generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 50000
actions:
generate_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
crMAIN:
run: stata-mp:latest analysis/cr_analysis_dataset.do
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: logs/cr_analysis_dataset.log
highly_sensitive:
data: output/cr_analysis_dataset.dta
crNEW:
run: stata-mp:latest analysis/cr_analysis_new.do
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: logs/cr_analysis_new.log
highly_sensitive:
data: output/cr_analysis_new.dta
crIMP:
run: stata-mp:latest analysis/cr_imputed_dataset.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/cr_imputed.log
highly_sensitive:
data: output/cr_imputed_dataset.dta
anSUMM:
run: stata-mp:latest analysis/an_summary.do
needs: [crNEW]
outputs:
moderately_sensitive:
log: logs/an_summary.log
#figure1: output/sgtf_perc_region.svg
#figure2: output/sgtf_perc_region.pdf
anRISK_TAB1:
run: stata-mp:latest analysis/an_risk28_table1.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_risk28_table1.log
table1text: output/table1_risk28.txt
table1xlsx: output/table1_risk28.xlsx
anCOX_TAB1:
run: stata-mp:latest analysis/an_cox_table1.do
needs: [crNEW]
outputs:
moderately_sensitive:
log: logs/an_cox_table1.log
table1text: output/table1_cox.txt
table1xlsx: output/table1_cox.xlsx
figure1: output/time_death_hist.svg
figure2: output/time_date_death_hist.svg
figure3: output/time_date_death_hist1.svg
figure4: output/hosp_hist.svg
figure5: output/hosp_kden.svg
figure6: output/icu_hist.svg
anHOSP_TAB1:
run: stata-mp:latest analysis/an_hosp_table1.do
needs: [crNEW]
outputs:
moderately_sensitive:
log: logs/an_hosp_table1.log
table1text: output/table1_hosp.txt
table1xlsx: output/table1_hosp.xlsx
figure1: output/time_death_hosp.svg
anCOX_STAB1:
run: stata-mp:latest analysis/an_cox_stable1.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_cox_stable1.log
table1text: output/stable1_cox.txt
table1xlsx: output/stable1_cox.xlsx
table2text: output/stable1_cox_short.txt
table2xlsx: output/stable1_cox_short.xlsx
# anRISK_MOD:
# run: stata-mp:latest analysis/an_risk_models.do
# needs: [crMAIN]
# outputs:
# moderately_sensitive:
# log: logs/an_risk_models.log
anODDS_MOD:
run: stata-mp:latest analysis/an_logit_models.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_logit_models.log
table1text: output/table3_abs_risk.txt
table1xlsx: output/table3_abs_risk.xlsx
anODDS_MOD40:
run: stata-mp:latest analysis/an_logit_models_40.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_logit_models_40.log
table1text: output/table3_abs_risk40.txt
table1xlsx: output/table3_abs_risk40.xlsx
anCOX_MOD:
run: stata-mp:latest analysis/an_cox_models.do
needs: [crNEW]
outputs:
moderately_sensitive:
log: logs/an_cox_models.log
figure1: output/cox_shoen.svg
figure2: output/cox_km.svg
figure3: output/cox_cumhaz.svg
figure4: output/cox_haz.svg
table1text: output/table2_hr.txt
table1xlsx: output/table2_hr.xlsx
anCOX_HOSP:
run: stata-mp:latest analysis/an_cox_hosp.do
needs: [crNEW]
outputs:
moderately_sensitive:
log: logs/an_cox_hosp.log
figure1: output/cox_shoen_hosp.svg
#figure2: output/cox_km.svg
#figure3: output/cox_cumhaz.svg
figure2: output/cox_haz_hosp.svg
table1text: output/table2_hr_hosp.txt
table1xlsx: output/table2_hr_hosp.xlsx
anCOX_DHOSP:
run: stata-mp:latest analysis/an_cox_deathhosp.do
needs: [crNEW]
outputs:
moderately_sensitive:
log: logs/an_cox_deathhosp.log
figure1: output/cox_shoen_deathhosp.svg
#figure2: output/cox_km.svg
#figure3: output/cox_cumhaz.svg
figure2: output/cox_haz_deathhosp.svg
table1text: output/table2_hr_deathhosp.txt
table1xlsx: output/table2_hr_deathhosp.xlsx
anCOX_SENS:
run: stata-mp:latest analysis/an_cox_models_sgtf_sens.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_cox_models_sgtf_sens.log
anCOX_IMP:
run: stata-mp:latest analysis/an_cox_imputed.do
needs: [crIMP]
outputs:
moderately_sensitive:
log: logs/an_cox_imputed.log
highly_sensitive:
data2: output/an_imputed_eth2.ster