generated from opensafely/research-template
/
project.yaml
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/
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 --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_*.feather
get_patient_count:
run: python:latest python analysis/get_patients_counts.py
needs: [generate_study_population]
outputs:
moderately_sensitive:
text: output/patient_count.json
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_ethnicity.feather
join_ethnicity:
run: python:latest python analysis/join_ethnicity.py
needs: [generate_study_population, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/input*.feather
generate_study_population_practice_count:
run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_practice_count.feather
generate_measures:
run: python:latest python analysis/calculate_measures.py
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure: output/combined_measure_*.csv
# generate_measures:
# run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
# needs: [join_ethnicity]
# outputs:
# moderately_sensitive:
# measure_csv: output/measure_*.csv
# generate_measure_ethnicity:
# run: python:latest python analysis/generate_measure_ethnicity.py
# needs: [join_ethnicity]
# outputs:
# moderately_sensitive:
# measure: output/measure_*_ethnicity.csv
get_practice_count:
run: python:latest python analysis/get_practice_count.py
needs: [generate_study_population_practice_count]
outputs:
moderately_sensitive:
text: output/practice_count.json
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_measures, get_practice_count, get_patient_count]
# outputs:
# moderately_sensitive:
# notebook: output/sentinel_measures.html
generate_notebook_demographics:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures_demographics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_measures, get_practice_count, get_patient_count]
outputs:
moderately_sensitive:
notebook: output/sentinel_measures_demographics.html
figures: output/test_*.png
# generate_notebook_practice:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures_by_practice.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_measures, get_practice_count, get_patient_count]
# outputs:
# moderately_sensitive:
# notebook: output/sentinel_measures_by_practice.html
# csvs: output/*_check.csv
# get_event_summary:
# run: python:latest python analysis/get_event_summary.py
# needs: [join_ethnicity]
# outputs:
# moderately_sensitive:
# text: output/*_event_summary.csv
# run_tests:
# run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
# outputs:
# moderately_sensitive:
# log: output/pytest.xml