generated from opensafely/research-template
/
project.yaml
46 lines (38 loc) · 1.28 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 30000
actions:
### study cohort ###
generate_study_population_case:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case
outputs:
highly_sensitive:
cohort: output/input_case.csv
generate_study_population_control:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control
outputs:
highly_sensitive:
cohort: output/input_control.csv
### extract patient_id & index_date in case ###
process_1:
run: r:latest analysis/process_1.R
needs: [generate_study_population_case,generate_study_population_control]
outputs:
moderately_sensitive:
table1: output/table_case_0.csv
table2: output/table_case_1.csv
table3: output/table_control_0.csv
table4: output/table_control_1.csv
highly_sensitive:
case_csv: output/case_csv.csv
match_csv: output/match_csv.csv
matching_1:
run: python:latest python analysis/matching.py
needs: [process_1]
outputs:
highly_sensitive:
table1: output/matched_cases.csv
table2: output/matched_matches.csv
table3: output/matched_combined.csv
moderately_sensitive:
report1: output/matching_report.txt