Job request: 1869

######################################

# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.

######################################

version: '3.0'

expectations:
  population_size: 1000000

actions:

  # Extract data for study population flow chart
  generate_study_population_flow_chart_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart.csv

  # Calculate numbers for study population flow chart
  flow_chart:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Study_definition_flow_chart.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population_flow_chart_data]
    outputs:
      moderately_sensitive:
        html: output/Study_definition_flow_chart.html
        
  # Extract study data
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  # Process data
  data_process:
    run: r:latest analysis/R/Scripts/00_process_data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        data2: output/data/data_modelling.rds
        
  # Summarise data
  data_properties:
    run: r:latest analysis/R/Scripts/01_data_properties.R output/data/data_all.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_all*.txt
        
  # More data summaries
  data_summaries:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Data_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population, data_process]
    outputs:
      moderately_sensitive:
        html: output/Data_summaries.html

  # Coxph models
  cox_models:
    run: r:latest analysis/R/Scripts/02_Models.R
    needs: [generate_study_population, data_process]
    outputs:
      highly_sensitive :
        models: output/models/testing/mod*.rds
        
  # # Coxme model
  # cox_models_sub:
  #   run: r:latest analysis/R/Scripts/02_Models_sub_test.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/testing/mod_test*.rds

  # Model summaries
  cox_models_summaries:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Model_comparisons.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population, data_process, cox_models]
    outputs:
      moderately_sensitive:
        html: output/Model_comparisons.html
        
  # Stratified cox model
  cox_model_final:
    run: r:latest analysis/R/Scripts/03_Final_model.R
    needs: [generate_study_population, data_process]
    outputs:
      highly_sensitive :
        models: output/models/final/mod*.rds
      # moderately_sensitive:
      #   tables: output/models/final/tab*.html
      #   data: output/models/final/tab*.csv
      #   plots: output/models/final/plot*.svg
        
  # Strata summaries
  strata_summary:
    run: r:latest analysis/R/Scripts/04_Strata_Summary.R
    needs: [data_process, cox_model_final]
    outputs:
      moderately_sensitive:
        plots: output/models/final/plot_strata*.svg
  
  # Results summary
  results_summary:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Results_summary.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population, data_process, cox_model_final]
    outputs:
      moderately_sensitive:
        html: output/Results_summary.html