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epi_additions.yaml
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epi_additions.yaml
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actions:
## # # # # # # # # # # # # # # # # # # #
## Metrics data
## # # # # # # # # # # # # # # # # # # #
metrics_generate_sro_dataset_winter:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sro
--param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_sro_2021-12-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_sro_2021-12-01.feather
metrics_generate_sro_dataset_summer:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sro
--param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_sro_2021-06-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_sro_2021-06-01.feather
metrics_generate_kids_dataset_winter:
run: cohortextractor:latest generate_cohort --study-definition study_definition_kids
--param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_kids_2021-12-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_kids_2021-12-01.feather
metrics_generate_kids_dataset_summer:
run: cohortextractor:latest generate_cohort --study-definition study_definition_kids
--param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_kids_2021-06-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_kids_2021-06-01.feather
metrics_generate_endpopulation_dataset_winter:
run: cohortextractor:latest generate_cohort --study-definition study_definition_endpopulation
--param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_endpopulation_2021-12-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_endpopulation_2021-12-01.feather
metrics_generate_endpopulation_dataset_summer:
run: cohortextractor:latest generate_cohort --study-definition study_definition_endpopulation
--param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_endpopulation_2021-06-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_endpopulation_2021-06-01.feather
metrics_generate_sro_measures:
run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
--param end_date='2021-09-30' --study-definition study_definition_sro --output-dir=output/metrics
needs:
- metrics_generate_sro_dataset_summer
- metrics_generate_sro_dataset_winter
outputs:
moderately_sensitive:
measure_csv: output/metrics/mea*.csv
metrics_generate_kids_measures:
run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
--param end_date='2021-09-30' --study-definition study_definition_kids --output-dir=output/metrics
needs:
- metrics_generate_kids_dataset_summer
- metrics_generate_kids_dataset_winter
outputs:
moderately_sensitive:
measure_csv: output/metrics/me*.csv
metrics_generate_endpopulation_measures:
run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
--param end_date='2021-09-30' --study-definition study_definition_endpopulation
--output-dir=output/metrics
needs:
- metrics_generate_endpopulation_dataset_summer
- metrics_generate_endpopulation_dataset_winter
outputs:
moderately_sensitive:
measure_csv: output/metrics/m*.csv
## #### End ####