generated from opensafely/research-template
/
project.yaml
105 lines (90 loc) · 4 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_event_counts:
run: cohortextractor:latest generate_cohort --study-definition study_definition_eventcounts --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_eventcounts.feather
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input.feather
preprocess_inputs:
run: python:latest python analysis/preprocess_inputs.py --output-format feather
needs: [generate_study_population]
outputs:
highly_sensitive:
cohort_with_duration: output/data/input_processed.feather
execute_validation_analyses:
run: python:latest python analysis/validation_script.py
needs: [preprocess_inputs]
outputs:
moderately_sensitive:
tables: output/phenotype_validation_bmi/tables/*.csv
figures: output/phenotype_validation_bmi/figures/*.png
generate_report_bmi:
run: python:latest jupyter nbconvert /workspace/notebooks/report_bmi.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [execute_validation_analyses]
outputs:
moderately_sensitive:
notebook: output/report_bmi.html
execute_validation_analyses_height:
run: python:latest python analysis/validation_script_height.py
needs: [preprocess_inputs]
outputs:
moderately_sensitive:
tables: output/phenotype_validation_height/tables/*.csv
figures: output/phenotype_validation_height/figures/*.png
generate_report_height:
run: python:latest jupyter nbconvert /workspace/notebooks/report_height.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [execute_validation_analyses_height]
outputs:
moderately_sensitive:
notebook: output/report_height.html
execute_validation_analyses_weight:
run: python:latest python analysis/validation_script_weight.py
needs: [preprocess_inputs]
outputs:
moderately_sensitive:
tables: output/phenotype_validation_weight/tables/*.csv
figures: output/phenotype_validation_weight/figures/*.png
generate_report_weight:
run: python:latest jupyter nbconvert /workspace/notebooks/report_weight.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [execute_validation_analyses_weight]
outputs:
moderately_sensitive:
notebook: output/report_weight.html
generate_histograms:
run: python:latest python analysis/validation_histograms.py
needs: [preprocess_inputs]
outputs:
moderately_sensitive:
tables1: output/histograms/tables/hist*.csv
tables2: output/histograms/tables/ct*.csv
figures1: output/histograms/figures/hist*.png
figures2: output/histograms/figures/cdf*.png
execute_validation_recency:
run: python:latest python analysis/validation_recency.py
needs: [preprocess_inputs]
outputs:
moderately_sensitive:
tables: output/histograms/tables/*.csv
figures: output/histograms/figures/*.png
generate_report_eventcounts:
run: python:latest jupyter nbconvert /workspace/notebooks/report_event_counts.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_event_counts]
outputs:
moderately_sensitive:
notebook: output/report_event_counts.html
generate_dataset_report:
run: >
dataset-report:v0.0.9
--input-files output/data/input.feather
--output-dir output/data
needs: [generate_study_population]
outputs:
moderately_sensitive:
dataset_report: output/data/input.html