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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format 'feather'
outputs:
highly_sensitive:
cohort: output/input.feather
generate_report:
run: cohort-report:v3.0.0 output/input.feather
needs: [generate_population]
config:
output_path: output/cohort_reports_outputs
outputs:
moderately_sensitive:
reports: output/cohort_reports_outputs/descriptives_input.html
# note not possible to execute and save notebook in a single action with `--execute --to notebook` because of self-dependency
# still possible to execute and save to html or md file
summary_html:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/data_summary.ipynb --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
needs: [generate_population]
outputs:
moderately_sensitive:
html: output/data_summary.html