generated from opensafely/research-template
/
project.yaml
33 lines (27 loc) · 1.07 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-06-01 by month"
outputs:
highly_sensitive:
cohort: output/input_*.csv
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measure_*.csv
describe:
run: python:latest python analysis/report.py
needs: [generate_study_population, calculate_measures]
outputs:
moderately_sensitive:
cohort: output/descriptive_*.png
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/hba1c_levels.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [calculate_measures]
outputs:
moderately_sensitive:
notebook: output/hba1c_levels.html