generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
# generate_study_population:
# run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
# outputs:
# highly_sensitive:
# cohort: output/measures/input_*.csv.gz
generate_study_population_hospitalisation:
run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation --index-date-range "2020-07-01 to 2020-09-01 by month" --skip-existing --output-dir=output/hospitalisation_data --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/hospitalisation_data/input_hospitalisation_*.csv.gz
# generate_study_population_elderly:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_elderly
# --output-format=csv.gz
# outputs:
# highly_sensitive:
# cohort: output/input_elderly.csv.gz
# generate_measures:
# run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# measure_csv: output/measures/measure_*.csv
# describe_elderly_agedis:
# run: r:latest analysis/tables/gen_csv_age_check.R
# needs: [generate_study_population_elderly]
# outputs:
# moderately_sensitive:
# agetable: output/age_quant.csv
# describe:
# run: r:latest analysis/plot/overall_ab_prescribing.R
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# cohort: output/overall.png
# boxplot: output/overallbox.png
# describe_percentile:
# run: r:latest analysis/plot/overall_ab_prescribing_2575percentile.R
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# percentile: output/overall_25th_75th_percentile.png
# describe_starpu:
# run: r:latest analysis/plot/starpu_ab_prescribing.R
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# cohort: output/starpuline.png
# boxplot: output/starpubox.png
#generate_notebook_starpu:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_risk --ExecutePreprocessor.timeout=86400
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# notebook: output/hospitalisation_risk/starpu.html
# figures: output/hospitalisation_risk/*
#tables: output/tables/*
#csvs: output/*/* # two possible subfolders
#text: output/text/*
# generate_notebook_hospitalisation_analysis:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_analysis.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_risk --ExecutePreprocessor.timeout=86400
# needs: [generate_study_population_hospitalisation]
# outputs:
# moderately_sensitive:
# notebook: output/hospitalisation_risk/hospitalisation_analysis.html
# figures: output/hospitalisation_risk/*
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]
outputs:
moderately_sensitive:
notebook: output/hospitalisation_prediction_uti/hospitalisation_prediction_uti.html
figures: output/hospitalisation_prediction_uti/*
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]
outputs:
moderately_sensitive:
notebook: output/hospitalisation_prediction_urti/hospitalisation_prediction_urti.html
figures: output/hospitalisation_prediction_urti/*
# generate_notebook_hospitalisation_prediction:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction --ExecutePreprocessor.timeout=86400
# needs: [generate_study_population_hospitalisation]
# outputs:
# moderately_sensitive:
# notebook: output/hospitalisation_prediction/hospitalisation_prediction.html
# figures: output/hospitalisation_prediction/*
# describe_infection_ab_UTI:
# run: r:latest analysis/plot/infection_ab_UTI.R
# needs: [generate_study_population, generate_measures]
# outputs:
# moderately_sensitive:
# plot: output/UTI.png