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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
# Study populations
# Extract latests ethnicity record for cohort
generate_study_population_ethnicity:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity
--output-dir=output/indicators
--output-format=feather
outputs:
highly_sensitive:
cohort: output/indicators/input_ethnicity.feather
# Extract cohort for indicator HYP001 by month
generate_study_population_hyp001:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_hyp001
--index-date-range "2019-01-01 to 2022-01-01 by month"
--output-dir=output/indicators
--output-format=feather
outputs:
highly_sensitive:
cohort: output/indicators/input_hyp001_*.feather
# Extract cohort for indicator HYP003 by month
generate_study_population_hyp003:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_hyp003
--index-date-range "2019-01-01 to 2022-01-01 by month"
--output-dir=output/indicators
--output-format=feather
outputs:
highly_sensitive:
cohort: output/indicators/input_hyp003_*.feather
# Extract cohort for indicator HYP007 by month
generate_study_population_hyp007:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_hyp007
--index-date-range "2019-01-01 to 2022-01-01 by month"
--output-dir=output/indicators
--output-format=feather
outputs:
highly_sensitive:
cohort: output/indicators/input_hyp007_*.feather
join_ethnicity:
run: >
cohort-joiner:v0.0.12
--lhs output/indicators/input_hyp*.feather
--rhs output/indicators/input_ethnicity.feather
--output-dir output/indicators/joined
needs: [generate_study_population_ethnicity, generate_study_population_hyp001, generate_study_population_hyp003, generate_study_population_hyp007]
outputs:
highly_sensitive:
cohort: output/indicators/joined/input_hyp*.feather
# Measures
# Generate measures for indicator HYP001 by month
generate_measures_hyp001:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition_hyp001
--output-dir=output/indicators/joined
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/indicators/joined/measure_hyp001_*_rate.csv
# Generate measures for indicator HYP003 by month
generate_measures_hyp003:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition_hyp003
--output-dir=output/indicators/joined
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/indicators/joined/measure_hyp003_*_rate.csv
# Generate measures for indicator HYP007 by month
generate_measures_hyp007:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition_hyp007
--output-dir=output/indicators/joined
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/indicators/joined/measure_hyp007_*_rate.csv
# Join all measure files for each indicator
join_measures:
run: r:latest analysis/join_measures.R
needs: [generate_measures_hyp001]
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_hyp001.csv
# Generate notebooks
generate_hyp_report:
run: r:latest -e 'rmarkdown::render("notebooks/qof-hypertension.Rmd", knit_root_dir = "/workspace", output_dir = "notebooks")'
needs: [join_measures]
outputs:
moderately_sensitive:
report: notebooks/qof-hypertension.html