Job request: 6332

version: '3.0'

expectations:

  population_size: 400000

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_electively_unvaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_electively_unvaccinated
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_electively_unvaccinated.feather

  generate_study_population_vaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
      --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_vaccinated.feather

  generate_study_population_index:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_index
      --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_index.feather

  preprocess_data_vaccinated:
    run: r:latest analysis/preprocess_data.R vaccinated
    needs:
    - generate_study_population_index
    - generate_study_population_vaccinated
    - generate_study_population_electively_unvaccinated
    outputs:
      moderately_sensitive:
        describe: output/describe_input_vaccinated_*.txt
      highly_sensitive:
        cohort: output/input_vaccinated.rds
        venn: output/venn_vaccinated.rds

  preprocess_data_electively_unvaccinated:
    run: r:latest analysis/preprocess_data.R electively_unvaccinated
    needs:
    - generate_study_population_index
    - generate_study_population_vaccinated
    - generate_study_population_electively_unvaccinated
    outputs:
      moderately_sensitive:
        describe: output/describe_input_electively_unvaccinated_*.txt
      highly_sensitive:
        cohort: output/input_electively_unvaccinated.rds
        venn: output/venn_electively_unvaccinated.rds

  stage1_data_cleaning_both:
    run: r:latest analysis/Stage1_data_cleaning.R both
    needs:
    - preprocess_data_vaccinated
    - preprocess_data_electively_unvaccinated
    outputs:
      moderately_sensitive:
        refactoring: output/meta_data_factors_*.csv
        QA_rules: output/QA_summary_*.csv
        IE_criteria: output/Cohort_flow_*.csv
      highly_sensitive:
        cohort: output/input_*_stage1.rds

  stage2_missing_table1_both:
    run: r:latest analysis/Stage2_missing_table1.R both
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/Check_missing_range_*.csv
        DateChecks: output/Check_dates_range_*.csv
        Descriptive_Table: output/Table1_*.csv

  stage4_table2_both:
    run: r:latest analysis/table_2.R both
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        table2: output/table2_*.csv

  stage4_venn_diagram_both:
    run: r:latest analysis/venn_diagram.R both
    needs:
    - preprocess_data_vaccinated
    - preprocess_data_electively_unvaccinated
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        venn_diagram: output/venn_diagram_*.svg
        venn_diagram_number_check: output/venn_diagram_number_check_*.csv

  ## Apply cox model for ami 

  Analysis_cox_ami:
    run: r:latest analysis/01_pipe.R ami
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_ami.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_ami.html
        analyses_not_run: output/analyses_not_run_ami.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_ami.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_ami.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_ami.csv
        compiled_event_counts: output/compiled_event_counts_ami.csv

  ## Apply cox model for stroke_isch 

  Analysis_cox_stroke_isch:
    run: r:latest analysis/01_pipe.R stroke_isch
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_stroke_isch.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_stroke_isch.html
        analyses_not_run: output/analyses_not_run_stroke_isch.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_stroke_isch.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_stroke_isch.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_stroke_isch.csv
        compiled_event_counts: output/compiled_event_counts_stroke_isch.csv

  ## Apply cox model for dvt 

  Analysis_cox_dvt:
    run: r:latest analysis/01_pipe.R dvt
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_dvt.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_dvt.html
        analyses_not_run: output/analyses_not_run_dvt.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_dvt.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_dvt.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_dvt.csv
        compiled_event_counts: output/compiled_event_counts_dvt.csv

  ## Apply cox model for pe 

  Analysis_cox_pe:
    run: r:latest analysis/01_pipe.R pe
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_pe.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_pe.html
        analyses_not_run: output/analyses_not_run_pe.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_pe.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_pe.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_pe.csv
        compiled_event_counts: output/compiled_event_counts_pe.csv

  ## Apply cox model for tia 

  Analysis_cox_tia:
    run: r:latest analysis/01_pipe.R tia
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_tia.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_tia.html
        analyses_not_run: output/analyses_not_run_tia.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_tia.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_tia.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_tia.csv
        compiled_event_counts: output/compiled_event_counts_tia.csv

  ## Apply cox model for stroke_sah_hs 

  Analysis_cox_stroke_sah_hs:
    run: r:latest analysis/01_pipe.R stroke_sah_hs
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_stroke_sah_hs.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_stroke_sah_hs.html
        analyses_not_run: output/analyses_not_run_stroke_sah_hs.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_stroke_sah_hs.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_stroke_sah_hs.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_stroke_sah_hs.csv
        compiled_event_counts: output/compiled_event_counts_stroke_sah_hs.csv

  ## Apply cox model for hf 

  Analysis_cox_hf:
    run: r:latest analysis/01_pipe.R hf
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_hf.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_hf.html
        analyses_not_run: output/analyses_not_run_hf.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_hf.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_hf.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_hf.csv
        compiled_event_counts: output/compiled_event_counts_hf.csv

  ## Apply cox model for angina 

  Analysis_cox_angina:
    run: r:latest analysis/01_pipe.R angina
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_angina.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_angina.html
        analyses_not_run: output/analyses_not_run_angina.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_angina.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_angina.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_angina.csv
        compiled_event_counts: output/compiled_event_counts_angina.csv

  ## Apply cox model for ate 

  Analysis_cox_ate:
    run: r:latest analysis/01_pipe.R ate
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_ate.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_ate.html
        analyses_not_run: output/analyses_not_run_ate.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_ate.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_ate.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_ate.csv
        compiled_event_counts: output/compiled_event_counts_ate.csv

  ## Apply cox model for vte 

  Analysis_cox_vte:
    run: r:latest analysis/01_pipe.R vte
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_vte.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_vte.html
        analyses_not_run: output/analyses_not_run_vte.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_vte.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_vte.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_vte.csv
        compiled_event_counts: output/compiled_event_counts_vte.csv

  ## Apply cox model for depression 

  Analysis_cox_depression:
    run: r:latest analysis/01_pipe.R depression
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_depression.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_depression.html
        analyses_not_run: output/analyses_not_run_depression.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_depression.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_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_anxiety_general.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_anxiety_general.html
        analyses_not_run: output/analyses_not_run_anxiety_general.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_general.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_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_anxiety_ocd.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_anxiety_ocd.html
        analyses_not_run: output/analyses_not_run_anxiety_ocd.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_ocd.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_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_anxiety_ptsd.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_anxiety_ptsd.html
        analyses_not_run: output/analyses_not_run_anxiety_ptsd.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_ptsd.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_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_eating_disorders.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_eating_disorders.html
        analyses_not_run: output/analyses_not_run_eating_disorders.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_eating_disorders.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_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_serious_mental_illness.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_serious_mental_illness.html
        analyses_not_run: output/analyses_not_run_serious_mental_illness.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_serious_mental_illness.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_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_self_harm_10plus.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_self_harm_10plus.html
        analyses_not_run: output/analyses_not_run_self_harm_10plus.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_self_harm_10plus.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_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_self_harm_15plus.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_self_harm_15plus.html
        analyses_not_run: output/analyses_not_run_self_harm_15plus.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_self_harm_15plus.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_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_suicide.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_suicide.html
        analyses_not_run: output/analyses_not_run_suicide.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_suicide.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_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/suppressed_compiled_HR_results_addiction.html
        compiled_event_counts_html: output/suppressed_compiled_event_counts_addiction.html
        analyses_not_run: output/analyses_not_run_addiction.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_addiction.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