r:latest analysis/model/km.R under12 prior_covid_infection emergency
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/prior_covid_infection/emergency/*.rds
        png: output/under12/models/km/prior_covid_infection/emergency/*.png

  km_under12_prior_covid_infection_covidemergency:
    run: r:latest analysis/model/km.R under12 prior_covid_infection covidemergency
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/prior_covid_infection/covidemergency/*.rds
        png: output/under12/models/km/prior_covid_infection/covidemergency/*.png

  km_under12_prior_covid_infection_covidadmitted:
    run: r:latest analysis/model/km.R under12 prior_covid_infection covidadmitted
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/prior_covid_infection/covidadmitted/*.rds
        png: output/under12/models/km/prior_covid_infection/covidadmitted/*.png

  km_under12_prior_covid_infection_covidcritcare:
    run: r:latest analysis/model/km.R under12 prior_covid_infection covidcritcare
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/prior_covid_infection/covidcritcare/*.rds
        png: output/under12/models/km/prior_covid_infection/covidcritcare/*.png

  km_under12_prior_covid_infection_coviddeath:
    run: r:latest analysis/model/km.R under12 prior_covid_infection coviddeath
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/prior_covid_infection/coviddeath/*.rds
        png: output/under12/models/km/prior_covid_infection/coviddeath/*.png

  km_under12_prior_covid_infection_noncoviddeath:
    run: r:latest analysis/model/km.R under12 prior_covid_infection noncoviddeath
    needs:
    - process_controlfinal_under12
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/prior_covid_infection/noncoviddeath/*.rds
        png: output/under12/models/km/prior_covid_infection/noncoviddeath/*.png

  combine_km_under12:
    run: r:latest analysis/model/km_combine.R under12
    needs:
    - km_under12_all_postest
    - km_under12_all_emergency
    - km_under12_all_covidemergency
    - km_under12_all_covidadmitted
    - km_under12_all_covidcritcare
    - km_under12_all_coviddeath
    - km_under12_all_noncoviddeath
    - km_under12_prior_covid_infection_postest
    - km_under12_prior_covid_infection_emergency
    - km_under12_prior_covid_infection_covidemergency
    - km_under12_prior_covid_infection_covidadmitted
    - km_under12_prior_covid_infection_covidcritcare
    - km_under12_prior_covid_infection_coviddeath
    - km_under12_prior_covid_infection_noncoviddeath
    outputs:
      moderately_sensitive:
        rds: output/under12/models/km/combined/*.csv
        png: output/under12/models/km/combined/*.png

  ## # # # # # # # # # # # # # # # # # # # 
  ## Move files for release 
  ## # # # # # # # # # # # # # # # # # # # 

  release:
    run: r:latest analysis/release_objects.R
    needs:
    - combine_km_over12
    - table1_over12
    - combine_km_under12
    - table1_under12
    outputs:
      moderately_sensitive:
        txt: output/meta-release/*.txt
        csv: output/release/*.csv

  ## #### End ####

Timeline

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Job information

Status
Failed
Job exited with error code 1
Backend
TPP
Requested by
Colm Andrews
Branch
main
Force run dependencies
No
Git commit hash
1581bdd
Requested actions
  • vax2_over12
  • vax2_under12