generated from opensafely/research-template
/
project.yaml
49 lines (40 loc) · 2.31 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
study_definition_hospitalisation_rate:
run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_rate --index-date-range "2019-01-01 to 2022-02-01 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_hospitalisation_rate --skip-existing --output-dir=output/measures
needs: [study_definition_hospitalisation_rate]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
generate_notebook_hospitalisation_rate:
run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_rate.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_rate --ExecutePreprocessor.timeout=86400
needs: [generate_measures]
outputs:
moderately_sensitive:
notebook: output/hospitalisation_rate/hospitalisation_rate.html
figures: output/hospitalisation_rate/*
# study_definition_hospitalisation_rate_hxdx:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_rate_hxdx --index-date-range "2019-01-01 to 2022-02-01 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
# outputs:
# highly_sensitive:
# cohort: output/measures/input*.csv.gz
# generate_measures_hxdx:
# run: cohortextractor:latest generate_measures --study-definition study_definition_hospitalisation_rate_hxdx --skip-existing --output-dir=output/measures
# needs: [study_definition_hospitalisation_rate_hxdx]
# outputs:
# moderately_sensitive:
# measure_csv: output/measures/measur_*.csv
# generate_notebook_hospitalisation_rate_hxdx:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_rate_hxdx.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_rate_hxdx --ExecutePreprocessor.timeout=86400
# needs: [generate_measures_hxdx]
# outputs:
# moderately_sensitive:
# notebook: output/hospitalisation_rate_hxdx/hospitalisation_rate_hxdx.html
# figures: output/hospitalisation_rate_hxdx/*