Job request: 294

version: "3.0"

expectations:
  population_size: 1000

actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_cohort_coverage:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_coverage
    outputs:
      highly_sensitive:
        cohort: output/input_coverage.csv

  calculate_coverage: 
    run: r:latest analysis/run_calculate_tpp_coverage.R output/input_coverage.csv data/msoa_pop.csv
    needs: [generate_cohort_coverage]
    outputs: 
      moderately_sensitive: 
        log: analysis/logfiles/calculate_tpp_coverage.txt
      highly_sensitive:
        data: data/tpp_msoa_coverage.csv
        
  feasibility_checks: 
    run: r:latest analysis/run_feasibility_checks.R output/input.csv data/tpp_msoa_coverage.csv
    needs: [generate_cohort, calculate_coverage]
    outputs: 
      moderately_sensitive: 
        log: analysis/logfiles/feasibility_checks.txt
        table1a: analysis/outfiles/table1a.txt
        table1b: analysis/outfiles/table1b.txt
        figure1a: analysis/outfiles/figure1a.png
        figure1b: analysis/outfiles/figure1b.png
        figure1c: analysis/outfiles/figure1c.png
        table2: analysis/outfiles/table2.txt
        table3: analysis/outfiles/table3.txt
        figure2: analysis/outfiles/figure2.png
        table4: analysis/outfiles/table4.txt


  run_all:
    needs: [feasibility_checks]
    # In order to be valid this action needs to define a run commmand and some
    # output. We don't really care what these are but the below does the trick.
    # In a future release of the platform, this special action won't need to be
    # defined at all.
    run: cohortextractor:latest --version
    outputs:
      moderately_sensitive:
        whatever: project.yaml