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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:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
cohort_checks:
run: python:latest python analysis/cohort_checks.py
needs: [generate_study_population]
outputs:
moderately_sensitive:
cohort: output/cohort_checks.csv
transform:
run: python:latest python analysis/transform.py output/input.csv
needs: [generate_study_population]
outputs:
highly_sensitive:
cohort: output/cohort.pickle
count_prevalences:
run: python:latest python analysis/count_prevalences.py
needs: [transform]
outputs:
moderately_sensitive:
table: output/*/tables/prevalences.csv
compute_uptake_for_paper:
run: python:latest python analysis/compute_uptake_for_paper.py
needs: [transform]
outputs:
moderately_sensitive:
cohort: output/*/cumulative_coverage/*/*/*.csv
generate_outputs:
run: python:latest python analysis/generate_all_charts_and_tables.py
needs: [transform, compute_uptake_for_paper]
outputs:
moderately_sensitive:
charts: output/*/charts/*.png
reports: output/*/reports/*.html
tables: output/*/tables/*.csv