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

  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=2021-10-04
    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_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=2
    needs:
    - process_controlactual_over12_2
    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
    - 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
        png: output/over12/table1/*.png

  ## # # # # # # # # # # # # # # # # # # # 
  ## 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_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_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

  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=2022-04-18
    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_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=2
    needs:
    - process_controlactual_under12_2
    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
    - 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
        png: output/under12/table1/*.png

  ## # # # # # # # # # # # # # # # # # # # 
  ## 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_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_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 over12
    needs:
    - combine_km_over12
    - combine_km_under12
    outputs:
      highly_sensitive:
        txt: output/release/*.txt
        csv: output/release/*.csv

  ## #### End ####