generated from opensafely/research-template
/
project.yaml
111 lines (93 loc) · 3.54 KB
/
project.yaml
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version: "3.0"
expectations:
population_size: 20000
actions:
generate_covid_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid
outputs:
highly_sensitive:
cohort: output/input_covid.csv
generate_covid_community_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_community
outputs:
highly_sensitive:
cohort: output/input_covid_community.csv
generate_pneumonia_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia
outputs:
highly_sensitive:
cohort: output/input_pneumonia.csv
generate_measure_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-02-01 to 2020-10-01 by month"
outputs:
highly_sensitive:
measure_data: output/input_measures*.csv
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_measures
needs: [generate_measure_cohort]
outputs:
moderately_sensitive:
measure: output/measure_*_rate.csv
draw_timeseries:
run: python:latest python analysis/time_series_plots.py
needs: [calculate_measures]
outputs:
moderately_sensitive:
graph: output/event_count_time_series.svg
covid_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
needs: [generate_covid_cohort]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_covid.dta
covid_community_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid_community"
needs: [generate_covid_community_cohort]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_covid_community.dta
pneumonia_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
needs: [generate_pneumonia_cohort]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_pneumonia.dta
covid_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
needs: [covid_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid.csv
covid_comm_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "covid_community"
needs: [covid_community_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid_community.csv
pneumonia_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
needs: [pneumonia_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_pneumonia.csv
baseline_characteristics:
run: stata-mp:latest analysis/400_baseline_characteristics.do
needs: [covid_rates_cohort, covid_community_rates_cohort, pneumonia_rates_cohort]
outputs:
moderately_sensitive:
tables: output/tabfig/an_descriptiveTable_*.txt
append_cohorts:
run: stata-mp:latest analysis/300_cr_data_management_matching.do
needs: [covid_rates_cohort, pneumonia_rates_cohort]
outputs:
moderately_sensitive:
log: output/append_cohorts.txt
highly_sensitive:
dataset: output/combined_covid_pneumonia.dta
cox_models:
run: stata-mp:latest analysis/302_cox_models.do
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cox_models.txt
dataset: output/tabfig/cox_model_summary.csv