generated from opensafely/research-template
/
project.yaml
138 lines (120 loc) · 4.54 KB
/
project.yaml
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version: "3.0"
expectations:
population_size: 20000
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
generate_measure_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-01-01 to 2020-12-01 by month"
outputs:
highly_sensitive:
measure_data: output/input_measures*.csv
generate_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: [generate_measures]
outputs:
moderately_sensitive:
graph: output/event_count_time_series.svg
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
matching_data_management:
run: stata-mp:latest analysis/300_cr_data_management_matching.do
needs: [generate_cohorts, matching_control_2019, matching_control_2020]
outputs:
highly_sensitive:
combined3: output/matched_combined_pneumonia.dta
combined4: output/matched_combined_control_2019.dta
combined5: output/matched_combined_control_2020.dta
301_pneumonia:
run: stata-mp:latest analysis/301_cr_define_covariates_matched_groups.do "pneumonia"
needs: [matching_data_management]
outputs:
highly_sensitive:
combined1: output/matched_cohort_pneumonia.dta
301_control_2019:
run: stata-mp:latest analysis/301_cr_define_covariates_matched_groups.do "control_2019"
needs: [matching_data_management]
outputs:
highly_sensitive:
combined1: output/matched_cohort_control_2019.dta
301_control_2020:
run: stata-mp:latest analysis/301_cr_define_covariates_matched_groups.do "control_2020"
needs: [matching_data_management]
outputs:
highly_sensitive:
combined1: output/matched_cohort_control_2020.dta
302_pneumonia:
run: stata-mp:latest analysis/302_cox_models.do "pneumonia"
needs: [301_pneumonia]
outputs:
moderately_sensitive:
log: output/cox_model_pneumonia.log
combined1: output/tabfig/cox_model_summary_pneumonia.csv
302_control_2019:
run: stata-mp:latest analysis/302_cox_models.do "control_2019"
needs: [301_control_2019]
outputs:
moderately_sensitive:
log: output/cox_model_control_2019.log
combined1: output/tabfig/cox_model_summary_control_2019.csv
302_control_2020:
run: stata-mp:latest analysis/302_cox_models.do "control_2020"
needs: [301_control_2020]
outputs:
moderately_sensitive:
log: output/cox_model_control_2020.log
combined1: output/tabfig/cox_model_summary_control_2020.csv