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knowledgesystems / cmo-pipelines

GNU Affero General Public License v3.0
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CDM Sample List Support #1130

Closed averyniceday closed 4 months ago

averyniceday commented 7 months ago

This PR updates the fetch-dmp-data-for-import.sh script to upload a CDM deliverable to the s3://cdm-deliverable bucket using the update-cdm-deliverable.sh script. This deliverable file contains: 

SAMPLE_ID PATIENT_ID CANCER_TYPE CANCER_TYPE_DETAILED

It also fetches CDM updates from the s3://cdm-deliverable bucket using the pull-cdm-data.sh script. The CDM files are then merged into the msk_solid_heme cohort.