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project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
## Descriptive info on vaccinated patients
extract_vaccinated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
outputs:
highly_sensitive:
cohort: output/input_vaccinated.csv
data_process_vaccinated:
run: r:latest analysis/R/data_process_vaccinated.R
needs: [extract_vaccinated]
outputs:
highly_sensitive:
cohort: output/data/data_vaccinated.rds
vaxdates: output/data/data_vaccinated_vax_dates.rds
data_properties_vaccinated:
run: r:latest analysis/R/data_properties.R output/data/data_vaccinated.rds output/data_properties
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
summary: output/data_properties/data_vaccinated*.txt
data_summarise_vaccinated:
run: r:latest analysis/R/data_summarise.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
summary1: output/variable_summary/categorical.txt
summary2: output/variable_summary/numeric.txt
summary3: output/variable_summary/date.txt
summarytables: output/variable_summary/tables/categorical_*.csv
summarystats: output/summary_stats.json
vaccine_tables:
run: r:latest analysis/R/vaccine_type.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
tables: output/vaccine_type/tables/vaccine_type_*.csv
tte_tables:
run: r:latest analysis/R/tte_tables.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
tables: output/tte/tables/event_rates_*.csv
tte_plots:
run: r:latest analysis/R/tte_plots.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
plots: output/tte/figures/plot_*.svg