Job request: 8680

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Will Hulme requested one or more actions to be run against real patient data in the COVID-19 Vaccine Effectiveness 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
iu4fkofuzxzo6r6v succeeded ci_A_all_covidadmitted
5pke7skvwuenkxf4 succeeded ci_A_all_covidadmittedproxy1
szjxtoh6xnxi5z3s succeeded ci_A_all_covidcritcare
gx2gwbsc3y2yobbc succeeded ci_A_all_coviddeath
zi7tgt6i6zi2y42n succeeded ci_A_all_covidemergency
hjihjqxiejiwrsqu succeeded ci_A_all_noncoviddeath
vich7uq65a5ao42q succeeded ci_A_all_postest
vsvaoxohc5af5sra succeeded ci_A_cev_cv_covidadmitted
cfutqi4lmtnhf4nu succeeded ci_A_cev_cv_covidadmittedproxy1
hmmdjvmtsitgz5ob succeeded ci_A_cev_cv_covidcritcare
atgsl4kkxd2dv6se succeeded ci_A_cev_cv_coviddeath
4he4sxnams3gogpe succeeded ci_A_cev_cv_covidemergency
hplpcyd5sot7jvfw succeeded ci_A_cev_cv_noncoviddeath
vkekhmjjccrlzv7y succeeded ci_A_cev_cv_postest
2aeubpvk2nxj6w6a succeeded ci_A_vax12_type_covidadmitted
icinnpem7vk27byd succeeded ci_A_vax12_type_covidadmittedproxy1
idpbxe2qhagf33wj succeeded ci_A_vax12_type_covidcritcare
zihtuodcbr7z5ygy succeeded ci_A_vax12_type_coviddeath
iac74ixriztosevl succeeded ci_A_vax12_type_covidemergency
uicqnxrce3xu4bb6 succeeded ci_A_vax12_type_noncoviddeath
en7fupoflinf4qsj succeeded ci_A_vax12_type_postest

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:

  population_size: 1000

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 
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  ## # # # # # # # # # # # # # # # # # # # 
  ## Pre-server scripts 
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  ## # # # # # # # # # # # # # # # # # # # 
  ## Extract and tidy 
  ## # # # # # # # # # # # # # # # # # # # 

  extract:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    needs: []
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  data_process:
    run: r:latest analysis/data_process.R
    needs:
    - extract
    outputs:
      highly_sensitive:
        rds: output/data/data_processed.rds
        vaxlong: output/data/data_vaxlong.rds

  skim_process:
    run: r:latest analysis/data_skim.R output/data/data_processed.rds output/data_properties
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/data_processed*.txt

  data_selection:
    run: r:latest analysis/data_selection.R
    needs:
    - data_process
    outputs:
      highly_sensitive:
        feather: output/data/data_cohort.feather
        cohortrds: output/data/data_cohort.rds
        criteriards: output/data/data_inclusioncriteria.rds
      moderately_sensitive:
        flow: output/data/flowchart.csv

  skim_selection:
    run: r:latest analysis/data_skim.R output/data/data_cohort.rds output/data_properties
    needs:
    - data_selection
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/data_cohort*.txt

  geography:
    run: r:latest analysis/geography.R
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        png: output/geography/*.png
        csv: output/geography/*.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## matching set A 
  ## # # # # # # # # # # # # # # # # # # # 

  match_A:
    run: r:latest analysis/match.R A
    needs:
    - data_selection
    outputs:
      highly_sensitive:
        rds: output/match/A/*.rds
      moderately_sensitive:
        txt: output/match/A/*.txt

  match_report_A:
    run: r:latest analysis/match_report.R A
    needs:
    - data_selection
    - match_A
    outputs:
      moderately_sensitive:
        txt: output/match/A/report/*.txt
        csv: output/match/A/report/*.csv
        png: output/match/A/report/*.png
        html: output/match/A/report/*.html

  ## ### Overall models (''all'') 

  ci_A_all_postest:
    run: r:latest analysis/ci.R A all postest
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/all/postest/*.txt
        csv: output/match/A/ci/all/postest/*.csv
        png: output/match/A/ci/all/postest/*.png

  ci_A_all_covidemergency:
    run: r:latest analysis/ci.R A all covidemergency
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/all/covidemergency/*.txt
        csv: output/match/A/ci/all/covidemergency/*.csv
        png: output/match/A/ci/all/covidemergency/*.png

  ci_A_all_covidadmittedproxy1:
    run: r:latest analysis/ci.R A all covidadmittedproxy1
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/all/covidadmittedproxy1/*.txt
        csv: output/match/A/ci/all/covidadmittedproxy1/*.csv
        png: output/match/A/ci/all/covidadmittedproxy1/*.png

  ci_A_all_covidadmitted:
    run: r:latest analysis/ci.R A all covidadmitted
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/all/covidadmitted/*.txt
        csv: output/match/A/ci/all/covidadmitted/*.csv
        png: output/match/A/ci/all/covidadmitted/*.png

  ci_A_all_covidcritcare:
    run: r:latest analysis/ci.R A all covidcritcare
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/all/covidcritcare/*.txt
        csv: output/match/A/ci/all/covidcritcare/*.csv
        png: output/match/A/ci/all/covidcritcare/*.png

  ci_A_all_coviddeath:
    run: r:latest analysis/ci.R A all coviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/all/coviddeath/*.txt
        csv: output/match/A/ci/all/coviddeath/*.csv
        png: output/match/A/ci/all/coviddeath/*.png

  ci_A_all_noncoviddeath:
    run: r:latest analysis/ci.R A all noncoviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/all/noncoviddeath/*.txt
        csv: output/match/A/ci/all/noncoviddeath/*.csv
        png: output/match/A/ci/all/noncoviddeath/*.png

  ## ### Models by primary course (''vax12_type'') 

  ci_A_vax12_type_postest:
    run: r:latest analysis/ci.R A vax12_type postest
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/vax12_type/postest/*.txt
        csv: output/match/A/ci/vax12_type/postest/*.csv
        png: output/match/A/ci/vax12_type/postest/*.png

  ci_A_vax12_type_covidemergency:
    run: r:latest analysis/ci.R A vax12_type covidemergency
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/vax12_type/covidemergency/*.txt
        csv: output/match/A/ci/vax12_type/covidemergency/*.csv
        png: output/match/A/ci/vax12_type/covidemergency/*.png

  ci_A_vax12_type_covidadmittedproxy1:
    run: r:latest analysis/ci.R A vax12_type covidadmittedproxy1
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/vax12_type/covidadmittedproxy1/*.txt
        csv: output/match/A/ci/vax12_type/covidadmittedproxy1/*.csv
        png: output/match/A/ci/vax12_type/covidadmittedproxy1/*.png

  ci_A_vax12_type_covidadmitted:
    run: r:latest analysis/ci.R A vax12_type covidadmitted
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/vax12_type/covidadmitted/*.txt
        csv: output/match/A/ci/vax12_type/covidadmitted/*.csv
        png: output/match/A/ci/vax12_type/covidadmitted/*.png

  ci_A_vax12_type_covidcritcare:
    run: r:latest analysis/ci.R A vax12_type covidcritcare
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/vax12_type/covidcritcare/*.txt
        csv: output/match/A/ci/vax12_type/covidcritcare/*.csv
        png: output/match/A/ci/vax12_type/covidcritcare/*.png

  ci_A_vax12_type_coviddeath:
    run: r:latest analysis/ci.R A vax12_type coviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/vax12_type/coviddeath/*.txt
        csv: output/match/A/ci/vax12_type/coviddeath/*.csv
        png: output/match/A/ci/vax12_type/coviddeath/*.png

  ci_A_vax12_type_noncoviddeath:
    run: r:latest analysis/ci.R A vax12_type noncoviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/vax12_type/noncoviddeath/*.txt
        csv: output/match/A/ci/vax12_type/noncoviddeath/*.csv
        png: output/match/A/ci/vax12_type/noncoviddeath/*.png

  ## ### Models by clinically vulnerable group (''cev_cv'') 

  ci_A_cev_cv_postest:
    run: r:latest analysis/ci.R A cev_cv postest
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/cev_cv/postest/*.txt
        csv: output/match/A/ci/cev_cv/postest/*.csv
        png: output/match/A/ci/cev_cv/postest/*.png

  ci_A_cev_cv_covidemergency:
    run: r:latest analysis/ci.R A cev_cv covidemergency
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/cev_cv/covidemergency/*.txt
        csv: output/match/A/ci/cev_cv/covidemergency/*.csv
        png: output/match/A/ci/cev_cv/covidemergency/*.png

  ci_A_cev_cv_covidadmittedproxy1:
    run: r:latest analysis/ci.R A cev_cv covidadmittedproxy1
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/cev_cv/covidadmittedproxy1/*.txt
        csv: output/match/A/ci/cev_cv/covidadmittedproxy1/*.csv
        png: output/match/A/ci/cev_cv/covidadmittedproxy1/*.png

  ci_A_cev_cv_covidadmitted:
    run: r:latest analysis/ci.R A cev_cv covidadmitted
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/cev_cv/covidadmitted/*.txt
        csv: output/match/A/ci/cev_cv/covidadmitted/*.csv
        png: output/match/A/ci/cev_cv/covidadmitted/*.png

  ci_A_cev_cv_covidcritcare:
    run: r:latest analysis/ci.R A cev_cv covidcritcare
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/cev_cv/covidcritcare/*.txt
        csv: output/match/A/ci/cev_cv/covidcritcare/*.csv
        png: output/match/A/ci/cev_cv/covidcritcare/*.png

  ci_A_cev_cv_coviddeath:
    run: r:latest analysis/ci.R A cev_cv coviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/cev_cv/coviddeath/*.txt
        csv: output/match/A/ci/cev_cv/coviddeath/*.csv
        png: output/match/A/ci/cev_cv/coviddeath/*.png

  ci_A_cev_cv_noncoviddeath:
    run: r:latest analysis/ci.R A cev_cv noncoviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/cev_cv/noncoviddeath/*.txt
        csv: output/match/A/ci/cev_cv/noncoviddeath/*.csv
        png: output/match/A/ci/cev_cv/noncoviddeath/*.png

  ## ### Models by prior infection (''prior_covid_infection'') 

  ci_A_prior_covid_infection_postest:
    run: r:latest analysis/ci.R A prior_covid_infection postest
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/prior_covid_infection/postest/*.txt
        csv: output/match/A/ci/prior_covid_infection/postest/*.csv
        png: output/match/A/ci/prior_covid_infection/postest/*.png

  ci_A_prior_covid_infection_covidemergency:
    run: r:latest analysis/ci.R A prior_covid_infection covidemergency
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/prior_covid_infection/covidemergency/*.txt
        csv: output/match/A/ci/prior_covid_infection/covidemergency/*.csv
        png: output/match/A/ci/prior_covid_infection/covidemergency/*.png

  ci_A_prior_covid_infection_covidadmittedproxy1:
    run: r:latest analysis/ci.R A prior_covid_infection covidadmittedproxy1
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/prior_covid_infection/covidadmittedproxy1/*.txt
        csv: output/match/A/ci/prior_covid_infection/covidadmittedproxy1/*.csv
        png: output/match/A/ci/prior_covid_infection/covidadmittedproxy1/*.png

  ci_A_prior_covid_infection_covidadmitted:
    run: r:latest analysis/ci.R A prior_covid_infection covidadmitted
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/prior_covid_infection/covidadmitted/*.txt
        csv: output/match/A/ci/prior_covid_infection/covidadmitted/*.csv
        png: output/match/A/ci/prior_covid_infection/covidadmitted/*.png

  ci_A_prior_covid_infection_covidcritcare:
    run: r:latest analysis/ci.R A prior_covid_infection covidcritcare
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/prior_covid_infection/covidcritcare/*.txt
        csv: output/match/A/ci/prior_covid_infection/covidcritcare/*.csv
        png: output/match/A/ci/prior_covid_infection/covidcritcare/*.png

  ci_A_prior_covid_infection_coviddeath:
    run: r:latest analysis/ci.R A prior_covid_infection coviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/prior_covid_infection/coviddeath/*.txt
        csv: output/match/A/ci/prior_covid_infection/coviddeath/*.csv
        png: output/match/A/ci/prior_covid_infection/coviddeath/*.png

  ci_A_prior_covid_infection_noncoviddeath:
    run: r:latest analysis/ci.R A prior_covid_infection noncoviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/prior_covid_infection/noncoviddeath/*.txt
        csv: output/match/A/ci/prior_covid_infection/noncoviddeath/*.csv
        png: output/match/A/ci/prior_covid_infection/noncoviddeath/*.png

  ## ### Models by age (''age65plus'') 

  ci_A_age65plus_postest:
    run: r:latest analysis/ci.R A age65plus postest
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/age65plus/postest/*.txt
        csv: output/match/A/ci/age65plus/postest/*.csv
        png: output/match/A/ci/age65plus/postest/*.png

  ci_A_age65plus_covidemergency:
    run: r:latest analysis/ci.R A age65plus covidemergency
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/age65plus/covidemergency/*.txt
        csv: output/match/A/ci/age65plus/covidemergency/*.csv
        png: output/match/A/ci/age65plus/covidemergency/*.png

  ci_A_age65plus_covidadmittedproxy1:
    run: r:latest analysis/ci.R A age65plus covidadmittedproxy1
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/age65plus/covidadmittedproxy1/*.txt
        csv: output/match/A/ci/age65plus/covidadmittedproxy1/*.csv
        png: output/match/A/ci/age65plus/covidadmittedproxy1/*.png

  ci_A_age65plus_covidadmitted:
    run: r:latest analysis/ci.R A age65plus covidadmitted
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/age65plus/covidadmitted/*.txt
        csv: output/match/A/ci/age65plus/covidadmitted/*.csv
        png: output/match/A/ci/age65plus/covidadmitted/*.png

  ci_A_age65plus_covidcritcare:
    run: r:latest analysis/ci.R A age65plus covidcritcare
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/age65plus/covidcritcare/*.txt
        csv: output/match/A/ci/age65plus/covidcritcare/*.csv
        png: output/match/A/ci/age65plus/covidcritcare/*.png

  ci_A_age65plus_coviddeath:
    run: r:latest analysis/ci.R A age65plus coviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/age65plus/coviddeath/*.txt
        csv: output/match/A/ci/age65plus/coviddeath/*.csv
        png: output/match/A/ci/age65plus/coviddeath/*.png

  ci_A_age65plus_noncoviddeath:
    run: r:latest analysis/ci.R A age65plus noncoviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/age65plus/noncoviddeath/*.txt
        csv: output/match/A/ci/age65plus/noncoviddeath/*.csv
        png: output/match/A/ci/age65plus/noncoviddeath/*.png

  ## ### Models by variant era (''variantera'') 

  ci_A_variantera_postest:
    run: r:latest analysis/ci.R A variantera postest
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/variantera/postest/*.txt
        csv: output/match/A/ci/variantera/postest/*.csv
        png: output/match/A/ci/variantera/postest/*.png

  ci_A_variantera_covidemergency:
    run: r:latest analysis/ci.R A variantera covidemergency
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/variantera/covidemergency/*.txt
        csv: output/match/A/ci/variantera/covidemergency/*.csv
        png: output/match/A/ci/variantera/covidemergency/*.png

  ci_A_variantera_covidadmittedproxy1:
    run: r:latest analysis/ci.R A variantera covidadmittedproxy1
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/variantera/covidadmittedproxy1/*.txt
        csv: output/match/A/ci/variantera/covidadmittedproxy1/*.csv
        png: output/match/A/ci/variantera/covidadmittedproxy1/*.png

  ci_A_variantera_covidadmitted:
    run: r:latest analysis/ci.R A variantera covidadmitted
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/variantera/covidadmitted/*.txt
        csv: output/match/A/ci/variantera/covidadmitted/*.csv
        png: output/match/A/ci/variantera/covidadmitted/*.png

  ci_A_variantera_covidcritcare:
    run: r:latest analysis/ci.R A variantera covidcritcare
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/variantera/covidcritcare/*.txt
        csv: output/match/A/ci/variantera/covidcritcare/*.csv
        png: output/match/A/ci/variantera/covidcritcare/*.png

  ci_A_variantera_coviddeath:
    run: r:latest analysis/ci.R A variantera coviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/variantera/coviddeath/*.txt
        csv: output/match/A/ci/variantera/coviddeath/*.csv
        png: output/match/A/ci/variantera/coviddeath/*.png

  ci_A_variantera_noncoviddeath:
    run: r:latest analysis/ci.R A variantera noncoviddeath
    needs:
    - match_A
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/A/ci/variantera/noncoviddeath/*.txt
        csv: output/match/A/ci/variantera/noncoviddeath/*.csv
        png: output/match/A/ci/variantera/noncoviddeath/*.png

  ## # # # # # # # # # # # # # # # # # # # 
  ## matching set B 
  ## # # # # # # # # # # # # # # # # # # # 

  match_B:
    run: r:latest analysis/match.R B
    needs:
    - data_selection
    outputs:
      highly_sensitive:
        rds: output/match/B/*.rds
      moderately_sensitive:
        txt: output/match/B/*.txt

  match_report_B:
    run: r:latest analysis/match_report.R B
    needs:
    - data_selection
    - match_B
    outputs:
      moderately_sensitive:
        txt: output/match/B/report/*.txt
        csv: output/match/B/report/*.csv
        png: output/match/B/report/*.png
        html: output/match/B/report/*.html

  ## ### Overall models (''all'') 

  ci_B_all_postest:
    run: r:latest analysis/ci.R B all postest
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/all/postest/*.txt
        csv: output/match/B/ci/all/postest/*.csv
        png: output/match/B/ci/all/postest/*.png

  ci_B_all_covidemergency:
    run: r:latest analysis/ci.R B all covidemergency
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/all/covidemergency/*.txt
        csv: output/match/B/ci/all/covidemergency/*.csv
        png: output/match/B/ci/all/covidemergency/*.png

  ci_B_all_covidadmittedproxy1:
    run: r:latest analysis/ci.R B all covidadmittedproxy1
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/all/covidadmittedproxy1/*.txt
        csv: output/match/B/ci/all/covidadmittedproxy1/*.csv
        png: output/match/B/ci/all/covidadmittedproxy1/*.png

  ci_B_all_covidadmitted:
    run: r:latest analysis/ci.R B all covidadmitted
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/all/covidadmitted/*.txt
        csv: output/match/B/ci/all/covidadmitted/*.csv
        png: output/match/B/ci/all/covidadmitted/*.png

  ci_B_all_covidcritcare:
    run: r:latest analysis/ci.R B all covidcritcare
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/all/covidcritcare/*.txt
        csv: output/match/B/ci/all/covidcritcare/*.csv
        png: output/match/B/ci/all/covidcritcare/*.png

  ci_B_all_coviddeath:
    run: r:latest analysis/ci.R B all coviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/all/coviddeath/*.txt
        csv: output/match/B/ci/all/coviddeath/*.csv
        png: output/match/B/ci/all/coviddeath/*.png

  ci_B_all_noncoviddeath:
    run: r:latest analysis/ci.R B all noncoviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/all/noncoviddeath/*.txt
        csv: output/match/B/ci/all/noncoviddeath/*.csv
        png: output/match/B/ci/all/noncoviddeath/*.png

  ## ### Models by primary course (''vax12_type'') 

  ci_B_vax12_type_postest:
    run: r:latest analysis/ci.R B vax12_type postest
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/vax12_type/postest/*.txt
        csv: output/match/B/ci/vax12_type/postest/*.csv
        png: output/match/B/ci/vax12_type/postest/*.png

  ci_B_vax12_type_covidemergency:
    run: r:latest analysis/ci.R B vax12_type covidemergency
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/vax12_type/covidemergency/*.txt
        csv: output/match/B/ci/vax12_type/covidemergency/*.csv
        png: output/match/B/ci/vax12_type/covidemergency/*.png

  ci_B_vax12_type_covidadmittedproxy1:
    run: r:latest analysis/ci.R B vax12_type covidadmittedproxy1
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/vax12_type/covidadmittedproxy1/*.txt
        csv: output/match/B/ci/vax12_type/covidadmittedproxy1/*.csv
        png: output/match/B/ci/vax12_type/covidadmittedproxy1/*.png

  ci_B_vax12_type_covidadmitted:
    run: r:latest analysis/ci.R B vax12_type covidadmitted
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/vax12_type/covidadmitted/*.txt
        csv: output/match/B/ci/vax12_type/covidadmitted/*.csv
        png: output/match/B/ci/vax12_type/covidadmitted/*.png

  ci_B_vax12_type_covidcritcare:
    run: r:latest analysis/ci.R B vax12_type covidcritcare
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/vax12_type/covidcritcare/*.txt
        csv: output/match/B/ci/vax12_type/covidcritcare/*.csv
        png: output/match/B/ci/vax12_type/covidcritcare/*.png

  ci_B_vax12_type_coviddeath:
    run: r:latest analysis/ci.R B vax12_type coviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/vax12_type/coviddeath/*.txt
        csv: output/match/B/ci/vax12_type/coviddeath/*.csv
        png: output/match/B/ci/vax12_type/coviddeath/*.png

  ci_B_vax12_type_noncoviddeath:
    run: r:latest analysis/ci.R B vax12_type noncoviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/vax12_type/noncoviddeath/*.txt
        csv: output/match/B/ci/vax12_type/noncoviddeath/*.csv
        png: output/match/B/ci/vax12_type/noncoviddeath/*.png

  ## ### Models by clinically vulnerable group (''cev_cv'') 

  ci_B_cev_cv_postest:
    run: r:latest analysis/ci.R B cev_cv postest
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/cev_cv/postest/*.txt
        csv: output/match/B/ci/cev_cv/postest/*.csv
        png: output/match/B/ci/cev_cv/postest/*.png

  ci_B_cev_cv_covidemergency:
    run: r:latest analysis/ci.R B cev_cv covidemergency
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/cev_cv/covidemergency/*.txt
        csv: output/match/B/ci/cev_cv/covidemergency/*.csv
        png: output/match/B/ci/cev_cv/covidemergency/*.png

  ci_B_cev_cv_covidadmittedproxy1:
    run: r:latest analysis/ci.R B cev_cv covidadmittedproxy1
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/cev_cv/covidadmittedproxy1/*.txt
        csv: output/match/B/ci/cev_cv/covidadmittedproxy1/*.csv
        png: output/match/B/ci/cev_cv/covidadmittedproxy1/*.png

  ci_B_cev_cv_covidadmitted:
    run: r:latest analysis/ci.R B cev_cv covidadmitted
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/cev_cv/covidadmitted/*.txt
        csv: output/match/B/ci/cev_cv/covidadmitted/*.csv
        png: output/match/B/ci/cev_cv/covidadmitted/*.png

  ci_B_cev_cv_covidcritcare:
    run: r:latest analysis/ci.R B cev_cv covidcritcare
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/cev_cv/covidcritcare/*.txt
        csv: output/match/B/ci/cev_cv/covidcritcare/*.csv
        png: output/match/B/ci/cev_cv/covidcritcare/*.png

  ci_B_cev_cv_coviddeath:
    run: r:latest analysis/ci.R B cev_cv coviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/cev_cv/coviddeath/*.txt
        csv: output/match/B/ci/cev_cv/coviddeath/*.csv
        png: output/match/B/ci/cev_cv/coviddeath/*.png

  ci_B_cev_cv_noncoviddeath:
    run: r:latest analysis/ci.R B cev_cv noncoviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/cev_cv/noncoviddeath/*.txt
        csv: output/match/B/ci/cev_cv/noncoviddeath/*.csv
        png: output/match/B/ci/cev_cv/noncoviddeath/*.png

  ## ### Models by prior infection (''prior_covid_infection'') 

  ci_B_prior_covid_infection_postest:
    run: r:latest analysis/ci.R B prior_covid_infection postest
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/prior_covid_infection/postest/*.txt
        csv: output/match/B/ci/prior_covid_infection/postest/*.csv
        png: output/match/B/ci/prior_covid_infection/postest/*.png

  ci_B_prior_covid_infection_covidemergency:
    run: r:latest analysis/ci.R B prior_covid_infection covidemergency
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/prior_covid_infection/covidemergency/*.txt
        csv: output/match/B/ci/prior_covid_infection/covidemergency/*.csv
        png: output/match/B/ci/prior_covid_infection/covidemergency/*.png

  ci_B_prior_covid_infection_covidadmittedproxy1:
    run: r:latest analysis/ci.R B prior_covid_infection covidadmittedproxy1
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/prior_covid_infection/covidadmittedproxy1/*.txt
        csv: output/match/B/ci/prior_covid_infection/covidadmittedproxy1/*.csv
        png: output/match/B/ci/prior_covid_infection/covidadmittedproxy1/*.png

  ci_B_prior_covid_infection_covidadmitted:
    run: r:latest analysis/ci.R B prior_covid_infection covidadmitted
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/prior_covid_infection/covidadmitted/*.txt
        csv: output/match/B/ci/prior_covid_infection/covidadmitted/*.csv
        png: output/match/B/ci/prior_covid_infection/covidadmitted/*.png

  ci_B_prior_covid_infection_covidcritcare:
    run: r:latest analysis/ci.R B prior_covid_infection covidcritcare
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/prior_covid_infection/covidcritcare/*.txt
        csv: output/match/B/ci/prior_covid_infection/covidcritcare/*.csv
        png: output/match/B/ci/prior_covid_infection/covidcritcare/*.png

  ci_B_prior_covid_infection_coviddeath:
    run: r:latest analysis/ci.R B prior_covid_infection coviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/prior_covid_infection/coviddeath/*.txt
        csv: output/match/B/ci/prior_covid_infection/coviddeath/*.csv
        png: output/match/B/ci/prior_covid_infection/coviddeath/*.png

  ci_B_prior_covid_infection_noncoviddeath:
    run: r:latest analysis/ci.R B prior_covid_infection noncoviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/prior_covid_infection/noncoviddeath/*.txt
        csv: output/match/B/ci/prior_covid_infection/noncoviddeath/*.csv
        png: output/match/B/ci/prior_covid_infection/noncoviddeath/*.png

  ## ### Models by age (''age65plus'') 

  ci_B_age65plus_postest:
    run: r:latest analysis/ci.R B age65plus postest
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/age65plus/postest/*.txt
        csv: output/match/B/ci/age65plus/postest/*.csv
        png: output/match/B/ci/age65plus/postest/*.png

  ci_B_age65plus_covidemergency:
    run: r:latest analysis/ci.R B age65plus covidemergency
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/age65plus/covidemergency/*.txt
        csv: output/match/B/ci/age65plus/covidemergency/*.csv
        png: output/match/B/ci/age65plus/covidemergency/*.png

  ci_B_age65plus_covidadmittedproxy1:
    run: r:latest analysis/ci.R B age65plus covidadmittedproxy1
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/age65plus/covidadmittedproxy1/*.txt
        csv: output/match/B/ci/age65plus/covidadmittedproxy1/*.csv
        png: output/match/B/ci/age65plus/covidadmittedproxy1/*.png

  ci_B_age65plus_covidadmitted:
    run: r:latest analysis/ci.R B age65plus covidadmitted
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/age65plus/covidadmitted/*.txt
        csv: output/match/B/ci/age65plus/covidadmitted/*.csv
        png: output/match/B/ci/age65plus/covidadmitted/*.png

  ci_B_age65plus_covidcritcare:
    run: r:latest analysis/ci.R B age65plus covidcritcare
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/age65plus/covidcritcare/*.txt
        csv: output/match/B/ci/age65plus/covidcritcare/*.csv
        png: output/match/B/ci/age65plus/covidcritcare/*.png

  ci_B_age65plus_coviddeath:
    run: r:latest analysis/ci.R B age65plus coviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/age65plus/coviddeath/*.txt
        csv: output/match/B/ci/age65plus/coviddeath/*.csv
        png: output/match/B/ci/age65plus/coviddeath/*.png

  ci_B_age65plus_noncoviddeath:
    run: r:latest analysis/ci.R B age65plus noncoviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/age65plus/noncoviddeath/*.txt
        csv: output/match/B/ci/age65plus/noncoviddeath/*.csv
        png: output/match/B/ci/age65plus/noncoviddeath/*.png

  ## ### Models by variant era (''variantera'') 

  ci_B_variantera_postest:
    run: r:latest analysis/ci.R B variantera postest
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/variantera/postest/*.txt
        csv: output/match/B/ci/variantera/postest/*.csv
        png: output/match/B/ci/variantera/postest/*.png

  ci_B_variantera_covidemergency:
    run: r:latest analysis/ci.R B variantera covidemergency
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/variantera/covidemergency/*.txt
        csv: output/match/B/ci/variantera/covidemergency/*.csv
        png: output/match/B/ci/variantera/covidemergency/*.png

  ci_B_variantera_covidadmittedproxy1:
    run: r:latest analysis/ci.R B variantera covidadmittedproxy1
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/variantera/covidadmittedproxy1/*.txt
        csv: output/match/B/ci/variantera/covidadmittedproxy1/*.csv
        png: output/match/B/ci/variantera/covidadmittedproxy1/*.png

  ci_B_variantera_covidadmitted:
    run: r:latest analysis/ci.R B variantera covidadmitted
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/variantera/covidadmitted/*.txt
        csv: output/match/B/ci/variantera/covidadmitted/*.csv
        png: output/match/B/ci/variantera/covidadmitted/*.png

  ci_B_variantera_covidcritcare:
    run: r:latest analysis/ci.R B variantera covidcritcare
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/variantera/covidcritcare/*.txt
        csv: output/match/B/ci/variantera/covidcritcare/*.csv
        png: output/match/B/ci/variantera/covidcritcare/*.png

  ci_B_variantera_coviddeath:
    run: r:latest analysis/ci.R B variantera coviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/variantera/coviddeath/*.txt
        csv: output/match/B/ci/variantera/coviddeath/*.csv
        png: output/match/B/ci/variantera/coviddeath/*.png

  ci_B_variantera_noncoviddeath:
    run: r:latest analysis/ci.R B variantera noncoviddeath
    needs:
    - match_B
    - data_selection
    outputs:
      moderately_sensitive:
        txt: output/match/B/ci/variantera/noncoviddeath/*.txt
        csv: output/match/B/ci/variantera/noncoviddeath/*.csv
        png: output/match/B/ci/variantera/noncoviddeath/*.png

  ## # # # # # # # # # # # # # # # # # # # 
  ## Combine KM / CI estimates across outcomes and subgroups 
  ## # # # # # # # # # # # # # # # # # # # 

  ci_combine_A:
    run: r:latest analysis/ci_combine.R A
    needs:
    - ci_A_all_postest
    - ci_A_all_covidemergency
    - ci_A_all_covidadmittedproxy1
    - ci_A_all_covidadmitted
    - ci_A_all_covidcritcare
    - ci_A_all_coviddeath
    - ci_A_all_noncoviddeath
    - ci_A_vax12_type_postest
    - ci_A_vax12_type_covidemergency
    - ci_A_vax12_type_covidadmittedproxy1
    - ci_A_vax12_type_covidadmitted
    - ci_A_vax12_type_covidcritcare
    - ci_A_vax12_type_coviddeath
    - ci_A_vax12_type_noncoviddeath
    - ci_A_prior_covid_infection_postest
    - ci_A_prior_covid_infection_covidemergency
    - ci_A_prior_covid_infection_covidadmittedproxy1
    - ci_A_prior_covid_infection_covidadmitted
    - ci_A_prior_covid_infection_covidcritcare
    - ci_A_prior_covid_infection_coviddeath
    - ci_A_prior_covid_infection_noncoviddeath
    - ci_A_age65plus_postest
    - ci_A_age65plus_covidemergency
    - ci_A_age65plus_covidadmittedproxy1
    - ci_A_age65plus_covidadmitted
    - ci_A_age65plus_covidcritcare
    - ci_A_age65plus_coviddeath
    - ci_A_age65plus_noncoviddeath
    - ci_A_cev_cv_postest
    - ci_A_cev_cv_covidemergency
    - ci_A_cev_cv_covidadmittedproxy1
    - ci_A_cev_cv_covidadmitted
    - ci_A_cev_cv_covidcritcare
    - ci_A_cev_cv_coviddeath
    - ci_A_cev_cv_noncoviddeath
    outputs:
      moderately_sensitive:
        csv: output/match/A/ci/combined/*.csv
        png: output/match/A/ci/combined/plots/*.png

  ci_combine_B:
    run: r:latest analysis/ci_combine.R B
    needs:
    - ci_B_all_postest
    - ci_B_all_covidemergency
    - ci_B_all_covidadmittedproxy1
    - ci_B_all_covidadmitted
    - ci_B_all_covidcritcare
    - ci_B_all_coviddeath
    - ci_B_all_noncoviddeath
    - ci_B_vax12_type_postest
    - ci_B_vax12_type_covidemergency
    - ci_B_vax12_type_covidadmittedproxy1
    - ci_B_vax12_type_covidadmitted
    - ci_B_vax12_type_covidcritcare
    - ci_B_vax12_type_coviddeath
    - ci_B_vax12_type_noncoviddeath
    - ci_B_prior_covid_infection_postest
    - ci_B_prior_covid_infection_covidemergency
    - ci_B_prior_covid_infection_covidadmittedproxy1
    - ci_B_prior_covid_infection_covidadmitted
    - ci_B_prior_covid_infection_covidcritcare
    - ci_B_prior_covid_infection_coviddeath
    - ci_B_prior_covid_infection_noncoviddeath
    - ci_B_age65plus_postest
    - ci_B_age65plus_covidemergency
    - ci_B_age65plus_covidadmittedproxy1
    - ci_B_age65plus_covidadmitted
    - ci_B_age65plus_covidcritcare
    - ci_B_age65plus_coviddeath
    - ci_B_age65plus_noncoviddeath
    - ci_B_cev_cv_postest
    - ci_B_cev_cv_covidemergency
    - ci_B_cev_cv_covidadmittedproxy1
    - ci_B_cev_cv_covidadmitted
    - ci_B_cev_cv_covidcritcare
    - ci_B_cev_cv_coviddeath
    - ci_B_cev_cv_noncoviddeath
    outputs:
      moderately_sensitive:
        csv: output/match/B/ci/combined/*.csv
        png: output/match/B/ci/combined/plots/*.png

  ## # # # # # # # # # # # # # # # # # # # 
  ## Files for release 
  ## # # # # # # # # # # # # # # # # # # # 

  release_objects:
    run: r:latest analysis/release_objects.R
    needs:
    - data_selection
    - match_report_A
    - match_report_B
    - ci_combine_A
    - ci_combine_B
    outputs:
      moderately_sensitive:
        txt: output/files-for-release.txt
        csv: output/release-objects/*/*.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## End 
  ## # # # # # # # # # # # # # # # # # # #

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 12:15:53

Config

  • Backend:
    TPP
  • Workspace:
    comparative-booster_main
  • Branch:
    main
  • Creator:
    wjchulme
  • Force run dependencies:
    False
  • Git Commit Hash:
    b4bf69a
  • Requested actions:
    • ci_A_all_postest
    • ci_A_all_covidemergency
    • ci_A_all_covidadmittedproxy1
    • ci_A_all_covidadmitted
    • ci_A_all_covidcritcare
    • ci_A_all_coviddeath
    • ci_A_all_noncoviddeath
    • ci_A_vax12_type_postest
    • ci_A_vax12_type_covidemergency
    • ci_A_vax12_type_covidadmittedproxy1
    • ci_A_vax12_type_covidadmitted
    • ci_A_vax12_type_covidcritcare
    • ci_A_vax12_type_coviddeath
    • ci_A_vax12_type_noncoviddeath
    • ci_A_cev_cv_postest
    • ci_A_cev_cv_covidemergency
    • ci_A_cev_cv_covidadmittedproxy1
    • ci_A_cev_cv_covidadmitted
    • ci_A_cev_cv_covidcritcare
    • ci_A_cev_cv_coviddeath
    • ci_A_cev_cv_noncoviddeath