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generated from opensafely/research-template
/
project.yaml
82 lines (70 loc) · 2.28 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition
--output-format=feather
outputs:
highly_sensitive:
cohort: output/input.feather
generate_study_population_monthly:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_monthly
--output-format=feather
--index-date-range "2021-01-01 to 2021-12-01 by month"
outputs:
highly_sensitive:
cohort: output/input_monthly_*.feather
generate_study_population_weekly:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_weekly
--output-format=feather
--index-date-range "2021-01-01 to 2021-12-24 by week"
outputs:
highly_sensitive:
cohort: output/input_weekly_*.feather
generate_study_counts_bp:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_counts_bp
--output-format=feather
outputs:
highly_sensitive:
cohort: output/input_counts_bp.feather
generate_study_counts_eth:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_counts_eth
--output-format=feather
outputs:
highly_sensitive:
cohort: output/input_counts_eth.feather
generate_study_counts_aaa:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_counts_aaa
--output-format=feather
outputs:
highly_sensitive:
cohort: output/input_counts_aaa.feather
generate_top_5_table:
run: python:latest python analysis/top_codes_table.py
needs: [generate_study_counts_bp, generate_study_counts_eth, generate_study_counts_aaa]
outputs:
moderately_sensitive:
table: output/top_5_code_table_*.csv
generate_codelist_report:
run: >
cohortextractor:latest generate_codelist_report
--output-dir=output
--codelist-path=codelists/opensafely-systolic-blood-pressure-qof.csv
--start-date=2021-01-01
--end-date=2021-12-31
outputs:
moderately_sensitive:
table: output/counts_per_*.csv