generated from opensafely/research-template
/
project.yaml
51 lines (44 loc) · 1.36 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
report_data:
run: r:latest analysis/report.R
needs:
- generate_study_population
outputs:
moderately_sensitive:
csv: output/report_*.csv
markdown_doc:
run: r:latest -e 'rmarkdown::render("analysis/markdown_report.Rmd", output_dir = "output")'
needs:
- generate_study_population
outputs:
moderately_sensitive:
report: output/markdown_report.html
generate_report:
run: cohort-report:v3.0.0 output/input.csv
needs: [generate_study_population]
config:
variable_types:
CVD_assess_latest_date: date
statins_prescribed: date
age: int
sex: categorical
CVD_assess_latest_number: float
CVD_assess_comparator: categorical
CKD_code: binary
CVD_code: binary
T1D_code: binary
T2D_code: binary
Overall_diab_code: binary
output_path: output/cohort_reports_outputs
outputs:
moderately_sensitive:
reports: output/cohort_reports_outputs/descriptives_input.html
reports_charts: output/cohort_reports_outputs/*.png