generated from opensafely/research-template
/
project.yaml
151 lines (129 loc) · 4.62 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 50000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
data_preparation:
run: stata-mp:latest analysis/data_preparation_and_descriptives.do
needs: [generate_study_population]
outputs:
moderately_sensitive:
log: logs/data_preparation.log
highly_sensitive:
data: output/main.dta
data2: output/sensitivity.dta
cox_regression:
run: stata-mp:latest analysis/cox.do
needs: [data_preparation]
outputs:
moderately_sensitive:
log: logs/cox.log
figure1: output/phtest.svg
figure2: output/phtest_psw.svg
figure3: output/psgraph.svg
multiple_imputation:
run: stata-mp:latest analysis/multiple_imputation.do
needs: [data_preparation]
outputs:
moderately_sensitive:
log: logs/MI.log
data_preparation_molnupiravir:
run: stata-mp:latest analysis/data_preparation_and_descriptives_molnupiravir.do
needs: [generate_study_population]
outputs:
moderately_sensitive:
log: logs/data_preparation_mol.log
highly_sensitive:
data: output/main_mol.dta
cox_regression_molnupiravir:
run: stata-mp:latest analysis/cox_molnupiravir.do
needs: [data_preparation_molnupiravir]
outputs:
moderately_sensitive:
log: logs/cox_mol.log
figure1: output/psgraph_mol.svg
plot:
run: stata-mp:latest analysis/plot.do
needs: [data_preparation, data_preparation_molnupiravir]
outputs:
moderately_sensitive:
log: logs/plot.log
figure1: output/kmcurve.svg
figure2: output/kmcurve_mol.svg
generate_study_population_update:
run: cohortextractor:latest generate_cohort --study-definition study_definition_update
outputs:
highly_sensitive:
cohort: output/input_update.csv
data_preparation_update:
run: stata-mp:latest analysis/data_preparation_and_descriptives_update.do
needs: [generate_study_population_update]
outputs:
moderately_sensitive:
log: logs/data_preparation_update.log
highly_sensitive:
data: output/main_update.dta
data2: output/sensitivity_update.dta
cox_regression_update:
run: stata-mp:latest analysis/cox_update.do
needs: [data_preparation_update]
outputs:
moderately_sensitive:
log: logs/cox_update.log
figure1: output/phtest_update.svg
figure2: output/phtest_psw_update.svg
figure3: output/psgraph_update.svg
multiple_imputation_update:
run: stata-mp:latest analysis/multiple_imputation_update.do
needs: [data_preparation_update]
outputs:
moderately_sensitive:
log: logs/MI_update.log
data_preparation_molnupiravir_update:
run: stata-mp:latest analysis/data_preparation_and_descriptives_molnupiravir_update.do
needs: [generate_study_population_update]
outputs:
moderately_sensitive:
log: logs/data_preparation_mol_update.log
highly_sensitive:
data: output/main_mol_update.dta
cox_regression_molnupiravir_update:
run: stata-mp:latest analysis/cox_molnupiravir_update.do
needs: [data_preparation_molnupiravir_update]
outputs:
moderately_sensitive:
log: logs/cox_mol_update.log
figure1: output/psgraph_mol_update.svg
generate_study_population_raw_rate:
run: cohortextractor:latest generate_cohort --study-definition study_definition_raw_rate
outputs:
highly_sensitive:
cohort: output/input_raw_rate.csv
data_preparation_raw_rate:
run: stata-mp:latest analysis/data_preparation_and_descriptives_raw_rate.do
needs: [generate_study_population_raw_rate]
outputs:
moderately_sensitive:
log: logs/data_preparation_raw_rate.log
table1: output/table.dta
table2: output/table.csv
generate_study_population_feasibility:
run: cohortextractor:latest generate_cohort --study-definition study_definition_feasibility
outputs:
highly_sensitive:
cohort: output/input_feasibility.csv
data_preparation_feasibility:
run: stata-mp:latest analysis/data_preparation_and_descriptives_feasibility.do
needs: [generate_study_population_feasibility]
outputs:
moderately_sensitive:
log: logs/data_preparation_feasibility.log
generate_study_population_feasibility_update:
run: cohortextractor:latest generate_cohort --study-definition study_definition_feasibility_update
outputs:
highly_sensitive:
cohort: output/input_feasibility_update.csv