generated from opensafely/research-template
/
project.yaml
129 lines (113 loc) · 6.65 KB
/
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 --output-format feather
outputs:
highly_sensitive:
cohort: output/input.feather
generate_flow_chart_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart --output-format feather
outputs:
highly_sensitive:
cohort: output/input_flow_chart.feather
generate_study_population_measures:
run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_measures --output-format feather --index-date-range "2019-03-01 to 2021-02-01 by month" --skip-existing --output-dir=output/practice_measures
outputs:
highly_sensitive:
cohort: output/practice_measures/input_*.feather
generate_practice_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_practice_measures --skip-existing --output-dir=output/practice_measures
needs: [generate_study_population_measures]
outputs:
moderately_sensitive:
measure_binary_csv: output/practice_measures/measure_*_binary.csv
measure_csv: output/practice_measures/measure_*_rate.csv
generate_report:
run: cohort-report:v3.0.0 output/input.feather
needs: [generate_study_population]
config:
output_path: output/cohort_reports_outputs
outputs:
moderately_sensitive:
report: output/cohort_reports_outputs/descriptives_input.html
report_charts: output/cohort_reports_outputs/*.png
flow_chart:
run: r:latest analysis/00_flow_chart_data.R
needs: [generate_flow_chart_population]
outputs:
moderately_sensitive:
flow_data: output/flow_chart_data/flow_chart_data.csv
describe_cohorts:
run: r:latest analysis/01_describe_cohorts.R
needs: [generate_study_population]
outputs:
moderately_sensitive:
deaths_data: output/describe_cohorts/overall_death_counts/deaths_data.csv
deaths_cohort: output/describe_cohorts/overall_death_counts/deaths_cohort.csv
deaths_quarter: output/describe_cohorts/overall_death_counts/deaths_quarter.csv
deaths_quarter_figure: output/describe_cohorts/overall_death_counts/deaths_quarter.png
deaths_data_pod: output/describe_cohorts/overall_death_counts/deaths_data_pod.csv
deaths_cohort_pod: output/describe_cohorts/overall_death_counts/deaths_cohort_pod*.csv
deaths_quarter_pod: output/describe_cohorts/overall_death_counts/deaths_quarter_pod.csv
deaths_pod_figures: output/describe_cohorts/overall_death_counts/deaths_pod_cohort*.png
deaths_quarter_characteristic: output/describe_cohorts/quarter_death_counts/deaths_quarter_*.csv
quarter_summary_table: output/describe_cohorts/quarter_summary_table.csv
quarter_pod_summary_table: output/describe_cohorts/quarter_pod_summary_table.csv
deaths_quarter_ons: output/describe_cohorts/ons_death_comparisons/deaths_ons_quarter*.csv
deaths_month_ons: output/describe_cohorts/ons_death_comparisons/deaths_ons_month*.csv
deaths_ons_plots: output/describe_cohorts/ons_death_comparisons/deaths_ons*.png
cohort_summary_table: output/describe_cohorts/cohorts_summary_table.csv
cohort_pod_summary_table: output/describe_cohorts/cohorts_pod_summary_table*.csv
death_ratios_cohort: output/describe_cohorts/death_ratios_cohort/death_ratio_cohort*.csv
death_ratios_pod_cohort: output/describe_cohorts/death_ratios_pod_cohort/death_ratio_pod_cohort*.csv
deaths_region_ethnicity: output/describe_cohorts/overall_death_counts/deaths_region*.csv
describe_service_use:
run: r:latest analysis/02_describe_service_use.R
needs: [generate_study_population]
outputs:
moderately_sensitive:
service_use_means: output/describe_service_use/service_use_mean*.csv
service_use_means_plots: output/describe_service_use/plots/service_use_mean*.pdf
gp_complete_service_use_means: output/describe_service_use/complete_gp_history/gp_service_use_mean*.csv
gp_complete_service_use_plots: output/describe_service_use/complete_gp_history/plots/gp_service_use_mean*.pdf
describe_service_use_home_cohort:
run: r:latest analysis/03_describe_service_use_home_cohort.R
needs: [generate_study_population]
outputs:
moderately_sensitive:
service_use_cohort: output/describe_service_use_home/service_use_cohort_home*.csv
service_use_cohort_plots: output/describe_service_use_home/plots/service_use_cohort_home_*.pdf
service_use_cohort_prop_plots: output/describe_service_use_home/plots/service_prop_cohort_home_*.pdf
describe_service_use_home_quarter:
run: r:latest analysis/04_describe_service_use_home_quarter.R
needs: [generate_study_population]
outputs:
moderately_sensitive:
service_use_quarter: output/describe_service_use_home/service_use_quart_home.csv
service_use_quarter_plots: output/describe_service_use_home/plots/service_use_quart_home*.pdf
service_use_quarter_prop_plots: output/describe_service_use_home/plots/service_prop_quart_home*.pdf
describe_service_use_home_gp_cohort:
run: r:latest analysis/05_describe_service_use_home_gp_cohort.R
needs: [generate_study_population]
outputs:
moderately_sensitive:
gp_complete_service_use_cohort: output/describe_service_use_home/complete_gp_history/gp_service_use_cohort_home*.csv
gp_complete_service_use_cohort_plots: output/describe_service_use_home/complete_gp_history/plots/gp_service_use_cohort_home_*.pdf
gp_complete_service_use_cohort_prop_plots: output/describe_service_use_home/complete_gp_history/plots/gp_service_prop_cohort_home_*.pdf
describe_service_use_home_gp_quarter:
run: r:latest analysis/06_describe_service_use_home_gp_quarter.R
needs: [generate_study_population]
outputs:
moderately_sensitive:
gp_complete_service_use_quarter: output/describe_service_use_home/complete_gp_history/gp_service_use_quart_home.csv
gp_complete_service_use_quarter_plots: output/describe_service_use_home/complete_gp_history/plots/gp_service_use_quart_home_*.pdf
gp_complete_service_use_quarter_prop_plots: output/describe_service_use_home/complete_gp_history/plots/gp_service_prop_quart_home_*.pdf
practice_measures_plots:
run: r:latest analysis/07_practice_measures_plots.R
needs: [generate_practice_measures]
outputs:
moderately_sensitive:
deciles_data: output/practice_measures/plots/deciles_*.csv
deciles_plots: output/practice_measures/plots/deciles_*.png