/
project.yaml
66 lines (51 loc) · 2.26 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --index-date-range "2019-03-01 to 2021-03-01 by month" --study-definition study_definition --output-dir=output/inputs
outputs:
highly_sensitive:
cohort: output/inputs/input_*.csv
generate_study_population_control:
run: cohortextractor:latest generate_cohort --index-date-range "2019-03-01 to 2021-03-01 by month" --study-definition study_definition_control --output-dir=output/control
outputs:
highly_sensitive:
cohort: output/control/input_control_*.csv
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/inputs
outputs:
highly_sensitive:
cohort: output/inputs/input_ethnicity.csv
join_ethnicity:
run: python:latest python analysis/join_ethnicity.py
needs: [generate_study_population, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/inputs/input*.csv
join_ethnicity_control:
run: python:latest python analysis/join_ethnicity_control.py
needs: [generate_study_population_control, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/control/input*.csv
# Generate measures
generate_measures_control:
run: cohortextractor:latest generate_measures --study-definition study_definition_control --output-dir=output/control
needs: [join_ethnicity_control]
outputs:
moderately_sensitive:
measure_csv: output/control/measure_control_*.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/inputs
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/inputs/measure_a*.csv
describe:
run: python:latest python analysis/descriptives.py
needs: [generate_measures,join_ethnicity,generate_measures_control]
outputs:
moderately_sensitive:
cohort: output/graphs/*.html
tables: output/descriptives/descriptive_statistics_*.csv