generated from opensafely/research-template
/
project.yaml
376 lines (324 loc) · 12.7 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 50000
actions:
generate_cohort1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01"
outputs:
highly_sensitive:
cohort: output/input_2020-03-01.csv
generate_cohort2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-09-01"
outputs:
highly_sensitive:
cohort: output/input_2020-09-01.csv
clean:
run: stata-mp:latest analysis/001_clean_input_data.do
needs: [generate_cohort1, generate_cohort2]
outputs:
highly_sensitive:
clean1: analysis/data_base_cohort1.dta
clean2: analysis/data_base_cohort2.dta
create_analysis:
run: stata-mp:latest analysis/002_create_ld_analysis_dataset.do
needs: [clean]
outputs:
highly_sensitive:
an_data1: analysis/data_ldanalysis_cohort1.dta
an_data2: analysis/data_ldanalysis_cohort2.dta
create_analysis_ar:
run: stata-mp:latest analysis/003_create_ar_analysis_dataset.do
needs: [clean]
outputs:
highly_sensitive:
an_data1: analysis/data_aranalysis_cohort1.dta
an_data2: analysis/data_aranalysis_cohort2.dta
describe_cohort:
run: stata-mp:latest analysis/AL001_describe_cohort.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL001_describe_cohort.log
tabulate_cohort:
run: stata-mp:latest analysis/AL002_tabulate_cohort_descriptives.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL002_tabulate_cohort_descriptives.log
model: output/basetable1.txt
cox_regression_child:
run: stata-mp:latest analysis/AL005_cox_regression_child.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL005_cox_regression_child.log
hrs_child: output/output_hrs_main_child.out
rates_child: output/output_rates_child.out
cumulative_incidence:
run: stata-mp:latest analysis/AL003_cumulative_incidence.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL003_cumulative_incidence.log
graph1: output/cumincidence_coviddeath.svg
graph2: output/cumincidence_composite.svg
cox_lda1:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission ldr
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_covidadmission_ldr.log
hrs: output/ldcox_wave1_covidadmission_ldr.out
cox_lda2:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission ldr
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_covidadmission_ldr.log
hrs: output/ldcox_wave2_covidadmission_ldr.out
cox_lda3:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission ldr_cat
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_covidadmission_ldr_cat.log
hrs: output/ldcox_wave1_covidadmission_ldr_cat.out
cox_lda4:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission ldr_cat
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_covidadmission_ldr_cat.log
hrs: output/ldcox_wave2_covidadmission_ldr_cat.out
cox_lda5:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission ldr_carecat
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_covidadmission_ldr_carecat.log
hrs: output/ldcox_wave1_covidadmission_ldr_carecat.out
cox_lda6:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission ldr_carecat
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_covidadmission_ldr_carecat.log
hrs: output/ldcox_wave2_covidadmission_ldr_carecat.out
cox_lda7:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission ds
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_covidadmission_ds.log
hrs: output/ldcox_wave1_covidadmission_ds.out
cox_lda8:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission ds
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_covidadmission_ds.log
hrs: output/ldcox_wave2_covidadmission_ds.out
cox_lda9:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission cp
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_covidadmission_cp.log
hrs: output/ldcox_wave1_covidadmission_cp.out
cox_lda10:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission cp
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_covidadmission_cp.log
hrs: output/ldcox_wave2_covidadmission_cp.out
cox_lda11:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission ldr_group
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_covidadmission_ldr_group.log
hrs: output/ldcox_wave1_covidadmission_ldr_group.out
cox_lda12:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission ldr_group
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_covidadmission_ldr_group.log
hrs: output/ldcox_wave2_covidadmission_ldr_group.out
cox_ldd1:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath ldr
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_coviddeath_ldr.log
hrs: output/ldcox_wave1_coviddeath_ldr.out
cox_ldd2:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath ldr
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_coviddeath_ldr.log
hrs: output/ldcox_wave2_coviddeath_ldr.out
cox_ldd3:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath ldr_cat
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_coviddeath_ldr_cat.log
hrs: output/ldcox_wave1_coviddeath_ldr_cat.out
cox_ldd4:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath ldr_cat
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_coviddeath_ldr_cat.log
hrs: output/ldcox_wave2_coviddeath_ldr_cat.out
cox_ldd5:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath ldr_carecat
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_coviddeath_ldr_carecat.log
hrs: output/ldcox_wave1_coviddeath_ldr_carecat.out
cox_ldd6:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath ldr_carecat
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_coviddeath_ldr_carecat.log
hrs: output/ldcox_wave2_coviddeath_ldr_carecat.out
cox_ldd7:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath ds
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_coviddeath_ds.log
hrs: output/ldcox_wave1_coviddeath_ds.out
cox_ldd8:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath ds
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_coviddeath_ds.log
hrs: output/ldcox_wave2_coviddeath_ds.out
cox_ldd9:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath cp
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_coviddeath_cp.log
hrs: output/ldcox_wave1_coviddeath_cp.out
cox_ldd10:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath cp
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_coviddeath_cp.log
hrs: output/ldcox_wave2_coviddeath_cp.out
cox_ldd11:
run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath ldr_group
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave1_coviddeath_ldr_group.log
hrs: output/ldcox_wave1_coviddeath_ldr_group.out
cox_ldd12:
run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath ldr_group
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression_wave2_coviddeath_ldr_group.log
hrs: output/ldcox_wave2_coviddeath_ldr_group.out
cox_ar1:
run: stata-mp:latest analysis/AAR001_cox_regression.do 1 covidadmission
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR001_cox_regression_wave1_covidadmission.log
hrs: output/hr_wave1_male*_covidadmission.txt
cox_ar2:
run: stata-mp:latest analysis/AAR001_cox_regression.do 2 covidadmission
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR001_cox_regression_wave2_covidadmission.log
hrs: output/hr_wave2_male*_covidadmission.txt
cox_ar3:
run: stata-mp:latest analysis/AAR001_cox_regression.do 1 coviddeath
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR001_cox_regression_wave1_coviddeath.log
hrs: output/hr_wave1_male*_coviddeath.txt
cox_ar4:
run: stata-mp:latest analysis/AAR001_cox_regression.do 2 coviddeath
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR001_cox_regression_wave2_coviddeath.log
hrs: output/hr_wave2_male*_coviddeath.txt
ar_1:
run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 0 covidadmission
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_risk_by_age_wave1_male0_covidadmission.log
absrisk: output/ar_wave1_male0_covidadmission.out
graph: output/ar_wave1_male0_covidadmission.svg
ar_2:
run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 1 covidadmission
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_risk_by_age_wave1_male1_covidadmission.log
absrisk: output/ar_wave1_male1_covidadmission.out
graph: output/ar_wave1_male1_covidadmission.svg
ar_3:
run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 0 covidadmission
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_risk_by_age_wave2_male0_covidadmission.log
absrisk: output/ar_wave2_male0_covidadmission.out
graph: output/ar_wave2_male0_covidadmission.svg
ar_4:
run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 1 covidadmission
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_risk_by_age_wave2_male1_covidadmission.log
absrisk: output/ar_wave2_male1_covidadmission.out
graph: output/ar_wave2_male1_covidadmission.svg
ar_5:
run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 0 coviddeath
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_risk_by_age_wave1_male0_coviddeath.log
absrisk: output/ar_wave1_male0_coviddeath.out
graph: output/ar_wave1_male0_coviddeath.svg
ar_6:
run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 1 coviddeath
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_risk_by_age_wave1_male1_coviddeath.log
absrisk: output/ar_wave1_male1_coviddeath.out
graph: output/ar_wave1_male1_coviddeath.svg
ar_7:
run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 0 coviddeath
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_risk_by_age_wave2_male0_coviddeath.log
absrisk: output/ar_wave2_male0_coviddeath.out
graph: output/ar_wave2_male0_coviddeath.svg
ar_8:
run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 1 coviddeath
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_risk_by_age_wave2_male1_coviddeath.log
absrisk: output/ar_wave2_male1_coviddeath.out
graph: output/ar_wave2_male1_coviddeath.svg