project.yaml

version: '3.0'

expectations:
  population_size: 10000

actions:

  ## WAVE 4 ##

  # Extract data
  generate_study_population_wave4:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_wave4
        --skip-existing
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_wave4.csv.gz

  # Process data
  process_data_wave4:
    run: r:latest analysis/data_process.R wave4
    needs: [generate_study_population_wave4]
    outputs:
      highly_sensitive:
        rds: output/processed/input_wave4.rds
        
  # Skim data
  skim_data_wave4:
    run: r:latest analysis/data_skim.R output/processed/input_wave4.rds output/data_properties
    needs: [process_data_wave4]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/input_wave4_skim.txt
        txt2: output/data_properties/input_wave4_coltypes.txt
        txt3: output/data_properties/input_wave4_tabulate.txt
        
  # Filter data
  filter_data_wave4:
    run: r:latest analysis/data_selection.R wave4
    needs: [process_data_wave4]
    outputs:
      highly_sensitive:
        rds: output/filtered/input_wave4.rds
      moderately_sensitive:
        csv: output/flowchart/flowchart_wave4.csv

  # Immunosuppression combinations
  imm_comb_wave4:
    run: r:latest analysis/imm_comb.R wave4
    needs: [filter_data_wave4]
    outputs:
      moderately_sensitive:
        csv1: output/imm_comb/imm_comb_wave4_broad.csv
        csv2: output/imm_comb/imm_comb_wave4_narrow.csv

  # Table 1
  table_1_wave4_all:
    run: r:latest analysis/table_1.R wave4 all
    needs: [filter_data_wave4]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave4_all.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave4_all.html
        csv: output/table_1/table_1_wave4_all.csv
        
  table_1_wave4_Tx:
    run: r:latest analysis/table_1.R wave4 Tx
    needs: [filter_data_wave4]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave4_Tx.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave4_Tx.html
        csv: output/table_1/table_1_wave4_Tx.csv

  table_1_wave4_HC:
    run: r:latest analysis/table_1.R wave4 HC
    needs: [filter_data_wave4]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave4_HC.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave4_HC.html
        csv: output/table_1/table_1_wave4_HC.csv

  table_1_wave4_RC:
    run: r:latest analysis/table_1.R wave4 RC
    needs: [filter_data_wave4]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave4_RC.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave4_RC.html
        csv: output/table_1/table_1_wave4_RC.csv
        
  table_1_wave4_IMM:
    run: r:latest analysis/table_1.R wave4 IMM
    needs: [filter_data_wave4]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave4_IMM.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave4_IMM.html
        csv: output/table_1/table_1_wave4_IMM.csv

  table_1_wave4_IMD:
    run: r:latest analysis/table_1.R wave4 IMD
    needs: [filter_data_wave4]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave4_IMD.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave4_IMD.html
        csv: output/table_1/table_1_wave4_IMD.csv

  collate_table_1_wave4:
    run: r:latest analysis/collate_table_1.R wave4
    needs: [table_1_wave4_all, table_1_wave4_Tx, table_1_wave4_HC, table_1_wave4_RC, table_1_wave4_IMM, table_1_wave4_IMD]
    outputs:
      moderately_sensitive:
        csv: output/table_1/table_1_wave4_collated.csv

  # Table - incidence rates
  calc_ir_hr_wave4_Tx:
    run: r:latest analysis/calc_ir_hr.R wave4 Tx
    needs: [filter_data_wave4]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave4_Tx.csv
        csv2: output/table_ir_hr/table_ir_hr_wave4_Tx_simple.csv

  calc_ir_hr_wave4_HC:
    run: r:latest analysis/calc_ir_hr.R wave4 HC
    needs: [filter_data_wave4]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave4_HC.csv
        csv2: output/table_ir_hr/table_ir_hr_wave4_HC_simple.csv

  calc_ir_hr_wave4_RC:
    run: r:latest analysis/calc_ir_hr.R wave4 RC
    needs: [filter_data_wave4]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave4_RC.csv
        csv2: output/table_ir_hr/table_ir_hr_wave4_RC_simple.csv

  calc_ir_hr_wave4_IMM:
    run: r:latest analysis/calc_ir_hr.R wave4 IMM
    needs: [filter_data_wave4]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave4_IMM.csv
        csv2: output/table_ir_hr/table_ir_hr_wave4_IMM_simple.csv

  calc_ir_hr_wave4_IMD:
    run: r:latest analysis/calc_ir_hr.R wave4 IMD
    needs: [filter_data_wave4]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave4_IMD.csv
        csv2: output/table_ir_hr/table_ir_hr_wave4_IMD_simple.csv



  ## WAVE 3 ##

  # Extract data
  generate_study_population_wave3:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_wave3
        --skip-existing
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_wave3.csv.gz

  # Process data
  process_data_wave3:
    run: r:latest analysis/data_process.R wave3
    needs: [generate_study_population_wave3]
    outputs:
      highly_sensitive:
        rds: output/processed/input_wave3.rds
        
  # Skim data
  skim_data_wave3:
    run: r:latest analysis/data_skim.R output/processed/input_wave3.rds output/data_properties
    needs: [process_data_wave3]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/input_wave3_skim.txt
        txt2: output/data_properties/input_wave3_coltypes.txt
        txt3: output/data_properties/input_wave3_tabulate.txt
        
  # Filter data
  filter_data_wave3:
    run: r:latest analysis/data_selection.R wave3
    needs: [process_data_wave3]
    outputs:
      highly_sensitive:
        rds: output/filtered/input_wave3.rds
      moderately_sensitive:
        csv: output/flowchart/flowchart_wave3.csv

  # Table 1
  table_1_wave3_all:
    run: r:latest analysis/table_1.R wave3 all
    needs: [filter_data_wave3]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave3_all.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave3_all.html
        csv: output/table_1/table_1_wave3_all.csv
        
  table_1_wave3_Tx:
    run: r:latest analysis/table_1.R wave3 Tx
    needs: [filter_data_wave3]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave3_Tx.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave3_Tx.html
        csv: output/table_1/table_1_wave3_Tx.csv

  table_1_wave3_HC:
    run: r:latest analysis/table_1.R wave3 HC
    needs: [filter_data_wave3]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave3_HC.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave3_HC.html
        csv: output/table_1/table_1_wave3_HC.csv

  table_1_wave3_RC:
    run: r:latest analysis/table_1.R wave3 RC
    needs: [filter_data_wave3]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave3_RC.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave3_RC.html
        csv: output/table_1/table_1_wave3_RC.csv
        
  table_1_wave3_IMM:
    run: r:latest analysis/table_1.R wave3 IMM
    needs: [filter_data_wave3]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave3_IMM.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave3_IMM.html
        csv: output/table_1/table_1_wave3_IMM.csv

  table_1_wave3_IMD:
    run: r:latest analysis/table_1.R wave3 IMD
    needs: [filter_data_wave3]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave3_IMD.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave3_IMD.html
        csv: output/table_1/table_1_wave3_IMD.csv

  collate_table_1_wave3:
    run: r:latest analysis/collate_table_1.R wave3
    needs: [table_1_wave3_all, table_1_wave3_Tx, table_1_wave3_HC, table_1_wave3_RC, table_1_wave3_IMM, table_1_wave3_IMD]
    outputs:
      moderately_sensitive:
        csv: output/table_1/table_1_wave3_collated.csv

  # Table - incidence rates
  calc_ir_hr_wave3_Tx:
    run: r:latest analysis/calc_ir_hr.R wave3 Tx
    needs: [filter_data_wave3]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave3_Tx.csv
        csv2: output/table_ir_hr/table_ir_hr_wave3_Tx_simple.csv

  calc_ir_hr_wave3_HC:
    run: r:latest analysis/calc_ir_hr.R wave3 HC
    needs: [filter_data_wave3]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave3_HC.csv
        csv2: output/table_ir_hr/table_ir_hr_wave3_HC_simple.csv

  calc_ir_hr_wave3_RC:
    run: r:latest analysis/calc_ir_hr.R wave3 RC
    needs: [filter_data_wave3]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave3_RC.csv
        csv2: output/table_ir_hr/table_ir_hr_wave3_RC_simple.csv

  calc_ir_hr_wave3_IMM:
    run: r:latest analysis/calc_ir_hr.R wave3 IMM
    needs: [filter_data_wave3]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave3_IMM.csv
        csv2: output/table_ir_hr/table_ir_hr_wave3_IMM_simple.csv

  calc_ir_hr_wave3_IMD:
    run: r:latest analysis/calc_ir_hr.R wave3 IMD
    needs: [filter_data_wave3]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave3_IMD.csv
        csv2: output/table_ir_hr/table_ir_hr_wave3_IMD_simple.csv



  ## WAVE 2 ##

  # Extract data
  generate_study_population_wave2:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_wave2
        --skip-existing
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_wave2.csv.gz

  # Process data
  process_data_wave2:
    run: r:latest analysis/data_process.R wave2
    needs: [generate_study_population_wave2]
    outputs:
      highly_sensitive:
        rds: output/processed/input_wave2.rds
        
  # Skim data
  skim_data_wave2:
    run: r:latest analysis/data_skim.R output/processed/input_wave2.rds output/data_properties
    needs: [process_data_wave2]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/input_wave2_skim.txt
        txt2: output/data_properties/input_wave2_coltypes.txt
        txt3: output/data_properties/input_wave2_tabulate.txt
        
  # Filter data
  filter_data_wave2:
    run: r:latest analysis/data_selection.R wave2
    needs: [process_data_wave2]
    outputs:
      highly_sensitive:
        rds: output/filtered/input_wave2.rds
      moderately_sensitive:
        csv: output/flowchart/flowchart_wave2.csv

  # Table 1
  table_1_wave2_all:
    run: r:latest analysis/table_1.R wave2 all
    needs: [filter_data_wave2]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave2_all.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave2_all.html
        csv: output/table_1/table_1_wave2_all.csv
        
  table_1_wave2_Tx:
    run: r:latest analysis/table_1.R wave2 Tx
    needs: [filter_data_wave2]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave2_Tx.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave2_Tx.html
        csv: output/table_1/table_1_wave2_Tx.csv

  table_1_wave2_HC:
    run: r:latest analysis/table_1.R wave2 HC
    needs: [filter_data_wave2]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave2_HC.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave2_HC.html
        csv: output/table_1/table_1_wave2_HC.csv

  table_1_wave2_RC:
    run: r:latest analysis/table_1.R wave2 RC
    needs: [filter_data_wave2]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave2_RC.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave2_RC.html
        csv: output/table_1/table_1_wave2_RC.csv
        
  table_1_wave2_IMM:
    run: r:latest analysis/table_1.R wave2 IMM
    needs: [filter_data_wave2]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave2_IMM.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave2_IMM.html
        csv: output/table_1/table_1_wave2_IMM.csv

  table_1_wave2_IMD:
    run: r:latest analysis/table_1.R wave2 IMD
    needs: [filter_data_wave2]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave2_IMD.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave2_IMD.html
        csv: output/table_1/table_1_wave2_IMD.csv

  collate_table_1_wave2:
    run: r:latest analysis/collate_table_1.R wave2
    needs: [table_1_wave2_all, table_1_wave2_Tx, table_1_wave2_HC, table_1_wave2_RC, table_1_wave2_IMM, table_1_wave2_IMD]
    outputs:
      moderately_sensitive:
        csv: output/table_1/table_1_wave2_collated.csv

  # Table - incidence rates
  calc_ir_hr_wave2_Tx:
    run: r:latest analysis/calc_ir_hr.R wave2 Tx
    needs: [filter_data_wave2]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave2_Tx.csv
        csv2: output/table_ir_hr/table_ir_hr_wave2_Tx_simple.csv

  calc_ir_hr_wave2_HC:
    run: r:latest analysis/calc_ir_hr.R wave2 HC
    needs: [filter_data_wave2]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave2_HC.csv
        csv2: output/table_ir_hr/table_ir_hr_wave2_HC_simple.csv

  calc_ir_hr_wave2_RC:
    run: r:latest analysis/calc_ir_hr.R wave2 RC
    needs: [filter_data_wave2]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave2_RC.csv
        csv2: output/table_ir_hr/table_ir_hr_wave2_RC_simple.csv

  calc_ir_hr_wave2_IMM:
    run: r:latest analysis/calc_ir_hr.R wave2 IMM
    needs: [filter_data_wave2]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave2_IMM.csv
        csv2: output/table_ir_hr/table_ir_hr_wave2_IMM_simple.csv

  calc_ir_hr_wave2_IMD:
    run: r:latest analysis/calc_ir_hr.R wave2 IMD
    needs: [filter_data_wave2]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave2_IMD.csv
        csv2: output/table_ir_hr/table_ir_hr_wave2_IMD_simple.csv



  ## WAVE 1 ##

  # Extract data
  generate_study_population_wave1:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_wave1
        --skip-existing
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_wave1.csv.gz

  # Process data
  process_data_wave1:
    run: r:latest analysis/data_process.R wave1
    needs: [generate_study_population_wave1]
    outputs:
      highly_sensitive:
        rds: output/processed/input_wave1.rds
        
  # Skim data
  skim_data_wave1:
    run: r:latest analysis/data_skim.R output/processed/input_wave1.rds output/data_properties
    needs: [process_data_wave1]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/input_wave1_skim.txt
        txt2: output/data_properties/input_wave1_coltypes.txt
        txt3: output/data_properties/input_wave1_tabulate.txt
        
  # Filter data
  filter_data_wave1:
    run: r:latest analysis/data_selection.R wave1
    needs: [process_data_wave1]
    outputs:
      highly_sensitive:
        rds: output/filtered/input_wave1.rds
      moderately_sensitive:
        csv: output/flowchart/flowchart_wave1.csv

  # Table 1
  table_1_wave1_all:
    run: r:latest analysis/table_1.R wave1 all
    needs: [filter_data_wave1]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave1_all.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave1_all.html
        csv: output/table_1/table_1_wave1_all.csv
        
  table_1_wave1_Tx:
    run: r:latest analysis/table_1.R wave1 Tx
    needs: [filter_data_wave1]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave1_Tx.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave1_Tx.html
        csv: output/table_1/table_1_wave1_Tx.csv

  table_1_wave1_HC:
    run: r:latest analysis/table_1.R wave1 HC
    needs: [filter_data_wave1]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave1_HC.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave1_HC.html
        csv: output/table_1/table_1_wave1_HC.csv

  table_1_wave1_RC:
    run: r:latest analysis/table_1.R wave1 RC
    needs: [filter_data_wave1]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave1_RC.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave1_RC.html
        csv: output/table_1/table_1_wave1_RC.csv
        
  table_1_wave1_IMM:
    run: r:latest analysis/table_1.R wave1 IMM
    needs: [filter_data_wave1]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave1_IMM.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave1_IMM.html
        csv: output/table_1/table_1_wave1_IMM.csv

  table_1_wave1_IMD:
    run: r:latest analysis/table_1.R wave1 IMD
    needs: [filter_data_wave1]
    outputs:
      highly_sensitive:
        data: output/table_1/table_1_wave1_IMD.rds
      moderately_sensitive:
        table: output/table_1/table_1_wave1_IMD.html
        csv: output/table_1/table_1_wave1_IMD.csv

  collate_table_1_wave1:
    run: r:latest analysis/collate_table_1.R wave1
    needs: [table_1_wave1_all, table_1_wave1_Tx, table_1_wave1_HC, table_1_wave1_RC, table_1_wave1_IMM, table_1_wave1_IMD]
    outputs:
      moderately_sensitive:
        csv: output/table_1/table_1_wave1_collated.csv

  # Table - incidence rates
  calc_ir_hr_wave1_Tx:
    run: r:latest analysis/calc_ir_hr.R wave1 Tx
    needs: [filter_data_wave1]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave1_Tx.csv
        csv2: output/table_ir_hr/table_ir_hr_wave1_Tx_simple.csv

  calc_ir_hr_wave1_HC:
    run: r:latest analysis/calc_ir_hr.R wave1 HC
    needs: [filter_data_wave1]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave1_HC.csv
        csv2: output/table_ir_hr/table_ir_hr_wave1_HC_simple.csv

  calc_ir_hr_wave1_RC:
    run: r:latest analysis/calc_ir_hr.R wave1 RC
    needs: [filter_data_wave1]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave1_RC.csv
        csv2: output/table_ir_hr/table_ir_hr_wave1_RC_simple.csv

  calc_ir_hr_wave1_IMM:
    run: r:latest analysis/calc_ir_hr.R wave1 IMM
    needs: [filter_data_wave1]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave1_IMM.csv
        csv2: output/table_ir_hr/table_ir_hr_wave1_IMM_simple.csv

  calc_ir_hr_wave1_IMD:
    run: r:latest analysis/calc_ir_hr.R wave1 IMD
    needs: [filter_data_wave1]
    outputs:
      moderately_sensitive:
        csv1: output/table_ir_hr/table_ir_hr_wave1_IMD.csv
        csv2: output/table_ir_hr/table_ir_hr_wave1_IMD_simple.csv