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DPL-973 [deprecated] Prevent 'donor clash' when pooling for sequencing
User story As a user of the scRNA Core pipeline, I would like the LIMS to help me prevent 'donor clash' when I am pooling together tubes for sequencing. This means that the pool should not contain more than one sample from the same donor. The donor is identified by the donor_id field in the sample metadata.
Who are the primary contacts for this story Lesley, Abby
Who is the nominated tester for UAT Lesley, Abby
Acceptance criteria To be considered successful the solution must allow:
- [ ] When pooling for sequencing in the scRNA Core pipeline, I am shown an error if the pool contains more than one sample with the same donor id.
- [ ] This logic applies only to the scRNA Core pipeline.
- [ ] If the pool is made up of compound samples, the relevant samples to look at for the donor id are the component samples that make up the compound samples.
Outstanding questions
- Where in the LIMS will the pooling for sequencing happen? Check the process for the current Chromium pipelines, as the library prep part of the scRNA Core pipeline is almost identical to these.
- If it's in a generic page (e.g. 'poolings/new'), how can we make sure we don't affect other pipelines?
This is how pooling for 10X pipelines is currently specified (From Liz H via email):
The service user provides a completed pooling document to say which samples need to go into each specific pool when they submit the samples. Then when I make the submissions each pool is given a specific submission name as usual for all submissions.
This is for both manual and semi-auto.
The final pooling step seems to be in Limber. Tube purposes as follows:
| Pipeline flavour | Penultimate tube | Final tube |
|---|---|---|
| 5' (semi-auto) | LBC 5p Pool Norm | LB Lib Pool Norm |
| 3' (semi-auto) | LBC 3pV3 GLibPS | LB Lib Pool Norm |
| BCR (semi-auto) | LBC BCR Pool Norm | LB Lib Pool Norm |
| TCR (semi-auto) | LBC TCR Pool Norm | LB Lib Pool Norm |
From Abby RE working group meeting on the 22nd Feb 2024:
It was agreed that samples can be pooled together at sequencing where donors are the same because at this point they will be tagged. We just need to have the donor clash prevention step for pooling before chip loading as at this point there will be no barcoding.
Therefore I am deprecating this story. Pooling prior to chip loading is covered by https://github.com/sanger/limber/issues/1390