generated from opensafely/research-template
/
project.yaml
131 lines (113 loc) · 4.03 KB
/
project.yaml
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version: "3.0"
expectations:
population_size: 10000
actions:
generate_cohorts:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
crmain:
run: stata-mp:latest analysis/01_eth_cr_analysis_dataset.do
needs: [generate_cohorts]
outputs:
highly_sensitive:
data: output/analysis_dataset.dta
moderately_sensitive:
log: logs/01_eth_cr_analysis_dataset.log
cr_sgss:
run: stata-mp:latest analysis/01b_eth_cr_stset_sgss.do
needs: [crmain]
outputs:
highly_sensitive:
stsettested: output/analysis_dataset_STSET_tested.dta
stsetpositiivetest: output/analysis_dataset_STSET_positivetest.dta
moderately_sensitive:
log: logs/01b_eth_cr_stset_sgss.log
cr_hes_covid:
run: stata-mp:latest analysis/01c_eth_cr_stset_hes.do
needs: [crmain]
outputs:
highly_sensitive:
stsethes: output/analysis_dataset_STSET_hes.dta
stsetonscoviddeath: output/analysis_dataset_STSET_onscoviddeath.dta
moderately_sensitive:
log: logs/01c_eth_cr_stset_hes_covid.log
cr_ons:
run: stata-mp:latest analysis/01d_eth_cr_stset_death.do
needs: [crmain]
outputs:
highly_sensitive:
stsetons_noncoviddeath: output/analysis_dataset_STSET_ons_noncoviddeath.dta
stsetonsdeath: output/analysis_dataset_STSET_onsdeath.dta
moderately_sensitive:
log: logs/01d_eth_cr_stset_death.log
check_eth16:
run: stata-mp:latest analysis/02a_eth_outcomes_checks_eth16.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/02a_outcomes_checks_eth16.log
table: output/table0_outcomes_eth16.txt
check_eth5:
run: stata-mp:latest analysis/02b_eth_outcomes_checks_eth5.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/02b_outcomes_checks_eth5.log
table: output/table0_outcomes_eth5.txt
check_region:
run: stata-mp:latest analysis/05a_eth_region_check.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/05_region_check.log
table: output/table3_region.txt
table1_eth16:
run: stata-mp:latest analysis/03a_eth_table1_descriptives_eth16_nocarehomes.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/03a_eth_table1_eth16_carehomes.log
table: output/table1_eth16.txt
table1_eth5:
run: stata-mp:latest analysis/03b_eth_table1_descriptives_eth5_nocarehomes.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/03b_eth_table1_eth5.log
table: output/table1_eth5.txt
table1_eth5_carehomes:
run: stata-mp:latest analysis/03d_eth_table1_descriptives_eth5_carehomes.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/03d_eth_table1_eth5_carehomes.log
table: output/table1_eth5_carehomes.txt
main_eth16:
run: stata-mp:latest analysis/04a_eth_an_multivariable_eth16_nocarehomes.do
needs: [cr_sgss, cr_hes_covid, cr_ons]
outputs:
moderately_sensitive:
log: logs/04a_eth_an_multivariable_eth16.log
table: output/table2_eth16.txt
estout: output/estout_table2_eth16.txt
graph: output/FP_multivariable_eth16.txt
main_eth5:
run: stata-mp:latest analysis/04b_eth_an_multivariable_eth5_nocarehomes.do
needs: [cr_sgss, cr_hes_covid, cr_ons]
outputs:
moderately_sensitive:
log: logs/04b_eth_an_multivariable_eth5.log
table: output/table2_eth5.txt
estout: output/estout_table2_eth5.txt
graph: output/FP_multivariable_eth5.txt
main_eth5_carehomes:
run: stata-mp:latest analysis/04d_eth_an_multivariable_eth5_carehomes.do
needs: [cr_sgss, cr_hes_covid, cr_ons]
outputs:
moderately_sensitive:
log: logs/04d_eth_an_multivariable_eth5_carehomes.log
table: output/table2_eth5_carehomes.txt
estout: output/estout_table2_eth5_carehomes.txt
graph: output/FP_multivariable_eth5_carehomes.txt