search

GTAC-MGI / GTAC-ESP-LIMS

3 stars 0 forks source link

CLE Lab: Pipeline script to trim ingest sheet #450

Open tim-snyder-wustl opened 2 months ago

tim-snyder-wustl commented 2 months ago

For CLE, ingest will compose of two steps.

  1. Trim a CSV ingest file down to only samples listed that do not currently exists.
  2. Do the actual ingest with the newly created trimmed-down list.

This ticket is for part 1.

How this will be done is TBD.

To be done before https://github.com/GTAC-MGI/GTAC-ESP-LIMS/issues/451

tim-snyder-wustl commented 1 week ago

Implement this as a stand-alone pipeline script.

Waiting on a sample file from @abohanno

abohanno commented 1 week ago

Hi Guys,

I do not have an update on the log file that would be delivered for GPS assays (SOMA and IDT Germline Exome). We plan to discuss this with Dr. Spencer at the next meeting. Hopefully I will have an update afterwards for our next meeting. In the meantime, we're working off the assumption that it will be structured very similarly to the MyeloSeq log. I have attached an example file with the column headers and what info they indicate. Any column header without an explanation is most likely unnecessary for our ingest purposes.

CLE_Ingest_Template.xlsx

Andy