generated from opensafely/research-template
/
project.yaml
104 lines (89 loc) · 6.24 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 200000
actions:
generate_study_population_hospitalisation_urti:
run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_urti --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/hospitalisation_data/input_hospitalisation_urti.csv.gz
generate_study_population_hospitalisation_lrti:
run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_lrti --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/hospitalisation_data/input_hospitalisation_lrti.csv.gz
generate_study_population_hospitalisation_uti:
run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_uti --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/hospitalisation_data/input_hospitalisation_uti.csv.gz
generate_study_population_hospitalisation_sinusitis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_sinusitis --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/hospitalisation_data/input_hospitalisation_sinusitis.csv.gz
generate_study_population_hospitalisation_ot_externa:
run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_ot_externa --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/hospitalisation_data/input_hospitalisation_ot_externa.csv.gz
generate_study_population_hospitalisation_otmedia:
run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_otmedia --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/hospitalisation_data/input_hospitalisation_otmedia.csv.gz
generate_notebook_hospitalisation_prediction_urti:
run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_urti.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_urti --ExecutePreprocessor.timeout=86400
# needs: [generate_study_population_hospitalisation_urti,generate_study_population_bmi]
needs: [generate_study_population_hospitalisation_urti]
outputs:
moderately_sensitive:
notebook: output/hospitalisation_prediction_urti/hospitalisation_prediction_urti.html
figures: output/hospitalisation_prediction_urti/*
generate_notebook_hospitalisation_prediction_lrti:
run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_lrti.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_lrti --ExecutePreprocessor.timeout=86400
# needs: [generate_study_population_hospitalisation_lrti,generate_study_population_bmi]
needs: [generate_study_population_hospitalisation_lrti]
outputs:
moderately_sensitive:
notebook: output/hospitalisation_prediction_lrti/hospitalisation_prediction_lrti.html
figures: output/hospitalisation_prediction_lrti/*
generate_notebook_hospitalisation_prediction_uti:
run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_uti.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_uti --ExecutePreprocessor.timeout=86400
# needs: [generate_study_population_hospitalisation_uti,generate_study_population_bmi]
needs: [generate_study_population_hospitalisation_uti]
outputs:
moderately_sensitive:
notebook: output/hospitalisation_prediction_uti/hospitalisation_prediction_uti.html
figures: output/hospitalisation_prediction_uti/*
generate_notebook_hospitalisation_prediction_sinusitis:
run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_sinusitis.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_sinusitis --ExecutePreprocessor.timeout=86400
# needs: [generate_study_population_hospitalisation_sinusitis,generate_study_population_bmi]
needs: [generate_study_population_hospitalisation_sinusitis]
outputs:
moderately_sensitive:
notebook: output/hospitalisation_prediction_sinusitis/hospitalisation_prediction_sinusitis.html
figures: output/hospitalisation_prediction_sinusitis/*
generate_notebook_hospitalisation_prediction_ot_externa:
run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_ot_externa.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_ot_externa --ExecutePreprocessor.timeout=86400
# needs: [generate_study_population_hospitalisation_ot_externa,generate_study_population_bmi]
needs: [generate_study_population_hospitalisation_ot_externa]
outputs:
moderately_sensitive:
notebook: output/hospitalisation_prediction_ot_externa/hospitalisation_prediction_ot_externa.html
figures: output/hospitalisation_prediction_ot_externa/*
generate_notebook_hospitalisation_prediction_otmedia:
run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_otmedia.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_otmedia --ExecutePreprocessor.timeout=86400
# needs: [generate_study_population_hospitalisation_otmedia,generate_study_population_bmi]
needs: [generate_study_population_hospitalisation_otmedia]
outputs:
moderately_sensitive:
notebook: output/hospitalisation_prediction_otmedia/hospitalisation_prediction_otmedia.html
figures: output/hospitalisation_prediction_otmedia/*
generate_notebook_hosp_plots:
run: jupyter:latest jupyter nbconvert /workspace/analysis/hosp_plots.ipynb --execute --to html --output-dir=/workspace/output/hosp_plots --ExecutePreprocessor.timeout=86400
needs: [generate_notebook_hospitalisation_prediction_urti,generate_notebook_hospitalisation_prediction_lrti,generate_notebook_hospitalisation_prediction_uti,generate_notebook_hospitalisation_prediction_sinusitis,generate_notebook_hospitalisation_prediction_otmedia,generate_notebook_hospitalisation_prediction_ot_externa]
outputs:
moderately_sensitive:
notebook: output/hospitalisation_prediction/hosp_plots.html
figures: output/hospitalisation_prediction/*