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Job request: 13489

Workspace:
vaccine-effectiveness-3dose
ID:
iarwn7zt7jyz37ie

This page shows the technical details of what happened when authorised researcher Elsie Horne requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show project.yaml
version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create-project.R 
  ## Edit and run create-project.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # 
  ##   
  ## # # # # # # # # # # # # # # # # # # # 
  ## Preliminaries 
  ## # # # # # # # # # # # # # # # # # # # 

  design:
    run: r:latest analysis/design.R
    outputs:
      moderately_sensitive:
        lib: lib/design/*.json

  ## # # # # # # # # # # # # # # # # # # # 
  ## Extract and process treated data 
  ## # # # # # # # # # # # # # # # # # # # 

  extract_treated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_treated
      --output-file output/treated/extract/input_treated.feather
    needs:
    - design
    outputs:
      highly_sensitive:
        extract: output/treated/extract/input_treated.feather

  process_treated:
    run: r:latest analysis/process_data.R treated
    needs:
    - extract_treated
    outputs:
      highly_sensitive:
        eligiblerds: output/treated/eligible/*.rds
        pfizer: output/pfizer/treated/*.rds
        moderna: output/moderna/treated/*.rds
      moderately_sensitive:
        eligiblecsv: output/treated/eligible/*.csv
        input_treated_skim: output/treated/extract/*.txt
        data_processed_skim: output/treated/process/*.txt
        data_eligible_skim: output/treated/eligible/*.txt

  ## # # # # # # # # # # # # # # # # # # # 
  ## mrna cohort 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Extract and match 

  extract_controlpotential_mrna_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround1/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=1 --param index_date=2021-09-16
    needs:
    - design
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround1/extract/input_controlpotential.feather

  process_controlpotential_mrna_1:
    run: r:latest analysis/process_data.R potential mrna 1
    needs:
    - extract_controlpotential_mrna_1
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround1/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround1/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround1/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround1/process/*.txt

  match_potential_mrna_1:
    run: r:latest analysis/matching/match_potential.R mrna 1
    needs:
    - process_treated
    - process_controlpotential_mrna_1
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround1/potential/*.rds
        csv: output/mrna/matchround1/potential/*.csv.gz

  extract_controlactual_mrna_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround1/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=1
    needs:
    - design
    - match_potential_mrna_1
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround1/extract/input_controlactual.feather

  process_controlactual_mrna_1:
    run: r:latest analysis/process_data.R actual mrna 1
    needs:
    - process_treated
    - match_potential_mrna_1
    - extract_controlpotential_mrna_1
    - process_controlpotential_mrna_1
    - extract_controlactual_mrna_1
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround1/actual/*.rds
        csv: output/mrna/matchround1/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround1/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround1/actual/*.txt

  extract_controlpotential_mrna_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround2/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=2 --param index_date=2021-09-30
    needs:
    - design
    - process_controlactual_mrna_1
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround2/extract/input_controlpotential.feather

  process_controlpotential_mrna_2:
    run: r:latest analysis/process_data.R potential mrna 2
    needs:
    - extract_controlpotential_mrna_2
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround2/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround2/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround2/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround2/process/*.txt

  match_potential_mrna_2:
    run: r:latest analysis/matching/match_potential.R mrna 2
    needs:
    - process_treated
    - process_controlpotential_mrna_2
    - process_controlactual_mrna_1
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround2/potential/*.rds
        csv: output/mrna/matchround2/potential/*.csv.gz

  extract_controlactual_mrna_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround2/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=2
    needs:
    - design
    - match_potential_mrna_2
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround2/extract/input_controlactual.feather

  process_controlactual_mrna_2:
    run: r:latest analysis/process_data.R actual mrna 2
    needs:
    - process_treated
    - match_potential_mrna_2
    - extract_controlpotential_mrna_2
    - process_controlpotential_mrna_2
    - extract_controlactual_mrna_2
    - process_controlactual_mrna_1
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround2/actual/*.rds
        csv: output/mrna/matchround2/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround2/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround2/actual/*.txt

  extract_controlpotential_mrna_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround3/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=3 --param index_date=2021-10-14
    needs:
    - design
    - process_controlactual_mrna_2
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround3/extract/input_controlpotential.feather

  process_controlpotential_mrna_3:
    run: r:latest analysis/process_data.R potential mrna 3
    needs:
    - extract_controlpotential_mrna_3
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround3/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround3/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround3/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround3/process/*.txt

  match_potential_mrna_3:
    run: r:latest analysis/matching/match_potential.R mrna 3
    needs:
    - process_treated
    - process_controlpotential_mrna_3
    - process_controlactual_mrna_2
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround3/potential/*.rds
        csv: output/mrna/matchround3/potential/*.csv.gz

  extract_controlactual_mrna_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround3/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=3
    needs:
    - design
    - match_potential_mrna_3
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround3/extract/input_controlactual.feather

  process_controlactual_mrna_3:
    run: r:latest analysis/process_data.R actual mrna 3
    needs:
    - process_treated
    - match_potential_mrna_3
    - extract_controlpotential_mrna_3
    - process_controlpotential_mrna_3
    - extract_controlactual_mrna_3
    - process_controlactual_mrna_2
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround3/actual/*.rds
        csv: output/mrna/matchround3/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround3/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround3/actual/*.txt

  extract_controlpotential_mrna_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround4/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=4 --param index_date=2021-10-28
    needs:
    - design
    - process_controlactual_mrna_3
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround4/extract/input_controlpotential.feather

  process_controlpotential_mrna_4:
    run: r:latest analysis/process_data.R potential mrna 4
    needs:
    - extract_controlpotential_mrna_4
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround4/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround4/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround4/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround4/process/*.txt

  match_potential_mrna_4:
    run: r:latest analysis/matching/match_potential.R mrna 4
    needs:
    - process_treated
    - process_controlpotential_mrna_4
    - process_controlactual_mrna_3
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround4/potential/*.rds
        csv: output/mrna/matchround4/potential/*.csv.gz

  extract_controlactual_mrna_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround4/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=4
    needs:
    - design
    - match_potential_mrna_4
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround4/extract/input_controlactual.feather

  process_controlactual_mrna_4:
    run: r:latest analysis/process_data.R actual mrna 4
    needs:
    - process_treated
    - match_potential_mrna_4
    - extract_controlpotential_mrna_4
    - process_controlpotential_mrna_4
    - extract_controlactual_mrna_4
    - process_controlactual_mrna_3
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround4/actual/*.rds
        csv: output/mrna/matchround4/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround4/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround4/actual/*.txt

  extract_controlpotential_mrna_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround5/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=5 --param index_date=2021-11-11
    needs:
    - design
    - process_controlactual_mrna_4
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround5/extract/input_controlpotential.feather

  process_controlpotential_mrna_5:
    run: r:latest analysis/process_data.R potential mrna 5
    needs:
    - extract_controlpotential_mrna_5
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround5/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround5/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround5/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround5/process/*.txt

  match_potential_mrna_5:
    run: r:latest analysis/matching/match_potential.R mrna 5
    needs:
    - process_treated
    - process_controlpotential_mrna_5
    - process_controlactual_mrna_4
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround5/potential/*.rds
        csv: output/mrna/matchround5/potential/*.csv.gz

  extract_controlactual_mrna_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround5/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=5
    needs:
    - design
    - match_potential_mrna_5
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround5/extract/input_controlactual.feather

  process_controlactual_mrna_5:
    run: r:latest analysis/process_data.R actual mrna 5
    needs:
    - process_treated
    - match_potential_mrna_5
    - extract_controlpotential_mrna_5
    - process_controlpotential_mrna_5
    - extract_controlactual_mrna_5
    - process_controlactual_mrna_4
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround5/actual/*.rds
        csv: output/mrna/matchround5/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround5/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround5/actual/*.txt

  extract_controlpotential_mrna_6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround6/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=6 --param index_date=2021-11-25
    needs:
    - design
    - process_controlactual_mrna_5
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround6/extract/input_controlpotential.feather

  process_controlpotential_mrna_6:
    run: r:latest analysis/process_data.R potential mrna 6
    needs:
    - extract_controlpotential_mrna_6
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround6/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround6/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround6/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround6/process/*.txt

  match_potential_mrna_6:
    run: r:latest analysis/matching/match_potential.R mrna 6
    needs:
    - process_treated
    - process_controlpotential_mrna_6
    - process_controlactual_mrna_5
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround6/potential/*.rds
        csv: output/mrna/matchround6/potential/*.csv.gz

  extract_controlactual_mrna_6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround6/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=6
    needs:
    - design
    - match_potential_mrna_6
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround6/extract/input_controlactual.feather

  process_controlactual_mrna_6:
    run: r:latest analysis/process_data.R actual mrna 6
    needs:
    - process_treated
    - match_potential_mrna_6
    - extract_controlpotential_mrna_6
    - process_controlpotential_mrna_6
    - extract_controlactual_mrna_6
    - process_controlactual_mrna_5
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround6/actual/*.rds
        csv: output/mrna/matchround6/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround6/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround6/actual/*.txt

  extract_controlpotential_mrna_7:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround7/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=7 --param index_date=2021-12-09
    needs:
    - design
    - process_controlactual_mrna_6
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround7/extract/input_controlpotential.feather

  process_controlpotential_mrna_7:
    run: r:latest analysis/process_data.R potential mrna 7
    needs:
    - extract_controlpotential_mrna_7
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround7/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround7/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround7/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround7/process/*.txt

  match_potential_mrna_7:
    run: r:latest analysis/matching/match_potential.R mrna 7
    needs:
    - process_treated
    - process_controlpotential_mrna_7
    - process_controlactual_mrna_6
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround7/potential/*.rds
        csv: output/mrna/matchround7/potential/*.csv.gz

  extract_controlactual_mrna_7:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround7/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=7
    needs:
    - design
    - match_potential_mrna_7
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround7/extract/input_controlactual.feather

  process_controlactual_mrna_7:
    run: r:latest analysis/process_data.R actual mrna 7
    needs:
    - process_treated
    - match_potential_mrna_7
    - extract_controlpotential_mrna_7
    - process_controlpotential_mrna_7
    - extract_controlactual_mrna_7
    - process_controlactual_mrna_6
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround7/actual/*.rds
        csv: output/mrna/matchround7/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround7/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround7/actual/*.txt

  extract_controlpotential_mrna_8:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround8/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=8 --param index_date=2021-12-23
    needs:
    - design
    - process_controlactual_mrna_7
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround8/extract/input_controlpotential.feather

  process_controlpotential_mrna_8:
    run: r:latest analysis/process_data.R potential mrna 8
    needs:
    - extract_controlpotential_mrna_8
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround8/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround8/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround8/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround8/process/*.txt

  match_potential_mrna_8:
    run: r:latest analysis/matching/match_potential.R mrna 8
    needs:
    - process_treated
    - process_controlpotential_mrna_8
    - process_controlactual_mrna_7
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround8/potential/*.rds
        csv: output/mrna/matchround8/potential/*.csv.gz

  extract_controlactual_mrna_8:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround8/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=8
    needs:
    - design
    - match_potential_mrna_8
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround8/extract/input_controlactual.feather

  process_controlactual_mrna_8:
    run: r:latest analysis/process_data.R actual mrna 8
    needs:
    - process_treated
    - match_potential_mrna_8
    - extract_controlpotential_mrna_8
    - process_controlpotential_mrna_8
    - extract_controlactual_mrna_8
    - process_controlactual_mrna_7
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround8/actual/*.rds
        csv: output/mrna/matchround8/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround8/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround8/actual/*.txt

  extract_controlpotential_mrna_9:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround9/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=9 --param index_date=2022-01-06
    needs:
    - design
    - process_controlactual_mrna_8
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround9/extract/input_controlpotential.feather

  process_controlpotential_mrna_9:
    run: r:latest analysis/process_data.R potential mrna 9
    needs:
    - extract_controlpotential_mrna_9
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround9/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround9/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround9/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround9/process/*.txt

  match_potential_mrna_9:
    run: r:latest analysis/matching/match_potential.R mrna 9
    needs:
    - process_treated
    - process_controlpotential_mrna_9
    - process_controlactual_mrna_8
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround9/potential/*.rds
        csv: output/mrna/matchround9/potential/*.csv.gz

  extract_controlactual_mrna_9:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround9/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=9
    needs:
    - design
    - match_potential_mrna_9
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround9/extract/input_controlactual.feather

  process_controlactual_mrna_9:
    run: r:latest analysis/process_data.R actual mrna 9
    needs:
    - process_treated
    - match_potential_mrna_9
    - extract_controlpotential_mrna_9
    - process_controlpotential_mrna_9
    - extract_controlactual_mrna_9
    - process_controlactual_mrna_8
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround9/actual/*.rds
        csv: output/mrna/matchround9/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround9/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround9/actual/*.txt

  extract_controlpotential_mrna_10:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround10/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=10 --param index_date=2022-01-20
    needs:
    - design
    - process_controlactual_mrna_9
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround10/extract/input_controlpotential.feather

  process_controlpotential_mrna_10:
    run: r:latest analysis/process_data.R potential mrna 10
    needs:
    - extract_controlpotential_mrna_10
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround10/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround10/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround10/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround10/process/*.txt

  match_potential_mrna_10:
    run: r:latest analysis/matching/match_potential.R mrna 10
    needs:
    - process_treated
    - process_controlpotential_mrna_10
    - process_controlactual_mrna_9
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround10/potential/*.rds
        csv: output/mrna/matchround10/potential/*.csv.gz

  extract_controlactual_mrna_10:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround10/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=10
    needs:
    - design
    - match_potential_mrna_10
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround10/extract/input_controlactual.feather

  process_controlactual_mrna_10:
    run: r:latest analysis/process_data.R actual mrna 10
    needs:
    - process_treated
    - match_potential_mrna_10
    - extract_controlpotential_mrna_10
    - process_controlpotential_mrna_10
    - extract_controlactual_mrna_10
    - process_controlactual_mrna_9
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround10/actual/*.rds
        csv: output/mrna/matchround10/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround10/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround10/actual/*.txt

  extract_controlpotential_mrna_11:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround11/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=11 --param index_date=2022-02-03
    needs:
    - design
    - process_controlactual_mrna_10
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround11/extract/input_controlpotential.feather

  process_controlpotential_mrna_11:
    run: r:latest analysis/process_data.R potential mrna 11
    needs:
    - extract_controlpotential_mrna_11
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround11/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround11/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround11/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround11/process/*.txt

  match_potential_mrna_11:
    run: r:latest analysis/matching/match_potential.R mrna 11
    needs:
    - process_treated
    - process_controlpotential_mrna_11
    - process_controlactual_mrna_10
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround11/potential/*.rds
        csv: output/mrna/matchround11/potential/*.csv.gz

  extract_controlactual_mrna_11:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround11/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=11
    needs:
    - design
    - match_potential_mrna_11
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround11/extract/input_controlactual.feather

  process_controlactual_mrna_11:
    run: r:latest analysis/process_data.R actual mrna 11
    needs:
    - process_treated
    - match_potential_mrna_11
    - extract_controlpotential_mrna_11
    - process_controlpotential_mrna_11
    - extract_controlactual_mrna_11
    - process_controlactual_mrna_10
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround11/actual/*.rds
        csv: output/mrna/matchround11/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround11/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround11/actual/*.txt

  extract_controlpotential_mrna_12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/mrna/matchround12/extract/input_controlpotential.feather
      --param cohort=mrna --param matching_round=12 --param index_date=2022-02-17
    needs:
    - design
    - process_controlactual_mrna_11
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround12/extract/input_controlpotential.feather

  process_controlpotential_mrna_12:
    run: r:latest analysis/process_data.R potential mrna 12
    needs:
    - extract_controlpotential_mrna_12
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround12/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/mrna/matchround12/extract/potential/*.txt
        data_processed_skim: output/mrna/matchround12/potential/*.txt
        data_controlpotential_skim: output/mrna/matchround12/process/*.txt

  match_potential_mrna_12:
    run: r:latest analysis/matching/match_potential.R mrna 12
    needs:
    - process_treated
    - process_controlpotential_mrna_12
    - process_controlactual_mrna_11
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround12/potential/*.rds
        csv: output/mrna/matchround12/potential/*.csv.gz

  extract_controlactual_mrna_12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/mrna/matchround12/extract/input_controlactual.feather --param
      cohort=mrna --param matching_round=12
    needs:
    - design
    - match_potential_mrna_12
    outputs:
      highly_sensitive:
        cohort: output/mrna/matchround12/extract/input_controlactual.feather

  process_controlactual_mrna_12:
    run: r:latest analysis/process_data.R actual mrna 12
    needs:
    - process_treated
    - match_potential_mrna_12
    - extract_controlpotential_mrna_12
    - process_controlpotential_mrna_12
    - extract_controlactual_mrna_12
    - process_controlactual_mrna_11
    outputs:
      highly_sensitive:
        rds: output/mrna/matchround12/actual/*.rds
        csv: output/mrna/matchround12/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/mrna/matchround12/extract/actual/*.txt
        data_actual_skim: output/mrna/matchround12/actual/*.txt

  extract_controlfinal_mrna:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlfinal
      --output-file output/mrna/extract/input_controlfinal.feather --param cohort=mrna
      --param n_matching_rounds=12
    needs:
    - design
    - process_controlactual_mrna_12
    outputs:
      highly_sensitive:
        extract: output/mrna/extract/input_controlfinal.feather

  dummydata_controlfinal_mrna:
    run: r:latest analysis/dummy/dummydata_controlfinal.R mrna
    needs:
    - process_controlactual_mrna_1
    - process_controlactual_mrna_2
    - process_controlactual_mrna_3
    - process_controlactual_mrna_4
    - process_controlactual_mrna_5
    - process_controlactual_mrna_6
    - process_controlactual_mrna_7
    - process_controlactual_mrna_8
    - process_controlactual_mrna_9
    - process_controlactual_mrna_10
    - process_controlactual_mrna_11
    - process_controlactual_mrna_12
    outputs:
      highly_sensitive:
        dummydata_controlfinal: output/mrna/dummydata/dummy_control_final.feather

  process_controlfinal_mrna:
    run: r:latest analysis/process_data.R final mrna
    needs:
    - process_controlactual_mrna_1
    - process_controlactual_mrna_2
    - process_controlactual_mrna_3
    - process_controlactual_mrna_4
    - process_controlactual_mrna_5
    - process_controlactual_mrna_6
    - process_controlactual_mrna_7
    - process_controlactual_mrna_8
    - process_controlactual_mrna_9
    - process_controlactual_mrna_10
    - process_controlactual_mrna_11
    - process_controlactual_mrna_12
    - extract_controlfinal_mrna
    - process_treated
    - dummydata_controlfinal_mrna
    outputs:
      highly_sensitive:
        extract: output/mrna/match/*.rds
        ids: output/mrna/match/*.csv.gz
      moderately_sensitive:
        input_controlfinal_skim: output/mrna/extract/*.txt
        data_matched_skim: output/mrna/match/*.txt

  table1_mrna:
    run: r:latest analysis/matching/table1.R mrna
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        csv: output/mrna/table1/*.csv
        html: output/mrna/table1/*.html

  coverage_mrna:
    run: r:latest analysis/matching/coverage.R mrna
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        csv: output/mrna/match/coverage/*.csv
        png: output/mrna/match/coverage/*.png

  ## # # # # # # # # # # # # # # # # # # # 
  ## Covid tests data 
  ## # # # # # # # # # # # # # # # # # # # 

  extract_covidtests_mrna_treated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covidtests
      --output-file output/mrna/covidtests/extract/input_covidtests_treated.feather
      --param cohort=mrna --param arm=treated
    needs:
    - design
    - process_controlfinal_mrna
    outputs:
      highly_sensitive:
        extract: output/mrna/covidtests/extract/input_covidtests_treated.feather

  extract_covidtests_mrna_control:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covidtests
      --output-file output/mrna/covidtests/extract/input_covidtests_control.feather
      --param cohort=mrna --param arm=control
    needs:
    - design
    - process_controlfinal_mrna
    outputs:
      highly_sensitive:
        extract: output/mrna/covidtests/extract/input_covidtests_control.feather

  process_covidtests_mrna:
    run: r:latest analysis/covidtests/process_covidtests.R mrna
    needs:
    - process_controlfinal_mrna
    - extract_covidtests_mrna_treated
    - extract_covidtests_mrna_control
    outputs:
      highly_sensitive:
        extract: output/mrna/covidtests/process/*.rds
      moderately_sensitive:
        skim: output/mrna/covidtests/extract/*.txt
        png: output/mrna/covidtests/checks/*.png

  summarise_covidtests_mrna:
    run: r:latest analysis/covidtests/summarise_covidtests.R mrna all
    needs:
    - process_covidtests_mrna
    outputs:
      moderately_sensitive:
        csv: output/mrna/covidtests/summary/all/*.csv
        png: output/mrna/covidtests/summary/all/*.png

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

  cinc_dose4_mrna:
    run: r:latest analysis/model/cinc_dose4.R mrna
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        csv: output/mrna/models/cinc_dose4/*.csv
        png: output/mrna/models/cinc_dose4/*.png

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  
  ## cohort: mrna; subgroup: all; variant option: ignore 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  

  km_mrna_all_ignore_postest:
    run: r:latest analysis/model/km.R mrna all ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/ignore/postest/*.rds
        png: output/mrna/models/km/all/ignore/postest/*.png

  cox_unadj_mrna_all_ignore_postest:
    run: r:latest analysis/model/cox.R mrna unadj all ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/ignore/postest/*.rds

  cox_adj_mrna_all_ignore_postest:
    run: r:latest analysis/model/cox.R mrna adj all ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/ignore/postest/*.rds

  km_mrna_all_ignore_covidadmitted:
    run: r:latest analysis/model/km.R mrna all ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/ignore/covidadmitted/*.rds
        png: output/mrna/models/km/all/ignore/covidadmitted/*.png

  cox_unadj_mrna_all_ignore_covidadmitted:
    run: r:latest analysis/model/cox.R mrna unadj all ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/ignore/covidadmitted/*.rds

  cox_adj_mrna_all_ignore_covidadmitted:
    run: r:latest analysis/model/cox.R mrna adj all ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/ignore/covidadmitted/*.rds

  km_mrna_all_ignore_covidcritcareordeath:
    run: r:latest analysis/model/km.R mrna all ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/ignore/covidcritcareordeath/*.rds
        png: output/mrna/models/km/all/ignore/covidcritcareordeath/*.png

  cox_unadj_mrna_all_ignore_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna unadj all ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/ignore/covidcritcareordeath/*.rds

  cox_adj_mrna_all_ignore_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna adj all ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/ignore/covidcritcareordeath/*.rds

  km_mrna_all_ignore_coviddeath:
    run: r:latest analysis/model/km.R mrna all ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/ignore/coviddeath/*.rds
        png: output/mrna/models/km/all/ignore/coviddeath/*.png

  cox_unadj_mrna_all_ignore_coviddeath:
    run: r:latest analysis/model/cox.R mrna unadj all ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/ignore/coviddeath/*.rds

  cox_adj_mrna_all_ignore_coviddeath:
    run: r:latest analysis/model/cox.R mrna adj all ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/ignore/coviddeath/*.rds

  km_mrna_all_ignore_emergency:
    run: r:latest analysis/model/km.R mrna all ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/ignore/emergency/*.rds
        png: output/mrna/models/km/all/ignore/emergency/*.png

  cox_unadj_mrna_all_ignore_emergency:
    run: r:latest analysis/model/cox.R mrna unadj all ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/ignore/emergency/*.rds

  cox_adj_mrna_all_ignore_emergency:
    run: r:latest analysis/model/cox.R mrna adj all ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/ignore/emergency/*.rds

  km_mrna_all_ignore_covidemergency:
    run: r:latest analysis/model/km.R mrna all ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/ignore/covidemergency/*.rds
        png: output/mrna/models/km/all/ignore/covidemergency/*.png

  cox_unadj_mrna_all_ignore_covidemergency:
    run: r:latest analysis/model/cox.R mrna unadj all ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/ignore/covidemergency/*.rds

  cox_adj_mrna_all_ignore_covidemergency:
    run: r:latest analysis/model/cox.R mrna adj all ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/ignore/covidemergency/*.rds

  km_mrna_all_ignore_noncoviddeath:
    run: r:latest analysis/model/km.R mrna all ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/ignore/noncoviddeath/*.rds
        png: output/mrna/models/km/all/ignore/noncoviddeath/*.png

  cox_unadj_mrna_all_ignore_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna unadj all ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/ignore/noncoviddeath/*.rds

  cox_adj_mrna_all_ignore_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna adj all ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/ignore/noncoviddeath/*.rds

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  
  ## cohort: mrna; subgroup: all; variant option: split 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  

  km_mrna_all_split_postest:
    run: r:latest analysis/model/km.R mrna all split postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/split/postest/*.rds
        png: output/mrna/models/km/all/split/postest/*.png

  cox_unadj_mrna_all_split_postest:
    run: r:latest analysis/model/cox.R mrna unadj all split postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/split/postest/*.rds

  cox_adj_mrna_all_split_postest:
    run: r:latest analysis/model/cox.R mrna adj all split postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/split/postest/*.rds

  km_mrna_all_split_covidadmitted:
    run: r:latest analysis/model/km.R mrna all split covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/split/covidadmitted/*.rds
        png: output/mrna/models/km/all/split/covidadmitted/*.png

  cox_unadj_mrna_all_split_covidadmitted:
    run: r:latest analysis/model/cox.R mrna unadj all split covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/split/covidadmitted/*.rds

  cox_adj_mrna_all_split_covidadmitted:
    run: r:latest analysis/model/cox.R mrna adj all split covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/split/covidadmitted/*.rds

  km_mrna_all_split_covidcritcareordeath:
    run: r:latest analysis/model/km.R mrna all split covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/split/covidcritcareordeath/*.rds
        png: output/mrna/models/km/all/split/covidcritcareordeath/*.png

  cox_unadj_mrna_all_split_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna unadj all split covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/split/covidcritcareordeath/*.rds

  cox_adj_mrna_all_split_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna adj all split covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/split/covidcritcareordeath/*.rds

  km_mrna_all_split_coviddeath:
    run: r:latest analysis/model/km.R mrna all split coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/split/coviddeath/*.rds
        png: output/mrna/models/km/all/split/coviddeath/*.png

  cox_unadj_mrna_all_split_coviddeath:
    run: r:latest analysis/model/cox.R mrna unadj all split coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/split/coviddeath/*.rds

  cox_adj_mrna_all_split_coviddeath:
    run: r:latest analysis/model/cox.R mrna adj all split coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/split/coviddeath/*.rds

  km_mrna_all_split_emergency:
    run: r:latest analysis/model/km.R mrna all split emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/split/emergency/*.rds
        png: output/mrna/models/km/all/split/emergency/*.png

  cox_unadj_mrna_all_split_emergency:
    run: r:latest analysis/model/cox.R mrna unadj all split emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/split/emergency/*.rds

  cox_adj_mrna_all_split_emergency:
    run: r:latest analysis/model/cox.R mrna adj all split emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/split/emergency/*.rds

  km_mrna_all_split_covidemergency:
    run: r:latest analysis/model/km.R mrna all split covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/split/covidemergency/*.rds
        png: output/mrna/models/km/all/split/covidemergency/*.png

  cox_unadj_mrna_all_split_covidemergency:
    run: r:latest analysis/model/cox.R mrna unadj all split covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/split/covidemergency/*.rds

  cox_adj_mrna_all_split_covidemergency:
    run: r:latest analysis/model/cox.R mrna adj all split covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/split/covidemergency/*.rds

  km_mrna_all_split_noncoviddeath:
    run: r:latest analysis/model/km.R mrna all split noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/split/noncoviddeath/*.rds
        png: output/mrna/models/km/all/split/noncoviddeath/*.png

  cox_unadj_mrna_all_split_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna unadj all split noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/split/noncoviddeath/*.rds

  cox_adj_mrna_all_split_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna adj all split noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/split/noncoviddeath/*.rds

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  
  ## cohort: mrna; subgroup: all; variant option: restrict 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  

  km_mrna_all_restrict_postest:
    run: r:latest analysis/model/km.R mrna all restrict postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/restrict/postest/*.rds
        png: output/mrna/models/km/all/restrict/postest/*.png

  cox_unadj_mrna_all_restrict_postest:
    run: r:latest analysis/model/cox.R mrna unadj all restrict postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/restrict/postest/*.rds

  cox_adj_mrna_all_restrict_postest:
    run: r:latest analysis/model/cox.R mrna adj all restrict postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/restrict/postest/*.rds

  km_mrna_all_restrict_covidadmitted:
    run: r:latest analysis/model/km.R mrna all restrict covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/restrict/covidadmitted/*.rds
        png: output/mrna/models/km/all/restrict/covidadmitted/*.png

  cox_unadj_mrna_all_restrict_covidadmitted:
    run: r:latest analysis/model/cox.R mrna unadj all restrict covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/restrict/covidadmitted/*.rds

  cox_adj_mrna_all_restrict_covidadmitted:
    run: r:latest analysis/model/cox.R mrna adj all restrict covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/restrict/covidadmitted/*.rds

  km_mrna_all_restrict_covidcritcareordeath:
    run: r:latest analysis/model/km.R mrna all restrict covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/restrict/covidcritcareordeath/*.rds
        png: output/mrna/models/km/all/restrict/covidcritcareordeath/*.png

  cox_unadj_mrna_all_restrict_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna unadj all restrict covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/restrict/covidcritcareordeath/*.rds

  cox_adj_mrna_all_restrict_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna adj all restrict covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/restrict/covidcritcareordeath/*.rds

  km_mrna_all_restrict_coviddeath:
    run: r:latest analysis/model/km.R mrna all restrict coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/restrict/coviddeath/*.rds
        png: output/mrna/models/km/all/restrict/coviddeath/*.png

  cox_unadj_mrna_all_restrict_coviddeath:
    run: r:latest analysis/model/cox.R mrna unadj all restrict coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/restrict/coviddeath/*.rds

  cox_adj_mrna_all_restrict_coviddeath:
    run: r:latest analysis/model/cox.R mrna adj all restrict coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/restrict/coviddeath/*.rds

  km_mrna_all_restrict_emergency:
    run: r:latest analysis/model/km.R mrna all restrict emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/restrict/emergency/*.rds
        png: output/mrna/models/km/all/restrict/emergency/*.png

  cox_unadj_mrna_all_restrict_emergency:
    run: r:latest analysis/model/cox.R mrna unadj all restrict emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/restrict/emergency/*.rds

  cox_adj_mrna_all_restrict_emergency:
    run: r:latest analysis/model/cox.R mrna adj all restrict emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/restrict/emergency/*.rds

  km_mrna_all_restrict_covidemergency:
    run: r:latest analysis/model/km.R mrna all restrict covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/restrict/covidemergency/*.rds
        png: output/mrna/models/km/all/restrict/covidemergency/*.png

  cox_unadj_mrna_all_restrict_covidemergency:
    run: r:latest analysis/model/cox.R mrna unadj all restrict covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/restrict/covidemergency/*.rds

  cox_adj_mrna_all_restrict_covidemergency:
    run: r:latest analysis/model/cox.R mrna adj all restrict covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/restrict/covidemergency/*.rds

  km_mrna_all_restrict_noncoviddeath:
    run: r:latest analysis/model/km.R mrna all restrict noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/all/restrict/noncoviddeath/*.rds
        png: output/mrna/models/km/all/restrict/noncoviddeath/*.png

  cox_unadj_mrna_all_restrict_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna unadj all restrict noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/all/restrict/noncoviddeath/*.rds

  cox_adj_mrna_all_restrict_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna adj all restrict noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/all/restrict/noncoviddeath/*.rds

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  
  ## cohort: mrna; subgroup: vax3_type; variant option: ignore 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  

  km_mrna_vax3_type_ignore_postest:
    run: r:latest analysis/model/km.R mrna vax3_type ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax3_type/ignore/postest/*.rds
        png: output/mrna/models/km/vax3_type/ignore/postest/*.png

  cox_unadj_mrna_vax3_type_ignore_postest:
    run: r:latest analysis/model/cox.R mrna unadj vax3_type ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax3_type/ignore/postest/*.rds

  cox_adj_mrna_vax3_type_ignore_postest:
    run: r:latest analysis/model/cox.R mrna adj vax3_type ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax3_type/ignore/postest/*.rds

  km_mrna_vax3_type_ignore_covidadmitted:
    run: r:latest analysis/model/km.R mrna vax3_type ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax3_type/ignore/covidadmitted/*.rds
        png: output/mrna/models/km/vax3_type/ignore/covidadmitted/*.png

  cox_unadj_mrna_vax3_type_ignore_covidadmitted:
    run: r:latest analysis/model/cox.R mrna unadj vax3_type ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax3_type/ignore/covidadmitted/*.rds

  cox_adj_mrna_vax3_type_ignore_covidadmitted:
    run: r:latest analysis/model/cox.R mrna adj vax3_type ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax3_type/ignore/covidadmitted/*.rds

  km_mrna_vax3_type_ignore_covidcritcareordeath:
    run: r:latest analysis/model/km.R mrna vax3_type ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax3_type/ignore/covidcritcareordeath/*.rds
        png: output/mrna/models/km/vax3_type/ignore/covidcritcareordeath/*.png

  cox_unadj_mrna_vax3_type_ignore_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna unadj vax3_type ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax3_type/ignore/covidcritcareordeath/*.rds

  cox_adj_mrna_vax3_type_ignore_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna adj vax3_type ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax3_type/ignore/covidcritcareordeath/*.rds

  km_mrna_vax3_type_ignore_coviddeath:
    run: r:latest analysis/model/km.R mrna vax3_type ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax3_type/ignore/coviddeath/*.rds
        png: output/mrna/models/km/vax3_type/ignore/coviddeath/*.png

  cox_unadj_mrna_vax3_type_ignore_coviddeath:
    run: r:latest analysis/model/cox.R mrna unadj vax3_type ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax3_type/ignore/coviddeath/*.rds

  cox_adj_mrna_vax3_type_ignore_coviddeath:
    run: r:latest analysis/model/cox.R mrna adj vax3_type ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax3_type/ignore/coviddeath/*.rds

  km_mrna_vax3_type_ignore_emergency:
    run: r:latest analysis/model/km.R mrna vax3_type ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax3_type/ignore/emergency/*.rds
        png: output/mrna/models/km/vax3_type/ignore/emergency/*.png

  cox_unadj_mrna_vax3_type_ignore_emergency:
    run: r:latest analysis/model/cox.R mrna unadj vax3_type ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax3_type/ignore/emergency/*.rds

  cox_adj_mrna_vax3_type_ignore_emergency:
    run: r:latest analysis/model/cox.R mrna adj vax3_type ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax3_type/ignore/emergency/*.rds

  km_mrna_vax3_type_ignore_covidemergency:
    run: r:latest analysis/model/km.R mrna vax3_type ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax3_type/ignore/covidemergency/*.rds
        png: output/mrna/models/km/vax3_type/ignore/covidemergency/*.png

  cox_unadj_mrna_vax3_type_ignore_covidemergency:
    run: r:latest analysis/model/cox.R mrna unadj vax3_type ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax3_type/ignore/covidemergency/*.rds

  cox_adj_mrna_vax3_type_ignore_covidemergency:
    run: r:latest analysis/model/cox.R mrna adj vax3_type ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax3_type/ignore/covidemergency/*.rds

  km_mrna_vax3_type_ignore_noncoviddeath:
    run: r:latest analysis/model/km.R mrna vax3_type ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax3_type/ignore/noncoviddeath/*.rds
        png: output/mrna/models/km/vax3_type/ignore/noncoviddeath/*.png

  cox_unadj_mrna_vax3_type_ignore_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna unadj vax3_type ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax3_type/ignore/noncoviddeath/*.rds

  cox_adj_mrna_vax3_type_ignore_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna adj vax3_type ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax3_type/ignore/noncoviddeath/*.rds

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  
  ## cohort: mrna; subgroup: prior_covid_infection; variant option: ignore 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  

  km_mrna_prior_covid_infection_ignore_postest:
    run: r:latest analysis/model/km.R mrna prior_covid_infection ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/prior_covid_infection/ignore/postest/*.rds
        png: output/mrna/models/km/prior_covid_infection/ignore/postest/*.png

  cox_unadj_mrna_prior_covid_infection_ignore_postest:
    run: r:latest analysis/model/cox.R mrna unadj prior_covid_infection ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/prior_covid_infection/ignore/postest/*.rds

  cox_adj_mrna_prior_covid_infection_ignore_postest:
    run: r:latest analysis/model/cox.R mrna adj prior_covid_infection ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/prior_covid_infection/ignore/postest/*.rds

  km_mrna_prior_covid_infection_ignore_covidadmitted:
    run: r:latest analysis/model/km.R mrna prior_covid_infection ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/prior_covid_infection/ignore/covidadmitted/*.rds
        png: output/mrna/models/km/prior_covid_infection/ignore/covidadmitted/*.png

  cox_unadj_mrna_prior_covid_infection_ignore_covidadmitted:
    run: r:latest analysis/model/cox.R mrna unadj prior_covid_infection ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/prior_covid_infection/ignore/covidadmitted/*.rds

  cox_adj_mrna_prior_covid_infection_ignore_covidadmitted:
    run: r:latest analysis/model/cox.R mrna adj prior_covid_infection ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/prior_covid_infection/ignore/covidadmitted/*.rds

  km_mrna_prior_covid_infection_ignore_covidcritcareordeath:
    run: r:latest analysis/model/km.R mrna prior_covid_infection ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/prior_covid_infection/ignore/covidcritcareordeath/*.rds
        png: output/mrna/models/km/prior_covid_infection/ignore/covidcritcareordeath/*.png

  cox_unadj_mrna_prior_covid_infection_ignore_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna unadj prior_covid_infection ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/prior_covid_infection/ignore/covidcritcareordeath/*.rds

  cox_adj_mrna_prior_covid_infection_ignore_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna adj prior_covid_infection ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/prior_covid_infection/ignore/covidcritcareordeath/*.rds

  km_mrna_prior_covid_infection_ignore_coviddeath:
    run: r:latest analysis/model/km.R mrna prior_covid_infection ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/prior_covid_infection/ignore/coviddeath/*.rds
        png: output/mrna/models/km/prior_covid_infection/ignore/coviddeath/*.png

  cox_unadj_mrna_prior_covid_infection_ignore_coviddeath:
    run: r:latest analysis/model/cox.R mrna unadj prior_covid_infection ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/prior_covid_infection/ignore/coviddeath/*.rds

  cox_adj_mrna_prior_covid_infection_ignore_coviddeath:
    run: r:latest analysis/model/cox.R mrna adj prior_covid_infection ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/prior_covid_infection/ignore/coviddeath/*.rds

  km_mrna_prior_covid_infection_ignore_emergency:
    run: r:latest analysis/model/km.R mrna prior_covid_infection ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/prior_covid_infection/ignore/emergency/*.rds
        png: output/mrna/models/km/prior_covid_infection/ignore/emergency/*.png

  cox_unadj_mrna_prior_covid_infection_ignore_emergency:
    run: r:latest analysis/model/cox.R mrna unadj prior_covid_infection ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/prior_covid_infection/ignore/emergency/*.rds

  cox_adj_mrna_prior_covid_infection_ignore_emergency:
    run: r:latest analysis/model/cox.R mrna adj prior_covid_infection ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/prior_covid_infection/ignore/emergency/*.rds

  km_mrna_prior_covid_infection_ignore_covidemergency:
    run: r:latest analysis/model/km.R mrna prior_covid_infection ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/prior_covid_infection/ignore/covidemergency/*.rds
        png: output/mrna/models/km/prior_covid_infection/ignore/covidemergency/*.png

  cox_unadj_mrna_prior_covid_infection_ignore_covidemergency:
    run: r:latest analysis/model/cox.R mrna unadj prior_covid_infection ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/prior_covid_infection/ignore/covidemergency/*.rds

  cox_adj_mrna_prior_covid_infection_ignore_covidemergency:
    run: r:latest analysis/model/cox.R mrna adj prior_covid_infection ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/prior_covid_infection/ignore/covidemergency/*.rds

  km_mrna_prior_covid_infection_ignore_noncoviddeath:
    run: r:latest analysis/model/km.R mrna prior_covid_infection ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/prior_covid_infection/ignore/noncoviddeath/*.rds
        png: output/mrna/models/km/prior_covid_infection/ignore/noncoviddeath/*.png

  cox_unadj_mrna_prior_covid_infection_ignore_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna unadj prior_covid_infection ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/prior_covid_infection/ignore/noncoviddeath/*.rds

  cox_adj_mrna_prior_covid_infection_ignore_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna adj prior_covid_infection ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/prior_covid_infection/ignore/noncoviddeath/*.rds

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  
  ## cohort: mrna; subgroup: vax12_type; variant option: ignore 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  

  km_mrna_vax12_type_ignore_postest:
    run: r:latest analysis/model/km.R mrna vax12_type ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax12_type/ignore/postest/*.rds
        png: output/mrna/models/km/vax12_type/ignore/postest/*.png

  cox_unadj_mrna_vax12_type_ignore_postest:
    run: r:latest analysis/model/cox.R mrna unadj vax12_type ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax12_type/ignore/postest/*.rds

  cox_adj_mrna_vax12_type_ignore_postest:
    run: r:latest analysis/model/cox.R mrna adj vax12_type ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax12_type/ignore/postest/*.rds

  km_mrna_vax12_type_ignore_covidadmitted:
    run: r:latest analysis/model/km.R mrna vax12_type ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax12_type/ignore/covidadmitted/*.rds
        png: output/mrna/models/km/vax12_type/ignore/covidadmitted/*.png

  cox_unadj_mrna_vax12_type_ignore_covidadmitted:
    run: r:latest analysis/model/cox.R mrna unadj vax12_type ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax12_type/ignore/covidadmitted/*.rds

  cox_adj_mrna_vax12_type_ignore_covidadmitted:
    run: r:latest analysis/model/cox.R mrna adj vax12_type ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax12_type/ignore/covidadmitted/*.rds

  km_mrna_vax12_type_ignore_covidcritcareordeath:
    run: r:latest analysis/model/km.R mrna vax12_type ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax12_type/ignore/covidcritcareordeath/*.rds
        png: output/mrna/models/km/vax12_type/ignore/covidcritcareordeath/*.png

  cox_unadj_mrna_vax12_type_ignore_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna unadj vax12_type ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax12_type/ignore/covidcritcareordeath/*.rds

  cox_adj_mrna_vax12_type_ignore_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna adj vax12_type ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax12_type/ignore/covidcritcareordeath/*.rds

  km_mrna_vax12_type_ignore_coviddeath:
    run: r:latest analysis/model/km.R mrna vax12_type ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax12_type/ignore/coviddeath/*.rds
        png: output/mrna/models/km/vax12_type/ignore/coviddeath/*.png

  cox_unadj_mrna_vax12_type_ignore_coviddeath:
    run: r:latest analysis/model/cox.R mrna unadj vax12_type ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax12_type/ignore/coviddeath/*.rds

  cox_adj_mrna_vax12_type_ignore_coviddeath:
    run: r:latest analysis/model/cox.R mrna adj vax12_type ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax12_type/ignore/coviddeath/*.rds

  km_mrna_vax12_type_ignore_emergency:
    run: r:latest analysis/model/km.R mrna vax12_type ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax12_type/ignore/emergency/*.rds
        png: output/mrna/models/km/vax12_type/ignore/emergency/*.png

  cox_unadj_mrna_vax12_type_ignore_emergency:
    run: r:latest analysis/model/cox.R mrna unadj vax12_type ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax12_type/ignore/emergency/*.rds

  cox_adj_mrna_vax12_type_ignore_emergency:
    run: r:latest analysis/model/cox.R mrna adj vax12_type ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax12_type/ignore/emergency/*.rds

  km_mrna_vax12_type_ignore_covidemergency:
    run: r:latest analysis/model/km.R mrna vax12_type ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax12_type/ignore/covidemergency/*.rds
        png: output/mrna/models/km/vax12_type/ignore/covidemergency/*.png

  cox_unadj_mrna_vax12_type_ignore_covidemergency:
    run: r:latest analysis/model/cox.R mrna unadj vax12_type ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax12_type/ignore/covidemergency/*.rds

  cox_adj_mrna_vax12_type_ignore_covidemergency:
    run: r:latest analysis/model/cox.R mrna adj vax12_type ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax12_type/ignore/covidemergency/*.rds

  km_mrna_vax12_type_ignore_noncoviddeath:
    run: r:latest analysis/model/km.R mrna vax12_type ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/vax12_type/ignore/noncoviddeath/*.rds
        png: output/mrna/models/km/vax12_type/ignore/noncoviddeath/*.png

  cox_unadj_mrna_vax12_type_ignore_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna unadj vax12_type ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/vax12_type/ignore/noncoviddeath/*.rds

  cox_adj_mrna_vax12_type_ignore_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna adj vax12_type ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/vax12_type/ignore/noncoviddeath/*.rds

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  
  ## cohort: mrna; subgroup: agegroup; variant option: ignore 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # #  

  km_mrna_agegroup_ignore_postest:
    run: r:latest analysis/model/km.R mrna agegroup ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/agegroup/ignore/postest/*.rds
        png: output/mrna/models/km/agegroup/ignore/postest/*.png

  cox_unadj_mrna_agegroup_ignore_postest:
    run: r:latest analysis/model/cox.R mrna unadj agegroup ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/agegroup/ignore/postest/*.rds

  cox_adj_mrna_agegroup_ignore_postest:
    run: r:latest analysis/model/cox.R mrna adj agegroup ignore postest
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/agegroup/ignore/postest/*.rds

  km_mrna_agegroup_ignore_covidadmitted:
    run: r:latest analysis/model/km.R mrna agegroup ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/agegroup/ignore/covidadmitted/*.rds
        png: output/mrna/models/km/agegroup/ignore/covidadmitted/*.png

  cox_unadj_mrna_agegroup_ignore_covidadmitted:
    run: r:latest analysis/model/cox.R mrna unadj agegroup ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/agegroup/ignore/covidadmitted/*.rds

  cox_adj_mrna_agegroup_ignore_covidadmitted:
    run: r:latest analysis/model/cox.R mrna adj agegroup ignore covidadmitted
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/agegroup/ignore/covidadmitted/*.rds

  km_mrna_agegroup_ignore_covidcritcareordeath:
    run: r:latest analysis/model/km.R mrna agegroup ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/agegroup/ignore/covidcritcareordeath/*.rds
        png: output/mrna/models/km/agegroup/ignore/covidcritcareordeath/*.png

  cox_unadj_mrna_agegroup_ignore_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna unadj agegroup ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/agegroup/ignore/covidcritcareordeath/*.rds

  cox_adj_mrna_agegroup_ignore_covidcritcareordeath:
    run: r:latest analysis/model/cox.R mrna adj agegroup ignore covidcritcareordeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/agegroup/ignore/covidcritcareordeath/*.rds

  km_mrna_agegroup_ignore_coviddeath:
    run: r:latest analysis/model/km.R mrna agegroup ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/agegroup/ignore/coviddeath/*.rds
        png: output/mrna/models/km/agegroup/ignore/coviddeath/*.png

  cox_unadj_mrna_agegroup_ignore_coviddeath:
    run: r:latest analysis/model/cox.R mrna unadj agegroup ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/agegroup/ignore/coviddeath/*.rds

  cox_adj_mrna_agegroup_ignore_coviddeath:
    run: r:latest analysis/model/cox.R mrna adj agegroup ignore coviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/agegroup/ignore/coviddeath/*.rds

  km_mrna_agegroup_ignore_emergency:
    run: r:latest analysis/model/km.R mrna agegroup ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/agegroup/ignore/emergency/*.rds
        png: output/mrna/models/km/agegroup/ignore/emergency/*.png

  cox_unadj_mrna_agegroup_ignore_emergency:
    run: r:latest analysis/model/cox.R mrna unadj agegroup ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/agegroup/ignore/emergency/*.rds

  cox_adj_mrna_agegroup_ignore_emergency:
    run: r:latest analysis/model/cox.R mrna adj agegroup ignore emergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/agegroup/ignore/emergency/*.rds

  km_mrna_agegroup_ignore_covidemergency:
    run: r:latest analysis/model/km.R mrna agegroup ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/agegroup/ignore/covidemergency/*.rds
        png: output/mrna/models/km/agegroup/ignore/covidemergency/*.png

  cox_unadj_mrna_agegroup_ignore_covidemergency:
    run: r:latest analysis/model/cox.R mrna unadj agegroup ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/agegroup/ignore/covidemergency/*.rds

  cox_adj_mrna_agegroup_ignore_covidemergency:
    run: r:latest analysis/model/cox.R mrna adj agegroup ignore covidemergency
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/agegroup/ignore/covidemergency/*.rds

  km_mrna_agegroup_ignore_noncoviddeath:
    run: r:latest analysis/model/km.R mrna agegroup ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/km/agegroup/ignore/noncoviddeath/*.rds
        png: output/mrna/models/km/agegroup/ignore/noncoviddeath/*.png

  cox_unadj_mrna_agegroup_ignore_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna unadj agegroup ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_unadj/agegroup/ignore/noncoviddeath/*.rds

  cox_adj_mrna_agegroup_ignore_noncoviddeath:
    run: r:latest analysis/model/cox.R mrna adj agegroup ignore noncoviddeath
    needs:
    - process_controlfinal_mrna
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/cox_adj/agegroup/ignore/noncoviddeath/*.rds

  ## # # # # # # # # # # # # # # # # # # # 
  ## combine all outputs for mrna cohort 
  ## # # # # # # # # # # # # # # # # # # # 

  combine_mrna:
    run: r:latest analysis/model/combine.R mrna
    needs:
    - km_mrna_all_ignore_postest
    - km_mrna_all_split_postest
    - km_mrna_all_restrict_postest
    - km_mrna_all_ignore_covidadmitted
    - km_mrna_all_split_covidadmitted
    - km_mrna_all_restrict_covidadmitted
    - km_mrna_all_ignore_covidcritcareordeath
    - km_mrna_all_split_covidcritcareordeath
    - km_mrna_all_restrict_covidcritcareordeath
    - km_mrna_all_ignore_coviddeath
    - km_mrna_all_split_coviddeath
    - km_mrna_all_restrict_coviddeath
    - km_mrna_all_ignore_emergency
    - km_mrna_all_split_emergency
    - km_mrna_all_restrict_emergency
    - km_mrna_all_ignore_covidemergency
    - km_mrna_all_split_covidemergency
    - km_mrna_all_restrict_covidemergency
    - km_mrna_all_ignore_noncoviddeath
    - km_mrna_all_split_noncoviddeath
    - km_mrna_all_restrict_noncoviddeath
    - km_mrna_vax3_type_ignore_postest
    - km_mrna_vax3_type_ignore_covidadmitted
    - km_mrna_vax3_type_ignore_covidcritcareordeath
    - km_mrna_vax3_type_ignore_coviddeath
    - km_mrna_vax3_type_ignore_emergency
    - km_mrna_vax3_type_ignore_covidemergency
    - km_mrna_vax3_type_ignore_noncoviddeath
    - km_mrna_prior_covid_infection_ignore_postest
    - km_mrna_prior_covid_infection_ignore_covidadmitted
    - km_mrna_prior_covid_infection_ignore_covidcritcareordeath
    - km_mrna_prior_covid_infection_ignore_coviddeath
    - km_mrna_prior_covid_infection_ignore_emergency
    - km_mrna_prior_covid_infection_ignore_covidemergency
    - km_mrna_prior_covid_infection_ignore_noncoviddeath
    - km_mrna_vax12_type_ignore_postest
    - km_mrna_vax12_type_ignore_covidadmitted
    - km_mrna_vax12_type_ignore_covidcritcareordeath
    - km_mrna_vax12_type_ignore_coviddeath
    - km_mrna_vax12_type_ignore_emergency
    - km_mrna_vax12_type_ignore_covidemergency
    - km_mrna_vax12_type_ignore_noncoviddeath
    - km_mrna_agegroup_ignore_postest
    - km_mrna_agegroup_ignore_covidadmitted
    - km_mrna_agegroup_ignore_covidcritcareordeath
    - km_mrna_agegroup_ignore_coviddeath
    - km_mrna_agegroup_ignore_emergency
    - km_mrna_agegroup_ignore_covidemergency
    - km_mrna_agegroup_ignore_noncoviddeath
    - cox_unadj_mrna_all_ignore_postest
    - cox_unadj_mrna_all_split_postest
    - cox_unadj_mrna_all_restrict_postest
    - cox_unadj_mrna_all_ignore_covidadmitted
    - cox_unadj_mrna_all_split_covidadmitted
    - cox_unadj_mrna_all_restrict_covidadmitted
    - cox_unadj_mrna_all_ignore_covidcritcareordeath
    - cox_unadj_mrna_all_split_covidcritcareordeath
    - cox_unadj_mrna_all_restrict_covidcritcareordeath
    - cox_unadj_mrna_all_ignore_coviddeath
    - cox_unadj_mrna_all_split_coviddeath
    - cox_unadj_mrna_all_restrict_coviddeath
    - cox_unadj_mrna_all_ignore_emergency
    - cox_unadj_mrna_all_split_emergency
    - cox_unadj_mrna_all_restrict_emergency
    - cox_unadj_mrna_all_ignore_covidemergency
    - cox_unadj_mrna_all_split_covidemergency
    - cox_unadj_mrna_all_restrict_covidemergency
    - cox_unadj_mrna_all_ignore_noncoviddeath
    - cox_unadj_mrna_all_split_noncoviddeath
    - cox_unadj_mrna_all_restrict_noncoviddeath
    - cox_unadj_mrna_vax3_type_ignore_postest
    - cox_unadj_mrna_vax3_type_ignore_covidadmitted
    - cox_unadj_mrna_vax3_type_ignore_covidcritcareordeath
    - cox_unadj_mrna_vax3_type_ignore_coviddeath
    - cox_unadj_mrna_vax3_type_ignore_emergency
    - cox_unadj_mrna_vax3_type_ignore_covidemergency
    - cox_unadj_mrna_vax3_type_ignore_noncoviddeath
    - cox_unadj_mrna_prior_covid_infection_ignore_postest
    - cox_unadj_mrna_prior_covid_infection_ignore_covidadmitted
    - cox_unadj_mrna_prior_covid_infection_ignore_covidcritcareordeath
    - cox_unadj_mrna_prior_covid_infection_ignore_coviddeath
    - cox_unadj_mrna_prior_covid_infection_ignore_emergency
    - cox_unadj_mrna_prior_covid_infection_ignore_covidemergency
    - cox_unadj_mrna_prior_covid_infection_ignore_noncoviddeath
    - cox_unadj_mrna_vax12_type_ignore_postest
    - cox_unadj_mrna_vax12_type_ignore_covidadmitted
    - cox_unadj_mrna_vax12_type_ignore_covidcritcareordeath
    - cox_unadj_mrna_vax12_type_ignore_coviddeath
    - cox_unadj_mrna_vax12_type_ignore_emergency
    - cox_unadj_mrna_vax12_type_ignore_covidemergency
    - cox_unadj_mrna_vax12_type_ignore_noncoviddeath
    - cox_unadj_mrna_agegroup_ignore_postest
    - cox_unadj_mrna_agegroup_ignore_covidadmitted
    - cox_unadj_mrna_agegroup_ignore_covidcritcareordeath
    - cox_unadj_mrna_agegroup_ignore_coviddeath
    - cox_unadj_mrna_agegroup_ignore_emergency
    - cox_unadj_mrna_agegroup_ignore_covidemergency
    - cox_unadj_mrna_agegroup_ignore_noncoviddeath
    - cox_adj_mrna_all_ignore_postest
    - cox_adj_mrna_all_split_postest
    - cox_adj_mrna_all_restrict_postest
    - cox_adj_mrna_all_ignore_covidadmitted
    - cox_adj_mrna_all_split_covidadmitted
    - cox_adj_mrna_all_restrict_covidadmitted
    - cox_adj_mrna_all_ignore_covidcritcareordeath
    - cox_adj_mrna_all_split_covidcritcareordeath
    - cox_adj_mrna_all_restrict_covidcritcareordeath
    - cox_adj_mrna_all_ignore_coviddeath
    - cox_adj_mrna_all_split_coviddeath
    - cox_adj_mrna_all_restrict_coviddeath
    - cox_adj_mrna_all_ignore_emergency
    - cox_adj_mrna_all_split_emergency
    - cox_adj_mrna_all_restrict_emergency
    - cox_adj_mrna_all_ignore_covidemergency
    - cox_adj_mrna_all_split_covidemergency
    - cox_adj_mrna_all_restrict_covidemergency
    - cox_adj_mrna_all_ignore_noncoviddeath
    - cox_adj_mrna_all_split_noncoviddeath
    - cox_adj_mrna_all_restrict_noncoviddeath
    - cox_adj_mrna_vax3_type_ignore_postest
    - cox_adj_mrna_vax3_type_ignore_covidadmitted
    - cox_adj_mrna_vax3_type_ignore_covidcritcareordeath
    - cox_adj_mrna_vax3_type_ignore_coviddeath
    - cox_adj_mrna_vax3_type_ignore_emergency
    - cox_adj_mrna_vax3_type_ignore_covidemergency
    - cox_adj_mrna_vax3_type_ignore_noncoviddeath
    - cox_adj_mrna_prior_covid_infection_ignore_postest
    - cox_adj_mrna_prior_covid_infection_ignore_covidadmitted
    - cox_adj_mrna_prior_covid_infection_ignore_covidcritcareordeath
    - cox_adj_mrna_prior_covid_infection_ignore_coviddeath
    - cox_adj_mrna_prior_covid_infection_ignore_emergency
    - cox_adj_mrna_prior_covid_infection_ignore_covidemergency
    - cox_adj_mrna_prior_covid_infection_ignore_noncoviddeath
    - cox_adj_mrna_vax12_type_ignore_postest
    - cox_adj_mrna_vax12_type_ignore_covidadmitted
    - cox_adj_mrna_vax12_type_ignore_covidcritcareordeath
    - cox_adj_mrna_vax12_type_ignore_coviddeath
    - cox_adj_mrna_vax12_type_ignore_emergency
    - cox_adj_mrna_vax12_type_ignore_covidemergency
    - cox_adj_mrna_vax12_type_ignore_noncoviddeath
    - cox_adj_mrna_agegroup_ignore_postest
    - cox_adj_mrna_agegroup_ignore_covidadmitted
    - cox_adj_mrna_agegroup_ignore_covidcritcareordeath
    - cox_adj_mrna_agegroup_ignore_coviddeath
    - cox_adj_mrna_agegroup_ignore_emergency
    - cox_adj_mrna_agegroup_ignore_covidemergency
    - cox_adj_mrna_agegroup_ignore_noncoviddeath
    outputs:
      moderately_sensitive:
        rds: output/mrna/models/combined/*.csv
        png: output/mrna/models/combined/*.png

  ## #### End ####

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Failed
Completed successfully
Backend
TPP
Requested by
Elsie Horne
Branch
main
Force run dependencies
No
Git commit hash
c7505f2
Requested actions
  • cox_unadj_mrna_all_ignore_coviddeath
  • cox_adj_mrna_all_ignore_coviddeath
  • cox_unadj_mrna_all_ignore_emergency
  • cox_adj_mrna_all_ignore_emergency
  • cox_unadj_mrna_all_ignore_covidemergency
  • cox_adj_mrna_all_ignore_covidemergency
  • cox_unadj_mrna_all_ignore_noncoviddeath
  • cox_adj_mrna_all_ignore_noncoviddeath
  • cox_unadj_mrna_all_split_postest
  • cox_adj_mrna_all_split_postest
  • cox_unadj_mrna_all_split_covidadmitted
  • cox_adj_mrna_all_split_covidadmitted
  • cox_unadj_mrna_all_split_covidcritcareordeath
  • cox_adj_mrna_all_split_covidcritcareordeath
  • cox_unadj_mrna_all_split_coviddeath
  • cox_adj_mrna_all_split_coviddeath
  • cox_unadj_mrna_all_split_emergency
  • cox_adj_mrna_all_split_emergency