generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
# Asthma indicator (AST007) actions
generate_study_population_ast007:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ast007 --index-date-range "2022-01-01 to 2022-03-31 by month" --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_ast007*.csv
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_ethnicity.csv
join_ethnicity_ast_reg:
run: >
cohort-joiner:v0.0.12
--lhs output/input_ast007*.csv
--rhs output/input_ethnicity*.csv
--output-dir output/joined
needs: [generate_study_population_ethnicity, generate_study_population_ast007]
outputs:
highly_sensitive:
cohort: output/joined/input_ast007*.csv
generate_measures_ast007:
run: cohortextractor:latest generate_measures
--study-definition study_definition_ast007
--output-dir=output/joined
needs: [generate_study_population_ast007, generate_study_population_ethnicity, join_ethnicity_ast_reg]
outputs:
moderately_sensitive:
measure_csv: output/joined/measure_*_rate.csv
calculate_rates_ast007:
run: python:latest python analysis/rate_calculations_ast007.py
needs: [join_ethnicity_ast_reg, generate_measures_ast007]
outputs:
moderately_sensitive:
tables: output/rate_table_*.csv
plots: output/plot_*.png
decile_chart: output/decile_chart.png
# generate_notebook_ast007:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/qof_notebook_ast007.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [calculate_rates_ast007]
# outputs:
# moderately_sensitive:
# notebook: output/qof_notebook_ast007.html
# Testing Asthma variables
generate_study_population_ast007_test_variables:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ast007_test_variables
--index-date-range "2022-01-01 to 2022-03-31 by month"
--output-dir=output/test
outputs:
highly_sensitive:
cohort: output/test/input_ast007_test*.csv
generate_measures_ast007_test:
run: cohortextractor:latest generate_measures
--study-definition study_definition_ast007_test_variables
--output-dir=output/test
needs: [generate_study_population_ast007_test_variables]
outputs:
moderately_sensitive:
measure_csv: output/test/measure_*_rate.csv
# Check with separate analysis script
# check_data:
# run: r:latest analysis/indicator_dates_testing.py
# outputs:
# moderately_sensitive:
# table_csv: output/test/test.csv