generated from opensafely/research-template
/
project.yaml
44 lines (34 loc) · 1.6 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 15000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-01 to 2021-04-01 by month" --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_*.csv
generate_study_population_demographics:
run: cohortextractor:latest generate_cohort --study-definition study_definition_demographics
outputs:
highly_sensitive:
cohort: output/input_demographics.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measure_*.csv
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/measures_notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_study_population, generate_measures]
# outputs:
# moderately_sensitive:
# notebook: output/measures_notebook.html
# measures_csv: output/measures_dropped.csv
# csv: output/check.csv
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_study_population, generate_study_population_demographics,generate_measures]
outputs:
moderately_sensitive:
notebook: output/notebook.html