project.yaml

version: '3.0'

expectations:
  population_size: 1000

actions:
  

  generate_study_population_covid_primarycare:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_primarycare
    outputs:
      highly_sensitive:
        cohort: output/input_covid_primarycare.csv
  
  generate_study_population_covid_SGSS:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_SGSS
    outputs:
      highly_sensitive:
        cohort: output/input_covid_SGSS.csv

  generate_study_population_covid_admission:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_admission
    outputs:
      highly_sensitive:
        cohort: output/input_covid_admission.csv

  process_1:  # Covid ons death
    run: r:latest analysis/process_1.R
    needs: [generate_study_population_covid_primarycare, generate_study_population_covid_SGSS,generate_study_population_covid_admission]
    outputs:
      highly_sensitive:
        case: output/case_covid_hosp.csv 
        control: output/control_covid_infection.csv 

  matching: #R MatchIt  matching with replacement
    run: r:latest -e 'rmarkdown::render("analysis/matching.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_1]
    outputs:
      moderately_sensitive:
        html: output/matching.html
      highly_sensitive: 
        rds1: output/matched_patients.rds
        rds2: output/unmatched_cases.rds
        csv: output/matched_patients_id.csv
        
  check_unmatched:
    run: r:latest -e 'rmarkdown::render("analysis/check_unmatched.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [matching]
    outputs:
      moderately_sensitive:
        html: output/check_unmatched.html

  extract_variables: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome
    needs: [matching]
    outputs:
      highly_sensitive:
        cohort: output/input_outcome.csv

  process_Rmatching: # add variables 
    run: r:latest analysis/process_Rmatching.R
    needs: [extract_variables,matching]
    outputs:
      highly_sensitive:
        cohort1: output/matched_outcome.rds
        cohort2: output/matched_outcome_check.rds # filter died $ de-regist again
        rds1: output/abtype79.rds
        rds2: output/comor17.rds

  table1: # compare before & after matching 
    run: r:latest -e 'rmarkdown::render("analysis/table1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_1,process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/table1.html

  table2: # confounders
    run: r:latest -e 'rmarkdown::render("analysis/table2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/table2.html

  table2_ab: # ab
    run: r:latest -e 'rmarkdown::render("analysis/table2_ab.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/table2_ab.html

  model: 
    run: r:latest -e 'rmarkdown::render("analysis/model.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/model.html

  model_subgroup: # by age and sex 
    run: r:latest -e 'rmarkdown::render("analysis/model_subgroup.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/model_subgroup.html 

  # abtype modeling
  model_abtype: 
    run: r:latest -e 'rmarkdown::render("analysis/model_abtype.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/model_abtype.html

  model_time: # adjust for last AB time
    run: r:latest -e 'rmarkdown::render("analysis/model_time.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/model_time.html

  model_disease: # adjust for individual
    run: r:latest -e 'rmarkdown::render("analysis/model_disease.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/model_disease.html
  
  model_wave: # separate wave
    run: r:latest -e 'rmarkdown::render("analysis/model_wave.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/model_wave.html
  
        ################# check ok###########

        #### addintional check for 6 weeks exclusion
  extract_variables_6w: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome_6w
    needs: [matching]
    outputs:
      highly_sensitive:
        cohort: output/input_outcome_6w.csv
  
  process_Rmatching_6w: # add variables 
    run: r:latest analysis/process_Rmatching_6w.R
    needs: [extract_variables_6w,matching,process_Rmatching]
    outputs:
      highly_sensitive:
        cohort1: output/matched_outcome_6w.rds
  
  model_6w: # adjust for last AB time
    run: r:latest -e 'rmarkdown::render("analysis/model_6w.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching_6w]
    outputs:
      moderately_sensitive:
        html: output/model_6w.html

          #### addintional check for 6 weeks exclusion


  process_2: # died any cause
    run: r:latest analysis/process_2.R
    needs: [generate_study_population_covid_primarycare, generate_study_population_covid_SGSS]
    outputs:
      highly_sensitive:
        control: output/control_covid_infection_2.csv

  check_input: # 
    run: r:latest -e 'rmarkdown::render("analysis/check_input.Rmd", knit_root_dir = "/workspace", output_dir = "output")'
    needs: [process_Rmatching,process_2,extract_variables,matching,process_matching,extract_variables_outcome_2_2,extract_variables_outcome_2_4,extract_variables_outcome_2_6,matching_2,process_1,generate_study_population_covid_primarycare, generate_study_population_covid_SGSS]
    outputs:
      moderately_sensitive:
        html: output/check_input.html
        
# OS matching without replacement, ratio 2-4-6
  matching_2:
    run: python:latest python analysis/matching_outcome_2.py
    needs: [process_1]
    outputs:
      moderately_sensitive: 
        matching_report2: output/matching_report_infection_hosp_2.txt
        matching_report4: output/matching_report_infection_hosp_4.txt
        matching_report6: output/matching_report_infection_hosp_6.txt
      highly_sensitive: 
        combined2: output/matched_combined_infection_hosp_2.csv
        combined4: output/matched_combined_infection_hosp_4.csv
        combined6: output/matched_combined_infection_hosp_6.csv

  extract_variables_outcome_2_2: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome_2_2
    needs: [matching_2]
    outputs:
      highly_sensitive:
        cohort: output/input_outcome_2_2.csv
    
  extract_variables_outcome_2_4: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome_2_4
    needs: [matching_2]
    outputs:
      highly_sensitive:
        cohort: output/input_outcome_2_4.csv
  
  extract_variables_outcome_2_6: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome_2_6
    needs: [matching_2]
    outputs:
      highly_sensitive:
        cohort: output/input_outcome_2_6.csv

  check_matching_2:
    run: r:latest -e 'rmarkdown::render("analysis/check_matching_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [matching_2]
    outputs:
      moderately_sensitive:
        html: output/check_matching_2.html

  process_matching: # add variables 
    run: r:latest analysis/process_matching.R
    needs: [extract_variables_outcome_2_6,extract_variables_outcome_2_4,extract_variables_outcome_2_2,matching_2]
    outputs:
      highly_sensitive:
        cohort1: output/matched_outcome_2.csv
        cohort2: output/matched_outcome_4.csv
        cohort3: output/matched_outcome_6.csv

  check_exposures_6:
    run: r:latest -e 'rmarkdown::render("analysis/check_exposures_6.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_matching]
    outputs:
      moderately_sensitive:
        html: output/check_exposures_6.html 

  check_exposures_4:
    run: r:latest -e 'rmarkdown::render("analysis/check_exposures_4.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_matching]
    outputs:
      moderately_sensitive:
        html: output/check_exposures_4.html 

  check_exposures_2:
    run: r:latest -e 'rmarkdown::render("analysis/check_exposures_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_matching]
    outputs:
      moderately_sensitive:
        html: output/check_exposures_2.html 

# # R MatchIt

#   matching: # matching with replacement
#     run: r:latest -e 'rmarkdown::render("analysis/matching.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
#     needs: [process_1]
#     outputs:
#       moderately_sensitive:
#         html: output/matching.html
#       highly_sensitive: 
#         rds1: output/matched_patients.rds
#         rds2: output/unmatched_patients.rds
#         csv: output/matched_patients_id.csv

  check_matching:
    run: r:latest -e 'rmarkdown::render("analysis/check_matching.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [matching]
    outputs:
      moderately_sensitive:
        html: output/check_matching.html

  # extract_variables: 
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome
  #   needs: [matching]
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/input_outcome.csv
  
  # process_Rmatching: # add variables 
  #   run: r:latest analysis/process_Rmatching.R
  #   needs: [extract_variables,matching]
  #   outputs:
  #     highly_sensitive:
  #       cohort1: output/matched_outcome.rds
  #       rds1: output/abtype79.rds
  #       rds2: output/comor17.rds

  check_exposures_cont: # continuous variables
    run: r:latest -e 'rmarkdown::render("analysis/check_exposures_cont.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/check_exposures_cont.html
  
  check_exposures_cat: # category variables
    run: r:latest -e 'rmarkdown::render("analysis/check_exposures_cat.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/check_exposures_cat.html

  modeling: # ab level
    run: r:latest -e 'rmarkdown::render("analysis/modeling.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/modeling.html

  modeling2: # ab level+ CCI + covid vaccine
    run: r:latest -e 'rmarkdown::render("analysis/modeling2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/modeling2.html

  modeling3: # all
    run: r:latest -e 'rmarkdown::render("analysis/modeling3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/modeling3.html

  describe_ab: 
    run: r:latest -e 'rmarkdown::render("analysis/describe_ab.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/describe_ab.html
  
  # abtype modeling
  modeling4: # all
    run: r:latest -e 'rmarkdown::render("analysis/modeling4.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/modeling4.html


    # broad ab modeling
  modeling5: # all
    run: r:latest -e 'rmarkdown::render("analysis/modeling5.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_Rmatching]
    outputs:
      moderately_sensitive:
        html: output/modeling5.html



# unmatched controls
  extract_variables_unmatched: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unmatched
    needs: [process_1]
    outputs:
      highly_sensitive:
        cohort: output/input_unmatched.csv
  
  process_unmatched: # add variables 
    run: r:latest analysis/process_unmatched.R
    needs: [extract_variables_unmatched]
    outputs:
      highly_sensitive:
        cohort1: output/unmatched_outcome.rds

  # check_exposures_cont_unmatched: # continuous variables
  #   run: r:latest -e 'rmarkdown::render("analysis/check_exposures_cont_unmatched.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
  #   needs: [process_unmatched]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/check_exposures_cont_unmatched.html
  
  check_exposures_cat_unmatched: # category variables
    run: r:latest -e 'rmarkdown::render("analysis/check_exposures_cat_unmatched.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [process_unmatched]
    outputs:
      moderately_sensitive:
        html: output/check_exposures_cat_unmatched.html