generated from opensafely/research-template
/
project.yaml
140 lines (119 loc) · 4.55 KB
/
project.yaml
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version: "3.0"
expectations:
population_size: 1000
actions:
generate_study_population_tests:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_tests
--output-format csv.gz
outputs:
highly_sensitive:
cohort: output/input_tests.csv.gz
test_counts:
run: python:latest python analysis/test_codelists.py
needs: [generate_study_population_tests]
outputs:
moderately_sensitive:
counts: output/tests*.csv
generate_study_population:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2019-01-01 to 2021-01-01 by month"
--output-format csv.gz
outputs:
highly_sensitive:
cohort: output/input*.csv.gz
# generate_study_population_2:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2021-02-01 to 2022-05-01 by month"
# --output-format csv.gz
# outputs:
# highly_sensitive:
# cohort: output/inpu*.csv.gz
generate_study_population_ethnicity_ukrr:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity_ukrr
--output-dir=output
--output-format csv.gz
outputs:
highly_sensitive:
cohort: output/input_ethnicity_ukrr.csv.gz
join_cohorts:
run: >
cohort-joiner:v0.0.9
--lhs output/input_20*.csv.gz
--rhs output/input_ethnicity_ukrr.csv.gz
--output-dir output/joined
needs: [generate_study_population, generate_study_population_ethnicity_ukrr]
outputs:
highly_sensitive:
cohort: output/joined/input_20*.csv.gz
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
get_counts:
run: python:latest python analysis/combine_operators.py
needs: [join_cohorts]
outputs:
moderately_sensitive:
counts: output/*_count.csv
generate_plots:
run: python:latest python analysis/plot_measures.py
needs: [generate_measures]
outputs:
moderately_sensitive:
counts: output/figures/plot_*.jpeg
generate_plots_numeric_values:
run: python:latest python analysis/plot_numeric_values.py
needs: [join_cohorts]
outputs:
moderately_sensitive:
figures: output/*dis*.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, 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_ethnicity_ukrr]
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_cohorts]
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_cohorts]
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_cohorts]
# 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: [join_cohorts]
outputs:
moderately_sensitive:
report: output/notebooks/ukrr-tables-figures.html
# generate_frequency_plots:
# run: r:latest analysis/test_frequency.R
# needs: [join_cohorts]
# outputs:
# moderately_sensitive:
# figures: output/figures/months_with_*.png