d3b-center/d3b-arcus-manifest-prep

🗃️ tool to generate manifests for transfering cbtn data to arcus

d3b-arcus-manifest-prep's Issues

five participants do not have MRNs

Describe the bug

five participants that are CHOP participants do not have MRNs but are CHOP participants.

C849807
C2785827
C992118
C819549
C580191

We have their 7316-numbers but need to figure out what auth ID to provide to ARCUS for these ones.

Version ID

None

Feature Request: Build File-Sample-Participant Mapping

Description

Use the file manifest received from ARCUS of all the submitted files and convert that into a manifest mapping file, sample, and participant. This mapping file should have the following columns:

• genomic_file_id for the file's genomic file ID
• sample_id for the kf_id of the sample associated with the file
• participant_id for the kf_id of the participant associated with the sample

This file should be the same format as the one for CDS.

The generated mapping file should be placed in the data/ directory and the script(s) used to build the manifest should be in the scripts/ directory.