Job request: 16390

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

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


version: '3.0'

expectations:
  population_size: 100000

actions:

# Generate study population and extract baseline characteristics 
  generate_study_pop_baseline:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_baseline
      --index-date-range "2022-09-03" 
      --output-dir=feather 
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_baseline_*.feather

# Generating study population at different index dates 
  # generate_study_pop_index:
  #   run: cohortextractor:latest generate_cohort
  #     --study-definition study_definition_index
  #     --index-date-range "2022-09-03 to 2023-01-28 by week" 
  #     --output-dir=feather 
  #     --output-format=feather
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/input_index_*.feather

# Data processing
  data_process_baseline:
    run: r:latest analysis/processing/data_processing_baseline.R
    needs: [generate_study_pop_baseline]
    outputs:
      highly_sensitive:
        cohort: output/cohort/cohort_*.csv
      moderately_sensitive:
        descriptive: output/descriptive/total_*.csv

# Join 
# join_cohorts:
#     run: >
#       cohort-joiner:v0.0.48
#         --lhs output/input_baseline_*.csv
#         --rhs output/input_index_*.csv
#         --output-dir output/data
#     needs: [generate_study_pop_baseline]
#     outputs:
#       highly_sensitive:
#         cohort: output/data/input_*.csv 

# Cumulative uptake of fourth dose #
  # cumulative_fourth_dose:
  #  run: r:latest analysis/descriptive/cumulative_vax_byage.R
  #  needs: [data_process]
  #  outputs:
  #     moderately_sensitive:
  #       rates_csv: output/cumulative_rates/final_*.csv 
  #       plot: output/cumulative_rates/plot_*.png

# Flu vaccine uptake #
  # flu_vax:
  #  run: r:latest analysis/descriptive/flu_vax_byage.R
  #  needs: [generate_study_pop]
  #  outputs:
  #     moderately_sensitive:
  #       measure_csv: output/cumulative_rates/flu_*.csv
  #       plot: output/cumulative_rates/plot_flu_vax_byage.png

# Discontinuity of demographics
  # demographics:
  #  run: r:latest analysis/descriptive/demographics_byage.R
  #  needs: [generate_study_pop]
  #  outputs:
  #     moderately_sensitive:
  #       measure_csv: output/variables_by_age/demographics_*.csv
  #       plot: output/variables_by_age/plot_*.png

# Outcome plots #
  # covid_outcomes:
  #  run: r:latest analysis/descriptive/covid_outcomes_byage.R
  #  needs: [generate_study_pop]
  #  outputs:
  #     moderately_sensitive:
  #       measure_csv: output/covid_outcomes/covid_*.csv
  #       plot: output/covid_outcomes/plot_outcomes_*.png
  

# ITT analysis #


# IV analysis #