generated from opensafely/research-template
/
project.yaml
52 lines (44 loc) · 1.5 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
generate_cohort:
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_cohort]
config:
output_path: output/cohort_reports_outputs
outputs:
moderately_sensitive:
reports: output/cohort_reports_outputs/descriptives_input.html
reports_charts: output/cohort_reports_outputs/*.png
counts:
run: python:latest python analysis/counts.py
needs: [generate_cohort]
outputs:
moderately_sensitive:
tabdata: output/tabledata.csv
cohort_2: output/codecounts_week.csv
freq_plots:
run: python:latest python analysis/freq_plot.py
needs: [counts]
outputs:
moderately_sensitive:
plots: output/plots.svg
# figs: output/figs.svg
km_plots:
run: python:latest python analysis/km_plot.py
needs: [generate_cohort]
outputs:
moderately_sensitive:
figs: output/figs.svg
notebook_md:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/primary-care-covid-codes.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_cohort,km_plots,counts]
outputs:
moderately_sensitive:
md: output/primary-care-covid-codes.html