Updated Achilles and added achilles concept count sql

FINNGEN / ETL

second version for the ETL of the detailed longitudinal data to the OMOP-CDM

https://finngen.github.io/ETL/

MIT License

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Closed shanmukhasampath closed 8 months ago

shanmukhasampath commented 8 months ago

This is for issue #126

Things corrected

Achilles updated to the commit that adds the person count for non-standard codes into analysis
Added the SQL script to calculate Achilles result concept count table
Modified the run_config_template to add this etl step
Modified the run_ETL_in_atlasdev.R to properly run the ETL followed by Achilles and then achilles_result_concept_count