Y24-493 - Add additional columns to 007c pools manifest

[KatyTaylor]

User story

As an SSR, I would like the pools plate / GEMs plate manifest in the scRNA Core pipeline to include more columns, as some data is needed for release to ENA/EGA.

Who are the primary contacts for this story

Liz H, Abby C

Who is the nominated tester for UAT

Liz H, Abby C

Acceptance criteria

• scRNA Core Pools Plate manifest includes extra columns:
  • DATE OF COLLECTION
  • COUNTRY OF ORIGIN
  • PHENOTYPE
  • GENDER
  • SAMPLE ACCESSION NUMBER
  • TAXON ID
  • SAMPLE COMMON NAME
• number of rows per sample is increased (>100) due to the expected size of pools coming through

Dependencies
Enhancement to:

• DPL-823 Import PBMC pool plates into Sequencescape #3857

Additional context

Came out of UAT testing of:

• Y24-428 - Change entry point (ready-pooled plates) limber#2027

There was some discussion about this, as we were originally considering not importing sample-level information at this stage (just one 'sample' per pool) - and, in that case, we wouldn't have imported any of this information. However, it sounds like if we do import this information then it might make the data release process easier, and it is easy enough since we are including sample-level information. It's not clear if the fields needed for accessioning are necessary or not - don't know how these samples are getting accessioned - via Sequencescape or not. However, since most of these fields are not mandatory on the manifest, and go-live is very soon, it seemed safer to include all the possible fields just in case.

Number of samples per pool - the maximum expected for the first samples going through is 100, but I've set it to 150 to be safe.

[KatyTaylor]

Liz C:

These are fields that we have previously included in all manifest types:
DATE OF COLLECTION
COUNTRY OF ORIGIN
We updated all manifests last year to include these are they are a requirement if sample data is to be released to ENA

PHENOTYPE
GENDER
These 2 are normally needed to allow samples to accession if they are a managed study (sample data to be released to EGA)

SAMPLE ACCESSION NUMBER
This is automatically generated for each sample, but is included in all other manifest types - if the sample data has been released elsewhere or previously, then SUs can over-write with their own sample accession number.

I have to admit I'm not an expert in the data release side of things, but these columns are in all other manifests and I don't want missing data/information to prevent any data release further down the line. Hope that helps