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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
test_action:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01 to 2020-03-01 by week" --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/inp*.csv.gz
generate_study_population_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01 to 2021-03-07 by week" --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_*.csv.gz
# gives until 2022-03-27. Only have ONS deaths until 2021-07-01
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-03-14 to 2022-03-20 by week" --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input*.csv.gz
generate_study_population_end:
run: cohortextractor:latest generate_cohort --study-definition study_definition_end --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_end.csv.gz
join_cohorts_weekly:
run: >
cohort-joiner:v0.0.44
--lhs output/input_20*.csv.gz
--rhs output/input_end.csv.gz
--output-dir output/joined
needs: [
generate_study_population_1,
generate_study_population_2,
generate_study_population_end]
outputs:
highly_sensitive:
cohort: output/joined/input_20*.csv.gz
generate_dataset_report:
run: >
dataset-report:v0.0.24
--input-files output/joined/input_2022-03-20.csv.gz
--output-dir output/joined
needs: [join_cohorts_weekly]
outputs:
moderately_sensitive:
dataset_report: output/joined/input_2022-03-20.html