generated from opensafely/research-template
/
project.yaml
263 lines (223 loc) · 8.54 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 500000
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
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
multiple_imputation:
run: stata-mp:latest analysis/multiple_imputation.do
needs: [data_preparation]
outputs:
moderately_sensitive:
log: logs/MI.log
generate_study_population_update_codelist:
run: cohortextractor:latest generate_cohort --study-definition study_definition_update_codelist
outputs:
highly_sensitive:
cohort: output/update_codelist/input_update_codelist.csv
data_preparation_update_codelist:
run: stata-mp:latest analysis/data_preparation_and_descriptives_update_codelist.do
needs: [generate_study_population_update_codelist]
outputs:
moderately_sensitive:
log: logs/data_preparation_update_codelist.log
highly_sensitive:
data: output/update_codelist/main_update_codelist.dta
cox_regression_update_codelist:
run: stata-mp:latest analysis/cox_update_codelist.do
needs: [data_preparation_update_codelist]
outputs:
moderately_sensitive:
log: logs/cox_update_codelist.log
figure1: output/update_codelist/phtest.svg
figure2: output/update_codelist/phtest_psw.svg
generate_study_population_BA2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_BA2
outputs:
highly_sensitive:
cohort: output/BA2/input_BA2.csv
data_preparation_BA2:
run: stata-mp:latest analysis/data_preparation_and_descriptives_BA2.do
needs: [generate_study_population_BA2]
outputs:
moderately_sensitive:
log: logs/data_preparation_BA2.log
highly_sensitive:
data: output/BA2/main_BA2.dta
cox_regression_BA2:
run: stata-mp:latest analysis/cox_BA2.do
needs: [data_preparation_BA2]
outputs:
moderately_sensitive:
log: logs/cox_BA2.log
figure1: output/BA2/phtest.svg
figure2: output/BA2/phtest_psw.svg
generate_study_population_ukrr:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ukrr
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukrr.csv
data_preparation_ukrr:
run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr.do
needs: [generate_study_population_ukrr]
outputs:
moderately_sensitive:
log: logs/data_preparation_ukrr.log
highly_sensitive:
data: output/ukrr/main_ukrr.dta
cox_regression_ukrr:
run: stata-mp:latest analysis/cox_ukrr.do
needs: [data_preparation_ukrr]
outputs:
moderately_sensitive:
log: logs/cox_ukrr.log
figure1: output/ukrr/phtest.svg
figure2: output/ukrr/phtest_psw.svg
figure3: output/ukrr/psgraph.svg
multiple_imputation_ukrr:
run: stata-mp:latest analysis/multiple_imputation_ukrr.do
needs: [data_preparation_ukrr]
outputs:
moderately_sensitive:
log: logs/MI_ukrr.log
generate_study_population_ukrr_untreated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ukrr_untreated
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukrr_untreated.csv
data_preparation_ukrr_untreated:
run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr_untreated.do
needs: [generate_study_population_ukrr_untreated, data_preparation_ukrr]
outputs:
moderately_sensitive:
log: logs/data_preparation_ukrr_untreated.log
highly_sensitive:
data1: output/ukrr/ukrr_untreated.dta
data2: output/ukrr/main_ukrr_untreated.dta
cox_regression_ukrr_untreated:
run: stata-mp:latest analysis/cox_ukrr_untreated.do
needs: [data_preparation_ukrr_untreated]
outputs:
moderately_sensitive:
log: logs/cox_ukrr_untreated.log
data_preparation_ukrr_raw_rate:
run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr_raw_rate.do
needs: [generate_study_population_ukrr]
outputs:
moderately_sensitive:
log: logs/data_preparation_ukrr_raw_rate.log
generate_study_population_ukrr_update:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ukrr_update
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukrr_update.csv
data_preparation_ukrr_update:
run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr_update.do
needs: [generate_study_population_ukrr_update]
outputs:
moderately_sensitive:
log: logs/data_preparation_ukrr_update.log
highly_sensitive:
data: output/ukrr/main_ukrr_update.dta
cox_regression_ukrr_update:
run: stata-mp:latest analysis/cox_ukrr_update.do
needs: [data_preparation_ukrr_update]
outputs:
moderately_sensitive:
log: logs/cox_ukrr_update.log
figure1: output/ukrr/phtest_update.svg
figure2: output/ukrr/phtest_psw_update.svg
figure3: output/ukrr/psgraph_update.svg
generate_study_population_anaphylaxis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_anaphylaxis
outputs:
highly_sensitive:
cohort: output/input_anaphylaxis.csv
anaphylaxis:
run: stata-mp:latest analysis/anaphylaxis.do
needs: [generate_study_population_anaphylaxis]
outputs:
moderately_sensitive:
log: logs/anaphylaxis.log
generate_study_population_anaphylaxis_untreated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_anaphylaxis_untreated
outputs:
highly_sensitive:
cohort: output/input_anaphylaxis_untreated.csv
anaphylaxis_untreated:
run: stata-mp:latest analysis/anaphylaxis_untreated.do
needs: [generate_study_population_anaphylaxis_untreated]
outputs:
moderately_sensitive:
log: logs/anaphylaxis_untreated.log
generate_study_population_anaphylaxis_update:
run: cohortextractor:latest generate_cohort --study-definition study_definition_anaphylaxis_update
outputs:
highly_sensitive:
cohort: output/input_anaphylaxis_update.csv
anaphylaxis_update:
run: stata-mp:latest analysis/anaphylaxis_update.do
needs: [generate_study_population_anaphylaxis_update]
outputs:
moderately_sensitive:
log: logs/anaphylaxis_update.log
anaphylaxis_update_R:
run: r:latest analysis/anaphylaxis_update.R
needs: [generate_study_population_anaphylaxis_update]
outputs:
moderately_sensitive:
log: logs/anaphylaxis_update.txt
generate_study_population_anaphylaxis_untreated_update:
run: cohortextractor:latest generate_cohort --study-definition study_definition_anaphylaxis_untreated_update
outputs:
highly_sensitive:
cohort: output/input_anaphylaxis_untreated_update.csv
anaphylaxis_untreated_update:
run: stata-mp:latest analysis/anaphylaxis_untreated_update.do
needs: [generate_study_population_anaphylaxis_untreated_update]
outputs:
moderately_sensitive:
log: logs/anaphylaxis_untreated_update.log
anaphylaxis_untreated_update_R:
run: r:latest analysis/anaphylaxis_untreated_update.r
needs: [generate_study_population_anaphylaxis_untreated_update]
outputs:
moderately_sensitive:
log: logs/anaphylaxis_untreated_update.txt
generate_study_population_feasibility:
run: cohortextractor:latest generate_cohort --study-definition study_definition_feasibility
outputs:
highly_sensitive:
cohort: output/input_feasibility.csv
# Study population for NICE figures 26th February 2024
generate_study_population_nice:
run: cohortextractor:latest generate_cohort --study-definition study_definition_nice
outputs:
highly_sensitive:
cohort: output/input_nice.csv
nice_data:
run: stata-mp:latest analysis/data_preparation_and_descriptives_nice.do
needs: [generate_study_population_nice]
outputs:
moderately_sensitive:
log: logs/data_preparation_nice.log
table: output/nice/mortality_nice.txt