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project.yaml
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project.yaml
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version: "3.0"
expectations:
population_size: 10000
actions:
generate_study_population_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-01-01 to 2019-12-01 by month" --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input*.feather
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-01 to 2022-06-01 by month" --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_*.feather
generate_study_population_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2022-07-01 to 2023-06-01 by month" --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/inp*.feather
generate_dose:
run: python:latest python analysis/calculate_dose_scaled_back.py
needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3]
outputs:
highly_sensitive:
cohort: output/inpu*.feather
filter_population:
run: python:latest python analysis/filter_population.py
needs: [generate_dose]
outputs:
highly_sensitive:
cohort: output/filtered/input*.feather
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/filtered
needs: [filter_population]
outputs:
moderately_sensitive:
measure_csv: output/filtered/measure_*_rate.csv
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/report.ipynb --execute --to html --template basic --output-dir=/workspace/output/filtered --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_measures]
outputs:
moderately_sensitive:
notebook: output/filtered/report.html
plots: output/filtered/*.png
tables: output/filtered/*.csv