generated from opensafely/research-template
/
project.yaml
64 lines (56 loc) · 1.98 KB
/
project.yaml
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version: "3.0"
expectations:
population_size: 10000
actions:
generate_cohorts:
run: cohortextractor:latest generate_cohort
outputs:
highly_sensitive:
covid_cohort: output/input_covid.csv
pneumonia_cohort: output/input_pneumonia.csv
ctrl_2019_cohort: output/input_control_2019.csv
ctrl_2020_cohort: output/input_control_2020.csv
000_covid:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
needs: [generate_cohorts]
outputs:
moderately_sensitive:
graph: output/length_of_stay_covid.svg
highly_sensitive:
analysis_dataset: output/cohort_rates_covid.dta
000_pneumonia:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
needs: [generate_cohorts]
outputs:
moderately_sensitive:
graph: output/length_of_stay_pneumonia.svg
highly_sensitive:
analysis_dataset: output/cohort_rates_pneumonia.dta
201_covid:
run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
needs: [000_covid]
outputs:
moderately_sensitive:
graph: output/tabfig/rates_summary_covid.csv
201_pneumonia:
run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
needs: [000_pneumonia]
outputs:
moderately_sensitive:
graph: output/tabfig/rates_summary_pneumonia.csv
matching_control_2019:
run: python:latest python analysis/match_running.py "control_2019"
needs: [generate_cohorts]
outputs:
moderately_sensitive:
matching_report: output/matching_report_control_2019.txt
highly_sensitive:
combined: output/matched_combined_control_2019.csv
matching_control_2020:
run: python:latest python analysis/match_running.py "control_2020"
needs: [generate_cohorts]
outputs:
moderately_sensitive:
matching_report: output/matching_report_control_2020.txt
highly_sensitive:
combined: output/matched_combined_control_2020.csv