generated from opensafely/research-template
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project.yaml
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/
project.yaml
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version: "3.0"
expectations:
population_size: 1000
actions:
generate_study_population_calculators:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_calculators
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_calculators.csv.gz
calculate_calculators:
run: python:latest python analysis/scripts/calculate_calculators.py
needs: [generate_study_population_calculators]
outputs:
highly_sensitive:
counts: output/input_calculators_calculated.csv.gz
crcl_gault:
run: python:latest python analysis/scripts/crcl_gault.py
needs: [calculate_calculators]
outputs:
moderately_sensitive:
plots: output/dist*.png
venn: output/venn*.png
counts: output/creatinine_vs_crlc.json
generate_study_population:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2019-01-01 to 2023-07-01 by month"
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input*.csv.gz
generate_study_population_ukrr_ethnicity:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ukrr_ethnicity
--output-dir=output
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_ukrr_ethnicity.csv.gz
join_cohorts:
run: >
cohort-joiner:v0.0.46
--lhs output/input_20*.csv.gz
--rhs output/input_ukrr_ethnicity.csv.gz
--output-dir output/joined
needs: [generate_study_population, generate_study_population_ukrr_ethnicity]
outputs:
highly_sensitive:
cohort: output/joined/input_20*.csv.gz
generate_table_1:
run: python:latest python analysis/scripts/table_1.py --study_def_paths="output/joined/input_*.csv.gz" --demographics="age_band,sex,region,imd,ethnicity"
needs: [join_cohorts]
outputs:
moderately_sensitive:
tables: output/pub/descriptive_tables/table_1*.csv
get_counts:
run: python:latest python analysis/scripts/combine_operators.py
needs: [join_cohorts]
outputs:
moderately_sensitive:
counts_pub: output/pub/operator_counts/*.csv
generate_top_5_tables:
run: python:latest python analysis/scripts/top_codes.py
needs: [get_counts]
outputs:
moderately_sensitive:
counts: output/pub/top_5_tables/top_5_code_table_*.csv
ckd_discrepancies:
run: python:latest python analysis/scripts/ckd_discrepancies.py
needs: [join_cohorts]
outputs:
moderately_sensitive:
tables: output/pub/ckd_overlap/ckd_staging_*.csv
ukrr_vs_prim_care_ckd:
run: python:latest python analysis/scripts/ukrr_prim_care_crossover_ckd.py
needs: [join_cohorts]
outputs:
moderately_sensitive:
upset: output/pub/ukrr_pc_overlap/*.jpeg
table: output/pub/ukrr_pc_overlap/*.csv
generate_measures:
run: cohortextractor:latest generate_measures
--study-definition study_definition
--output-dir=output/joined
needs: [join_cohorts]
outputs:
moderately_sensitive:
measure_csv: output/joined/measure_*_rate.csv
generate_plots:
run: python:latest python analysis/scripts/plot_measures.py
needs: [generate_measures, join_cohorts]
outputs:
moderately_sensitive:
counts: output/pub/deciles/figures/plot_*.jpeg
csv: output/pub/deciles/data/plot_*.csv
ckd_stage: output/pub/ckd_stage/plot_ckd_stage.jpeg
ckd_stage_csv: output/pub/ckd_stage/plot_ckd_stage.csv
tests_ckd_stage: output/pub/tests_by_ckd_stage/*.jpeg
tests_ckd_stage_csv: output/pub/tests_by_ckd_stage/*.csv
ukrr: output/pub/ukrr_testing/*.jpeg
ukrr_data: output/pub/ukrr_testing/*.csv
practice_numbers:
run: python:latest python analysis/scripts/practice_numbers_deciles.py
needs: [generate_measures]
outputs:
moderately_sensitive:
tables: output/pub/deciles/num_practices*.csv
generate_plots_numeric_values:
run: python:latest python analysis/scripts/plot_numeric_values.py
needs: [join_cohorts]
outputs:
moderately_sensitive:
figures: output/pub/numeric_values/*dis*.jpeg
tables: output/pub/numeric_values/*dis*.csv
generate_study_population_ukrr_jul_22:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ukrr
--index-date-range "2022-07-01"
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukrr_2022-07-01.csv.gz
generate_study_population_ukrr:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ukrr
--index-date-range "2020-01-01"
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukrr*.csv.gz
generate_study_population_ukrr_1:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ukrr_short
--index-date-range "2021-01-01"
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukr*.csv.gz
generate_study_population_ukrr_2:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ukrr_short
--index-date-range "2022-01-01"
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/ukrr/input_uk*.csv.gz
generate_study_population_paeds:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_paeds
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_paeds.csv.gz
generate_study_population_check_SC:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_check_SC
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_check_SC.csv.gz
# 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, get_counts]
# outputs:
# moderately_sensitive:
# notebook: output/report.html
# generate_ukrr_checks:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-checks.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population, generate_study_population_ukrr_ethnicity]
# outputs:
# moderately_sensitive:
# report: output/notebooks/ukrr-checks.html
#generate_ukrr_report:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-report.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [join_acr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/ukrr-report.html
# generate_ukrr_discrepancies:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-discrepancies.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [join_acr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/ukrr-discrepancies.html
# generate_kidney_week:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/kidney_week.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [join_acr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/kidney_week.html
# generate_ukrr_tables_figures:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/ukrr-tables-figures.html
generate_ukrr_tables_figures_1:
run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures-2021.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
needs: [generate_study_population_ukrr_1]
outputs:
moderately_sensitive:
report: output/notebooks/ukrr-tables-figures-2021.html
generate_ukrr_tables_figures_2:
run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures-2022.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
needs: [generate_study_population_ukrr_2]
outputs:
moderately_sensitive:
report: output/notebooks/ukrr-tables-figures-2022.html
generate_false_positives_ckd:
run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/false-positives-ckd.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
needs: [generate_study_population_ukrr]
outputs:
moderately_sensitive:
report: output/notebooks/false-positives-ckd.html
generate_agreement_by_eGFR:
run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/agreement-by-eGFR.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
needs: [generate_study_population_ukrr]
outputs:
moderately_sensitive:
report: output/notebooks/agreement-by-eGFR.html
# generate_pc_sc_codes1a:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes1a.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes1a.html
# generate_pc_sc_codes1b:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes1b.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes1b.html
# generate_pc_sc_codes2:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes2.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes2.html
# generate_pc_sc_codes3:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes3.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes3.html
# generate_pc_sc_codes4a:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes4a.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes4a.html
# generate_pc_sc_codes4b:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes4b.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes4b.html
# generate_pc_sc_codes4c:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes4c.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes4c.html
# generate_pc_sc_codes5a:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes5a.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes5a.html
# generate_pc_sc_codes5b:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes5b.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes5b.html
# generate_ukrr_tables_figures_paeds:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures-paeds.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_paeds]
# outputs:
# moderately_sensitive:
# report: output/notebooks/ukrr-tables-figures-paeds.html
# generate_check_SC:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/check-SC.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_check_SC, generate_study_population_ukrr_ethnicity]
# outputs:
# moderately_sensitive:
# report: output/notebooks/check-SC.html
# generate_modality_difference_table:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/modality-difference-table.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/modality-difference-table.html
# generate_incident_analysis:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/incident-analysis.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/incident-analysis.html
# generate_study_population_flowchart:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition_flowchart
# --output-format csv.gz
# outputs:
# highly_sensitive:
# cohort: output/input_flowchart.csv.gz
# generate_median_age:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/median_age.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/median_age.html