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_data.R
    needs:
    - generate_study_population
    outputs:
      highly_sensitive:
        cohort: output/input.rds
        venn: output/venn.rds

  stage1_data_cleaning:
    run: r:latest analysis/Stage1_data_cleaning.R
    needs:
    - preprocess_data
    outputs:
      moderately_sensitive:
        QA_rules: output/QA_summary.csv
        refactoring: output/meta_data_factors.csv
        IE_criteria: output/cohort_flow.csv
      highly_sensitive:
        cohort: output/input_stage1.rds

  stage2_missing_table1:
    run: r:latest analysis/Stage2_Missing_Table1.R
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/Check_missing_range.csv
        DateChecks: output/Check_dates_range.csv
        Descriptive_Table: output/Table1*.csv

  stage3_diabetes_flow:
    run: r:latest analysis/diabetes_flowchart.R
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        flow_df: output/diabetes_flow_values.csv

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

  ## Apply cox model for t1dm 

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

  ## Apply cox model for t2dm 

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

  ## Apply cox model for otherdm 

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

  ## Apply cox model for gestationaldm 

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

  ## Apply cox model for depression 

  Analysis_cox_depression:
    run: r:latest analysis/01_pipe.R depression
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_depression.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_depression.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_depression_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_depression.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_depression.csv
        compiled_event_counts: output/compiled_event_counts_depression.csv

  ## Apply cox model for anxiety_general 

  Analysis_cox_anxiety_general:
    run: r:latest analysis/01_pipe.R anxiety_general
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_anxiety_general.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_general.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_anxiety_general_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_anxiety_general.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_anxiety_general.csv
        compiled_event_counts: output/compiled_event_counts_anxiety_general.csv

  ## Apply cox model for anxiety_ocd 

  Analysis_cox_anxiety_ocd:
    run: r:latest analysis/01_pipe.R anxiety_ocd
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_anxiety_ocd.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_ocd.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_anxiety_ocd_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_anxiety_ocd.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_anxiety_ocd.csv
        compiled_event_counts: output/compiled_event_counts_anxiety_ocd.csv

  ## Apply cox model for anxiety_ptsd 

  Analysis_cox_anxiety_ptsd:
    run: r:latest analysis/01_pipe.R anxiety_ptsd
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_anxiety_ptsd.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_ptsd.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_anxiety_ptsd_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_anxiety_ptsd.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_anxiety_ptsd.csv
        compiled_event_counts: output/compiled_event_counts_anxiety_ptsd.csv

  ## Apply cox model for eating_disorders 

  Analysis_cox_eating_disorders:
    run: r:latest analysis/01_pipe.R eating_disorders
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_eating_disorders.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_eating_disorders.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_eating_disorders_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_eating_disorders.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_eating_disorders.csv
        compiled_event_counts: output/compiled_event_counts_eating_disorders.csv

  ## Apply cox model for serious_mental_illness 

  Analysis_cox_serious_mental_illness:
    run: r:latest analysis/01_pipe.R serious_mental_illness
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_serious_mental_illness.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_serious_mental_illness.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_serious_mental_illness_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_serious_mental_illness.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_serious_mental_illness.csv
        compiled_event_counts: output/compiled_event_counts_serious_mental_illness.csv

  ## Apply cox model for self_harm_10plus 

  Analysis_cox_self_harm_10plus:
    run: r:latest analysis/01_pipe.R self_harm_10plus
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_self_harm_10plus.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_self_harm_10plus.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_self_harm_10plus_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_self_harm_10plus.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_self_harm_10plus.csv
        compiled_event_counts: output/compiled_event_counts_self_harm_10plus.csv

  ## Apply cox model for self_harm_15plus 

  Analysis_cox_self_harm_15plus:
    run: r:latest analysis/01_pipe.R self_harm_15plus
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_self_harm_15plus.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_self_harm_15plus.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_self_harm_15plus_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_self_harm_15plus.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_self_harm_15plus.csv
        compiled_event_counts: output/compiled_event_counts_self_harm_15plus.csv

  ## Apply cox model for suicide 

  Analysis_cox_suicide:
    run: r:latest analysis/01_pipe.R suicide
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_suicide.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_suicide.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_suicide_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_suicide.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_suicide.csv
        compiled_event_counts: output/compiled_event_counts_suicide.csv

  ## Apply cox model for addiction 

  Analysis_cox_addiction:
    run: r:latest analysis/01_pipe.R addiction
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_addiction.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_addiction.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_addiction_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_addiction.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_addiction.csv
        compiled_event_counts: output/compiled_event_counts_addiction.csv