generated from opensafely/research-template
/
project.yaml
110 lines (89 loc) · 3.88 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
generate_cohort_imd_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_imd_ethnicity
outputs:
highly_sensitive:
cohort: output/input_imd_ethnicity.csv
generate_test_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_check
outputs:
highly_sensitive:
cohort: output/input_check.csv
generate_cohort_1:
# week 1 2019 to 21 2019 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-12-31 to 2019-05-26 by week"
outputs:
highly_sensitive:
cohort: output/input_*.csv
generate_cohort_2:
# week 22 2019 to 42 2019 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-05-27 to 2019-10-20 by week"
outputs:
highly_sensitive:
cohort: output/input*.csv
generate_cohort_3:
# week 43 2019 to 11 2020 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-10-21 to 2020-03-15 by week"
outputs:
highly_sensitive:
cohort: output/inpu*.csv
generate_cohort_4:
# week 12 2020 to 32 2020 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-16 to 2020-08-09 by week"
outputs:
highly_sensitive:
cohort: output/inp*.csv
generate_cohort_5:
# week 33 2020 to week 53 2020 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-08-10 to 2021-01-03 by week"
outputs:
highly_sensitive:
cohort: output/in*.csv
join_ethnicity_imd:
run: python:latest python analysis/join_ethnicity_imd.py
needs: [generate_cohort_1, generate_cohort_2, generate_cohort_3, generate_cohort_4, generate_cohort_5, generate_cohort_imd_ethnicity]
outputs:
highly_sensitive:
cohort: output/i*.csv
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition
needs: [join_ethnicity_imd]
outputs:
moderately_sensitive:
measure: output/measure_*_rate.csv
calculate_measures_demographics:
run: python:latest python analysis/generate_measures_demographics.py
needs: [join_ethnicity_imd]
outputs:
moderately_sensitive:
csvs: output/measure_*_rate_*.csv
standardise_and_plot:
run: python:latest python analysis/time_series_plots.py
needs: [calculate_measures]
outputs:
moderately_sensitive:
tables: output/*_rate_table.csv
graph: output/*_time_series_plot.svg
standardise_and_plot_demographics:
run: python:latest python analysis/time_series_plots_demographics.py
needs: [calculate_measures, calculate_measures_demographics]
outputs:
moderately_sensitive:
tables: output/*_breakdown.csv
tables_combined: output/combined_disease_*_table.csv
combined_graph: output/*_combined_diseases_time_series_plot.svg
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/investigate_discrepancies.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [join_ethnicity_imd]
outputs:
moderately_sensitive:
notebook: output/investigate_discrepancies.html
generate_notebook_admission_method:
run: jupyter:latest jupyter nbconvert /workspace/analysis/investigate_admission_method.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_test_cohort]
outputs:
moderately_sensitive:
notebook: output/investigate_admission_method.html