generated from opensafely/research-template
/
project.yaml
58 lines (46 loc) · 1.81 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 5000
actions:
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
00_apply_exclusion_criteria:
run: stata-mp:latest analysis/00_apply_exclusion_criteria.do
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: output/logs/00_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_pfizer_cases.csv
cohort_moderna_cases: output/input_moderna_cases.csv
SCCS_first_dose_only_analyses_neuro:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro.do
needs: [00_apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses.log
results: output/tables/results_summary.csv
highly_sensitive:
sccs_pop_BP: output/temp_data/sccs_popn_BP.dta
sccs_pop_TM: output/temp_data/sccs_popn_TM.dta
sccs_pop_GBS: output/temp_data/sccs_popn_GBS.dta
SCCS_baseline_tables:
run: stata-mp:latest analysis/SCCS_baseline_tables.do
needs: [SCCS_first_dose_only_analyses_neuro]
outputs:
moderately_sensitive:
log: output/logs/SCCS_baseline_tables.log
tables: output/tables/table1*
SCCS_assumption_checking:
run: stata-mp:latest analysis/SCCS_assumption_checking.do
needs: [SCCS_first_dose_only_analyses_neuro]
outputs:
moderately_sensitive:
log: output/logs/SCCS_assumption_checking.log
plots_S1: output/plots/S1*
plots_S2: output/plots/S2*