generated from opensafely/research-template
/
project.yaml
69 lines (61 loc) · 1.95 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
# Extract data
# When argument --index-date-range is changed, change has to be made in ./analysis/config.json too
generate_study_population:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition
--skip-existing
--output-format=csv.gz
--index-date-range "2020-03-01 to 2021-12-01 by month"
outputs:
highly_sensitive:
cohort: output/input_*.csv.gz
# Extract ethnicity
generate_study_population_ethnicity:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_ethnicity.csv.gz
# Join data
join_cohorts:
run: >
cohort-joiner:v0.0.7
--lhs output/input_202*.csv.gz
--rhs output/input_ethnicity.csv.gz
--output-dir=output/joined
needs: [generate_study_population, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/joined/input_202*.csv.gz
# Calculate mortality rates (crude + subgroup specific)
calculate_measures:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition
--skip-existing
--output-dir=output/joined
needs: [join_cohorts]
outputs:
moderately_sensitive:
measure: output/joined/measure_*_mortality_rate.csv
# Standardise crude mortality rate
standardise_crude_rates:
run: r:latest analysis/crude_rates_standardise.R
needs: [calculate_measures]
outputs:
moderately_sensitive:
csvs: output/rates/crude_*monthly_std.csv
# Standardise subgroup specific mortality rates
standardise_subgroup_rates:
run: r:latest analysis/subgroups_rates_standardise.R
needs: [calculate_measures]
outputs:
moderately_sensitive:
csvs: output/rates/*_monthly_std.csv