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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_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
generate_study_population_prim_cov:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prim_cov
outputs:
highly_sensitive:
cohort: output/input_prim_cov.csv
generate_results:
run: jupyter:latest jupyter nbconvert /workspace/analysis/generate_results.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_study_population, generate_study_population_prim_cov]
outputs:
moderately_sensitive:
notebook: output/generate_results.html
tables: output/summary_tabl*.csv
id_tables: output/identification_table_*.csv
cm: output/cm_*.jpeg