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_definition_static:
run: cohortextractor:latest generate_cohort --study-definition study_definition_static
outputs:
highly_sensitive:
cohort: output/input_static.csv
# Oximetry
generate_study_population_oximetry:
run: cohortextractor:latest generate_cohort --study-definition study_definition_oximetry --index-date-range "2019-04-01 to 2022-05-30 by week"
outputs:
highly_sensitive:
oximetry_cohort: output/oximetry/0.1_generate_study_population/input_oximetry*.csv
join_cohorts_oximetry:
run: cohort-joiner:v0.0.30 --lhs output/oximetry/0.1_generate_study_population/input_oximetry*.csv --rhs output/input_static.csv --output-dir output/oximetry/0.2_join_cohorts/
needs:
[generate_study_population_oximetry, generate_study_definition_static]
outputs:
highly_sensitive:
cohort: output/oximetry/0.2_join_cohorts/input_oximetry*.csv
# BP
generate_study_population_bp:
run: cohortextractor:latest generate_cohort --study-definition study_definition_bp --index-date-range "2019-04-01 to 2022-05-30 by week"
outputs:
highly_sensitive:
bp_cohort: output/bp/0.1_generate_study_population/input_bp*.csv
join_cohorts_bp:
run: cohort-joiner:v0.0.30 --lhs output/bp/0.1_generate_study_population/input_bp*.csv --rhs output/input_static.csv --output-dir output/bp/0.2_join_cohorts/
needs: [generate_study_population_bp, generate_study_definition_static]
outputs:
highly_sensitive:
cohort: output/bp/0.2_join_cohorts/input_bp*.csv
# Proactive
generate_study_population_proactive:
run: cohortextractor:latest generate_cohort --study-definition study_definition_proactive --index-date-range "2019-04-01 to 2022-05-30 by week"
outputs:
highly_sensitive:
proactive_cohort: output/proactive/0.1_generate_study_population/input_proactive*.csv
join_cohorts_proactive:
run: cohort-joiner:v0.0.30 --lhs output/proactive/0.1_generate_study_population/input_proactive*.csv --rhs output/input_static.csv --output-dir output/proactive/0.2_join_cohorts/
needs:
[generate_study_population_proactive, generate_study_definition_static]
outputs:
highly_sensitive:
cohort: output/proactive/0.2_join_cohorts/input_proactive*.csv
# # Analysis
# generate_oximetry_timeseries:
# run: python:latest python analysis/analysis_oximetry_timeseries.py
# needs: [join_cohorts_oximetry]
# outputs:
# moderately_sensitive:
# oximetry_table_counts: output/oximetry_table_counts.csv
# oximetry_plot_timeseries: output/oximetry_plot_timeseries.png
# generate_oximetry_regional_timeseries:
# run: python:latest python analysis/analysis_oximetry_region.py
# needs: [join_cohorts_oximetry]
# outputs:
# moderately_sensitive:
# oximetry_table_counts_region: output/oximetry_table_counts_*.csv
# oximetry_plot_timeseries_region: output/oximetry_plot_timeseries_region_*.png
# generate_oximetry_breakdowns:
# run: python:latest python analysis/analysis_oximetry_breakdowns.py
# needs: [join_cohorts_oximetry]
# outputs:
# moderately_sensitive:
# oximetry_table_breakdowns: output/oximetry_table_code_*.csv
# oximetry_plot_breakdowns: output/oximetry_plot_code_*.png
# generate_oximetry_codes_analysis:
# run: python:latest python analysis/analysis_oximetry_codes.py
# needs: [join_cohorts_oximetry]
# outputs:
# moderately_sensitive:
# oximetry_table_code_counts: output/oximetry_table_code_counts_*.csv
# oximetry_table_code_combinations: output/oximetry_table_code_combinations.csv
# generate_oximetry_no_codes_analysis:
# run: python:latest python analysis/analysis_oximetry_no_codes.py
# needs: [join_cohorts_oximetry]
# outputs:
# moderately_sensitive:
# oximetry_table_no_codes_used: output/oximetry_table_no_codes_used.csv
# generate_bp_timeseries:
# run: python:latest python analysis/analysis_bp_timeseries.py
# needs: [join_cohorts_bp]
# outputs:
# moderately_sensitive:
# bp_table_counts: output/bp_table_counts.csv
# bp_plot_timeseries: output/bp_plot_timeseries.png
# generate_bp_regional_timeseries:
# run: python:latest python analysis/analysis_bp_region.py
# needs: [join_cohorts_bp]
# outputs:
# moderately_sensitive:
# bp_table_counts_region: output/bp_table_counts_*.csv
# bp_plot_timeseries_region: output/bp_plot_timeseries_region_*.png
# generate_bp_breakdowns:
# run: python:latest python analysis/analysis_bp_breakdowns.py
# needs: [join_cohorts_bp]
# outputs:
# moderately_sensitive:
# bp_table_breakdowns: output/bp_table_code_*.csv
# bp_plot_breakdowns: output/bp_plot_code_*.png
# generate_bp_codes_analysis:
# run: python:latest python analysis/analysis_bp_codes.py
# needs: [join_cohorts_bp]
# outputs:
# moderately_sensitive:
# bp_table_code_counts: output/bp_table_code_counts_*.csv
# bp_table_code_combinations: output/bp_table_code_combinations.csv
# generate_bp_no_codes_analysis:
# run: python:latest python analysis/analysis_bp_no_codes.py
# needs: [join_cohorts_bp]
# outputs:
# moderately_sensitive:
# bp_table_no_codes_used: output/bp_table_no_codes_used.csv
# generate_proactive_timeseries:
# run: python:latest python analysis/analysis_proactive_timeseries.py
# needs: [join_cohorts_proactive]
# outputs:
# moderately_sensitive:
# proactive_table_counts: output/proactive_table_counts.csv
# proactive_plot_timeseries: output/proactive_plot_timeseries.png
# generate_proactive_regional_timeseries:
# run: python:latest python analysis/analysis_proactive_region.py
# needs: [join_cohorts_proactive]
# outputs:
# moderately_sensitive:
# proactive_table_counts_region: output/proactive_table_counts_*.csv
# proactive_plot_timeseries_region: output/proactive_plot_timeseries_region_*.png
# generate_proactive_breakdowns:
# run: python:latest python analysis/analysis_proactive_breakdowns.py
# needs: [join_cohorts_proactive]
# outputs:
# moderately_sensitive:
# proactive_table_breakdowns: output/proactive_table_code_*.csv
# proactive_plot_breakdowns: output/proactive_plot_code_*.png
# generate_proactive_codes_analysis:
# run: python:latest python analysis/analysis_proactive_codes.py
# needs: [join_cohorts_proactive]
# outputs:
# moderately_sensitive:
# proactive_table_code_counts: output/proactive_table_code_counts_*.csv
# generate_proactive_no_codes_analysis:
# run: python:latest python analysis/analysis_proactive_no_codes.py
# needs: [join_cohorts_proactive]
# outputs:
# moderately_sensitive:
# proactive_table_no_codes_used: output/proactive_table_no_codes_used.csv