generated from opensafely/research-template
/
project.yaml
257 lines (220 loc) · 12.9 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-01 to 2020-05-01 by month" --output-format feather
outputs:
highly_sensitive:
cohort: output/input_*.feather
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-06-01 to 2020-12-01 by month" --output-format feather
outputs:
highly_sensitive:
cohort: output/input*.feather
generate_study_population_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-01-01 to 2021-07-01 by month" --output-format feather
outputs:
highly_sensitive:
cohort: output/inpu*.feather
check_EGFR:
run: python:latest python analysis/check_EGFR.py
needs: [join_ethnicity_region]
outputs:
moderately_sensitive:
counts: output/egfr_tabulation.csv
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format feather
outputs:
highly_sensitive:
cohort: output/input_ethnicity.feather
join_ethnicity_region:
run: python:latest python analysis/join_ethnicity_region.py
needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/inp*.feather
generate_study_population_lithium:
run: cohortextractor:latest generate_cohort --study-definition study_definition_lithium --index-date-range "2019-09-01 to 2021-07-01 by month" --output-format feather
outputs:
highly_sensitive:
cohort: output/input_lithium_*.feather
calculate_numerators:
run: python:latest python analysis/calculate_numerators.py
needs: [join_ethnicity_region]
outputs:
highly_sensitive:
cohort: output/indicator_e_f_*.feather
calculate_composite_indicators:
run: python:latest python analysis/composite_indicators.py
needs: [calculate_numerators, join_ethnicity_region]
outputs:
moderately_sensitive:
counts: output/*_composite_measure.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
needs: [join_ethnicity_region]
outputs:
moderately_sensitive:
measure_csv: output/measure_*_rate.csv
check_asthma:
run: python:latest python analysis/check_asthma.py
needs: [generate_measures]
outputs:
moderately_sensitive:
csv: output/asthma_sum.csv
generate_measures_demographics:
run: python:latest python analysis/calculate_measures.py
needs: [calculate_numerators, join_ethnicity_region, generate_study_population_lithium]
outputs:
moderately_sensitive:
counts: output/indicator_measure_*.csv
measure_csv: output/measure*_rate.csv
generate_plots:
run: python:latest python analysis/plot_measures.py
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
counts: output/plot_*.jpeg
cusum:
run: python:latest python analysis/cusum.py
needs: [generate_measures, generate_measures_demographics]
outputs:
moderately_sensitive:
cusum: output/cusum_results.json
plot_cusum:
run: python:latest python analysis/plot_cusum.py
needs: [cusum, generate_measures, generate_measures_demographics]
outputs:
moderately_sensitive:
cusum: output/cusum_indicator_*.jpeg
alert: output/alerts_indicator_*.jpeg
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/report.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_plots]
outputs:
moderately_sensitive:
notebook: output/report.html
indicator_saturation_a:
run: r:latest analysis/indicator_saturation_analysis.R -I a -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_a_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
highly_sensitive:
plots: output/indicator_saturation/indicator_saturation_*_a/figures/*.png
rdat: output/indicator_saturation/indicator_saturation_*_a/*.RData
csv: output/indicator_saturation/indicator_saturation_*_a/*_output_*.csv
# indicator_saturation_b:
# run: r:latest analysis/indicator_saturation_analysis.R -I b -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_b_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_b/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_b/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_b/*_output_*.csv
# indicator_saturation_c:
# run: r:latest analysis/indicator_saturation_analysis.R -I c -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_c_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_c/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_c/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_c/*_output_*.csv
# indicator_saturation_d:
# run: r:latest analysis/indicator_saturation_analysis.R -I d -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_d_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_d/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_d/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_d/*_output_*.csv
# indicator_saturation_e:
# run: r:latest analysis/indicator_saturation_analysis.R -I e -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_e_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_e/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_e/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_e/*_output_*.csv
# indicator_saturation_f:
# run: r:latest analysis/indicator_saturation_analysis.R -I f -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_f_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_f/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_f/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_f/*_output_*.csv
# indicator_saturation_g:
# run: r:latest analysis/indicator_saturation_analysis.R -I g -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_g_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_g/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_g/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_g/*_output_*.csv
# indicator_saturation_i:
# run: r:latest analysis/indicator_saturation_analysis.R -I i -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_i_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_i/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_i/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_i/*_output_*.csv
# indicator_saturation_k:
# run: r:latest analysis/indicator_saturation_analysis.R -I k -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_k_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_k/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_k/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_k/*_output_*.csv
# indicator_saturation_ac:
# run: r:latest analysis/indicator_saturation_analysis.R -I ac -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_ac_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_ac/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_ac/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_ac/*_output_*.csv
# indicator_saturation_me_no_fbc:
# run: r:latest analysis/indicator_saturation_analysis.R -I me_no_fbc -T date -C practice -B indicator_me_denominator -f -v -i output -o output/indicator_saturation measure_indicator_me_no_fbc_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_me_no_fbc/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_me_no_fbc/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_me_no_fbc/*_output_*.csv
# indicator_saturation_me_no_lft:
# run: r:latest analysis/indicator_saturation_analysis.R -I me_no_lft -T date -C practice -B indicator_me_denominator -f -v -i output -o output/indicator_saturation measure_indicator_me_no_lft_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_me_no_lft/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_me_no_lft/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_me_no_lft/*_output_*.csv
# indicator_saturation_li:
# run: r:latest analysis/indicator_saturation_analysis.R -I li -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_li_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_li/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_li/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_li/*_output_*.csv
# indicator_saturation_am:
# run: r:latest analysis/indicator_saturation_analysis.R -I am -T date -C practice -f -v -i output -o output/indicator_saturation measure_indicator_am_rate.csv
# needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
# outputs:
# highly_sensitive:
# plots: output/indicator_saturation/indicator_saturation_*_am/figures/*.png
# rdat: output/indicator_saturation/indicator_saturation_*_am/*.RData
# csv: output/indicator_saturation/indicator_saturation_*_am/*_output_*.csv
# combine_indicator_saturation_data:
# run: r:latest analysis/combine_indicator_saturation_output.R output/indicator_saturation output/indicator_saturation/combined
# needs: [indicator_saturation_a, indicator_saturation_b, indicator_saturation_c, indicator_saturation_d, indicator_saturation_e, indicator_saturation_f, indicator_saturation_g, indicator_saturation_i, indicator_saturation_k, indicator_saturation_ac, indicator_saturation_me_no_fbc, indicator_saturation_me_no_lft, indicator_saturation_li, indicator_saturation_am]
# outputs:
# highly_sensitive:
# compiled_indicator_saturation: output/indicator_saturation/combined/*
run_tests:
run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
outputs:
moderately_sensitive:
log: output/pytest.xml