generated from opensafely/research-template
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project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 5000
actions:
# extract relevant cohorts
generate_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sccs_and_historical_cohort
outputs:
highly_sensitive:
cohort: output/input_sccs_and_historical_cohort.csv
apply_exclusion_criteria:
run: stata-mp:latest analysis/apply_exclusion_criteria.do
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: output/logs/apply_exclusion_criteria.log
highly_sensitive:
cohort_controls: output/input_historical_controls.csv
cohort_az_cases: output/input_AZ_cases.csv
cohort_pfizer_cases: output/input_PF_cases.csv
cohort_moderna_cases: output/input_MOD_cases.csv
# main analyses
SCCS_first_dose_only_primary_AZ:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do AZ
needs: [apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_AZ.log
results: output/tables/results_summary_primary_AZ*
highly_sensitive:
sccs_pop_BP: output/temp_data/sccs_popn_BP_AZ*
sccs_pop_TM: output/temp_data/sccs_popn_TM_AZ*
sccs_pop_GBS: output/temp_data/sccs_popn_GBS_AZ*
sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_AZ*
sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_AZ*
sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_AZ*
SCCS_first_dose_only_primary_PF:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do PF
needs: [apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_PF.log
results: output/tables/results_summary_primary_PF*
highly_sensitive:
sccs_pop_BP: output/temp_data/sccs_popn_BP_PF*
sccs_pop_TM: output/temp_data/sccs_popn_TM_PF*
sccs_pop_GBS: output/temp_data/sccs_popn_GBS_PF*
sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_PF*
sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_PF*
sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_PF*
SCCS_first_dose_only_primary_MOD:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do MOD
needs: [apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_MOD.log
results: output/tables/results_summary_primary_MOD*
highly_sensitive:
sccs_pop_BP: output/temp_data/sccs_popn_BP_MOD*
sccs_pop_TM: output/temp_data/sccs_popn_TM_MOD*
sccs_pop_GBS: output/temp_data/sccs_popn_GBS_MOD*
sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_MOD*
sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_MOD*
sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_MOD*
# baseline tables (AZ and PF only due to small MOD numbers)
SCCS_baseline_tables_AZ:
run: stata-mp:latest analysis/SCCS_baseline_tables.do AZ
needs: [SCCS_first_dose_only_primary_AZ]
outputs:
moderately_sensitive:
log: output/logs/SCCS_baseline_tables_AZ.log
tables: output/tables/baseline_AZ/*
SCCS_baseline_tables_PF:
run: stata-mp:latest analysis/SCCS_baseline_tables.do PF
needs: [SCCS_first_dose_only_primary_PF]
outputs:
moderately_sensitive:
log: output/logs/SCCS_baseline_tables_PF.log
tables: output/tables/baseline_PF/*
# check assumptions
SCCS_assumption_checking_AZ:
run: stata-mp:latest analysis/SCCS_assumption_checking.do AZ
needs: [SCCS_first_dose_only_primary_AZ]
outputs:
moderately_sensitive:
log: output/logs/SCCS_assumption_checking_AZ.log
plots_S1: output/plots/S1_exposure_centered_interval_AZ*
plots_S2: output/plots/S2_censored_futime_AZ*
SCCS_assumption_checking_PF:
run: stata-mp:latest analysis/SCCS_assumption_checking.do PF
needs: [SCCS_first_dose_only_primary_PF]
outputs:
moderately_sensitive:
log: output/logs/SCCS_assumption_checking_PF.log
plots_S1: output/plots/S1_exposure_centered_interval_PF*
plots_S2: output/plots/S2_censored_futime_PF*
# sensitivity analyses
## stratified analyses
SCCS_stratified_analyses_AZ:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_stratified.do AZ
needs: [SCCS_first_dose_only_primary_AZ]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_stratified_AZ.log
results: output/tables/results_summary_stratified_AZ.csv
SCCS_stratified_analyses_PF:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_stratified.do PF
needs: [SCCS_first_dose_only_primary_PF]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_stratified_PF.log
results: output/tables/results_summary_stratified_PF.csv
## changing risk windows
SCCS_vary_risk_windows_AZ:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_risk.do AZ
needs: [SCCS_first_dose_only_primary_AZ]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_risk_AZ.log
results: output/tables/results_summary_sens_risk_AZ.csv
SCCS_vary_risk_windows_PF:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_risk.do PF
needs: [SCCS_first_dose_only_primary_PF]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_risk_PF.log
results: output/tables/results_summary_sens_risk_PF.csv
## second doses
SCCS_second_dose_AZ:
run: stata-mp:latest analysis/SCCS_first_second_dose_analyses_neuro.do AZ
needs: [SCCS_first_dose_only_primary_AZ, apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_second_dose_analyses_neuro_AZ.log
results: output/tables/results_summary_second_doses_AZ.csv
SCCS_second_dose_PF:
run: stata-mp:latest analysis/SCCS_first_second_dose_analyses_neuro.do PF
needs: [SCCS_first_dose_only_primary_PF, apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_second_dose_analyses_neuro_PF.log
results: output/tables/results_summary_second_doses_PF*
## AZ vs Pfizer
SCCS_comparative_AZ_Pfizer:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_sens_AZ_vs_PF.do
needs: [SCCS_first_dose_only_primary_AZ, SCCS_first_dose_only_primary_PF]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_sens_AZ_vs_PF.log
results: output/tables/results_summary_sens_AZ_vs_PF.csv