generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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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: 10000
actions:
generate_study_pop:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_fourth
--output-format=feather
outputs:
highly_sensitive:
cohort: output/input_fourth.feather
cumulative_fourth_dose:
run: r:latest analysis/descriptive/cumulative_vax_byage.R
needs: [generate_study_pop]
outputs:
moderately_sensitive:
measure_csv: output/cumulative_rates/final_*.csv
plot: output/cumulative_rates/plot_*.png
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
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
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