generated from opensafely/research-template
/
project.yaml
397 lines (338 loc) · 21.3 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
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
demographics: output/demographics_summary.csv
generate_summary_counts:
run: python:latest python analysis/summary_statistics.py
needs: [join_ethnicity_region, generate_measures, generate_measures_demographics, calculate_numerators, generate_study_population_lithium]
outputs:
highly_sensitive:
patient_count: output/patient_count.json
practice_count: output/practice_count.json
summary: output/indicator_summary_statistics.json
generate_plots:
run: python:latest python analysis/plot_measures.py
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
counts: output/figures/plot_*.jpeg
combined: output/figures/combined_plot_*.png
cusum:
run: python:latest python analysis/cusum.py
needs: [generate_measures, generate_measures_demographics]
outputs:
moderately_sensitive:
cusum: output/cusum/cusum_results.json
alerts: output/cusum/cusum_alerts_summary.json
by_date: output/cusum/cusum_alerts_by_date.json
plot_cusum:
run: python:latest python analysis/plot_cusum.py
needs: [cusum, generate_measures, generate_measures_demographics]
outputs:
moderately_sensitive:
cusum: output/cusum/cusum/cusum_indicator_*.jpeg
alert: output/cusum/alerts/alerts_indicator_*.jpeg
combined_cusum: output/cusum/combined_cusum_count.png
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, generate_summary_counts]
outputs:
moderately_sensitive:
notebook: output/report.html
indicator_saturation_a:
run: r:latest analysis/indicator_saturation_analysis.R -I a -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_a_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_a/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_a/plot_data.csv
indicator_saturation_b:
run: r:latest analysis/indicator_saturation_analysis.R -I b -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_b_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_b/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_b/plot_data.csv
indicator_saturation_c:
run: r:latest analysis/indicator_saturation_analysis.R -I c -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_c_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_c/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_c/plot_data.csv
indicator_saturation_d:
run: r:latest analysis/indicator_saturation_analysis.R -I d -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_d_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_d/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_d/plot_data.csv
indicator_saturation_e:
run: r:latest analysis/indicator_saturation_analysis.R -I e -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_e_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_e/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_e/plot_data.csv
indicator_saturation_f:
run: r:latest analysis/indicator_saturation_analysis.R -I f -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_f_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_f/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_f/plot_data.csv
indicator_saturation_g:
run: r:latest analysis/indicator_saturation_analysis.R -I g -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_g_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_g/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_g/plot_data.csv
indicator_saturation_i:
run: r:latest analysis/indicator_saturation_analysis.R -I i -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_i_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_i/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_i/plot_data.csv
indicator_saturation_k:
run: r:latest analysis/indicator_saturation_analysis.R -I k -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_k_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_k/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_k/plot_data.csv
indicator_saturation_ac:
run: r:latest analysis/indicator_saturation_analysis.R -I ac -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_ac_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_ac/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_ac/plot_data.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 -v -i output -o output/indicator_saturation measure_indicator_me_no_fbc_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_me_no_fbc/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_me_no_fbc/plot_data.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 -v -i output -o output/indicator_saturation measure_indicator_me_no_lft_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_me_no_lft/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_me_no_lft/plot_data.csv
indicator_saturation_li:
run: r:latest analysis/indicator_saturation_analysis.R -I li -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_li_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_li/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_li/plot_data.csv
indicator_saturation_am:
run: r:latest analysis/indicator_saturation_analysis.R -I am -T date -C practice -v -i output -o output/indicator_saturation measure_indicator_am_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation/indicator_saturation_*_am/summary_output.csv
plot_csv: output/indicator_saturation/indicator_saturation_*_am/plot_data.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:
moderately_sensitive:
counts: output/indicator_saturation/combined/*.csv
# plots: output/indicator_saturation/combined/CDPLOT_*.png
# summary: output/indicator_saturation/combined/SUMMARY_*.png
# Rdat: output/indicator_saturation/combined/ANALYSIS_OUTPUT.Rdat
generate_indicator_saturation_plots:
run: r:latest analysis/generate_indicator_saturation_plots.R output/indicator_saturation output/indicator_saturation/combined
needs: [combine_indicator_saturation_data]
outputs:
moderately_sensitive:
plots: output/indicator_saturation/combined/BREAK-COUNT_*.png
###
### REVERSED ANALYSIS
###
indicator_saturation_a_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I a -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_a_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_a/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_a/plot_data.csv
indicator_saturation_b_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I b -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_b_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_b/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_b/plot_data.csv
indicator_saturation_c_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I c -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_c_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_c/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_c/plot_data.csv
indicator_saturation_d_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I d -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_d_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_d/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_d/plot_data.csv
indicator_saturation_e_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I e -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_e_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_e/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_e/plot_data.csv
indicator_saturation_f_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I f -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_f_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_f/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_f/plot_data.csv
indicator_saturation_g_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I g -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_g_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_g/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_g/plot_data.csv
indicator_saturation_i_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I i -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_i_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_i/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_i/plot_data.csv
indicator_saturation_k_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I k -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_k_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_k/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_k/plot_data.csv
indicator_saturation_ac_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I ac -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_ac_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_ac/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_ac/plot_data.csv
indicator_saturation_am_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I am -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_am_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_am/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_am/plot_data.csv
indicator_saturation_li_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I li -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_li_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_li/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_li/plot_data.csv
indicator_saturation_me_no_fbc_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I me_no_fbc -T date -C practice -B indicator_me_denominator -v -Q -i output -o output/indicator_saturation_rev measure_indicator_me_no_fbc_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_me_no_fbc/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_me_no_fbc/plot_data.csv
indicator_saturation_me_no_lft_rev:
run: r:latest analysis/indicator_saturation_analysis.R -I me_no_lft -T date -C practice -B indicator_me_denominator -v -Q -i output -o output/indicator_saturation_rev measure_indicator_me_no_lft_rate.csv
needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
outputs:
moderately_sensitive:
out_csv: output/indicator_saturation_rev/indicator_saturation_*_me_no_lft/summary_output.csv
plot_csv: output/indicator_saturation_rev/indicator_saturation_*_me_no_lft/plot_data.csv
combine_indicator_saturation_data_rev:
run: r:latest analysis/combine_indicator_saturation_output.R output/indicator_saturation_rev output/indicator_saturation_rev/combined
needs: [indicator_saturation_a_rev, indicator_saturation_b_rev, indicator_saturation_c_rev, indicator_saturation_d_rev, indicator_saturation_e_rev, indicator_saturation_f_rev, indicator_saturation_g_rev, indicator_saturation_i_rev, indicator_saturation_k_rev, indicator_saturation_ac_rev, indicator_saturation_me_no_fbc_rev, indicator_saturation_me_no_lft_rev, indicator_saturation_li_rev, indicator_saturation_am_rev]
outputs:
moderately_sensitive:
counts: output/indicator_saturation_rev/combined/*.csv
# plots: output/indicator_saturation/combined/CDPLOT_*.png
# summary: output/indicator_saturation/combined/SUMMARY_*.png
# Rdat: output/indicator_saturation/combined/ANALYSIS_OUTPUT.Rdat
generate_indicator_saturation_plots_rev:
run: r:latest analysis/generate_indicator_saturation_plots.R output/indicator_saturation_rev output/indicator_saturation_rev/combined
needs: [combine_indicator_saturation_data_rev]
outputs:
moderately_sensitive:
plots: output/indicator_saturation_rev/combined/BREAK-COUNT_*.png
run_tests:
run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
outputs:
moderately_sensitive:
log: output/pytest.xml