project.yaml

version: '3.0'

expectations:

  population_size: 100000

actions:

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

  vax_eligibility_inputs:
    run: r:latest analysis/vax_eligibility_inputs.R
    outputs:
      highly_sensitive:
        vax_study_dates_json: output/vax_study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  preprocess_data:
    run: r:latest analysis/preprocess/preprocess_data.R
    needs:
    - generate_study_population
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_stage0.txt
      highly_sensitive:
        cohort: output/input.rds
        venn: output/venn.rds

  stage1_data_cleaning:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R
    needs:
    - preprocess_data
    outputs:
      moderately_sensitive:
        QA_rules: output/review/descriptives/QA_summary.csv
        refactoring: output/not-for-review/meta_data_factors.csv
        IE_criteria: output/review/descriptives/cohort_flow*.csv
      highly_sensitive:
        cohort: output/input_stage1*.rds

  stage1_end_date_table:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates*.rds

  stage2_missing_table1:
    run: r:latest analysis/descriptives/Stage2_Missing_Table1.R
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/not-for-review/Check_missing_range*.csv
        DateChecks: output/not-for-review/Check_dates_range*.csv
        Descriptive_Table: output/review/descriptives/Table1*.csv

  stage3_diabetes_flow:
    run: r:latest analysis/descriptives/diabetes_flowchart.R
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values*.csv

  ## Stage 4 - Table 2 

  stage4_table_2:
    run: 'r:latest analysis/descriptives/table_2.R '
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2*.csv

  stage4_venn_diagram:
    run: r:latest analysis/descriptives/venn_diagram.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_*.svg
        venn_diagram_number_check: output/review/venn-diagrams/venn_diagram_number_check*.csv

  ## Apply cox model for t1dm 

  Analysis_cox_t1dm:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_t1dm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_t1dm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_t1dm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_t1dm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_t1dm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_t1dm.csv

  ## Apply cox model for t2dm 

  Analysis_cox_t2dm:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_t2dm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_t2dm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_t2dm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_t2dm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_t2dm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_t2dm.csv

  ## Apply cox model for otherdm 

  Analysis_cox_otherdm:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_otherdm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_otherdm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_otherdm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_otherdm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_otherdm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_otherdm.csv

  ## Apply cox model for gestationaldm 

  Analysis_cox_gestationaldm:
    run: r:latest analysis/model/01_cox_pipeline.R gestationaldm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_gestationaldm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_gestationaldm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_gestationaldm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_gestationaldm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_gestationaldm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_gestationaldm.csv