generated from opensafely/research-template
/
project.yaml
51 lines (45 loc) · 2.45 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_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
describe_cohorts:
run: r:latest analysis/01_describe_cohorts.R
needs: [generate_study_population]
outputs:
moderately_sensitive:
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_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
quarters_summary_table: output/describe_cohorts/quarters_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
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
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
gp_complete_service_use_means: output/describe_service_use/complete_gp_history/gp_service_use_mean*.csv
service_use_ratios: output/describe_service_use/service_use_ratio*.csv