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sanger / limber

A config-driven LIMS built on Sequencescape, primarily for running library preparation pipelines in the laboratory
MIT License
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DPL-903 BIOSCAN automated library prep submissions of DNAP extracted lysates #1381

Open neilsycamore opened 1 year ago

neilsycamore commented 1 year ago

User Story

As R&D (Scott T) I would like an automated method to generate library preparation submissions for LBSN-96 Lysate plates generated by Limber extraction pipelines in order to simplify the submission process and reduce the burden on the SSRs.

Who are the primary contacts for this story Scott T (R&D) Emma B (R&D)

Knowledge or Stake holders Lena (SSR)

Acceptance Criteria In order to be successful, this story should:

Remove the requirement for a separate BIOSCAN library prep submission template to be completed for LBSN-96 Lysate plates created by the Limber extraction process.

We should still be able to fail wells on the Lysate plate (see https://github.com/sanger/limber/issues/1434 for when this was implemented).

Any wells that have been failed on the Lysate plate should not be included in the automated submission, and this should not cause an issue with the transfer to the next plate (sometimes requests are required on all wells).

Additional context or information There are two input routes into the BIOSCAN pipeline: LBSN-96 Lysate plates containing pre-extracted samples or LILYS-96-Stock plates containing insects in ethanol.

For the LILYS-96-Stock plate entry point, two sequencescape submissions are required in total. One submission is required for the extraction process (where a LILYS-96-Stock plate generates a LBSN-96 Lysate plate), and a separate submission is required for the LBSN-96 Lysate plate to proceed to BIOSCAN library preparation.

We are currently aiming to process 2 BIOSCAN batches per month for the next several months, this requires the SSRs to create 2x submissions for 192 plates each month. This story would halve the number of submissions for the SSR and enable the process scale up throughput in the future.

This feature was initially requested as part of the original BIOSCAN LIMS request (DPL-450),investigated in DPL-562, but was dropped for the revised LIMS MVP due to time constraints.

DPL-450 Initial BIOSCAN process map DPL-562

andrewsparkes commented 1 year ago

This is difficult to do because the LBSN-96 Lysate plates are created by two routes and have an unusual configuration and state change model already. The automated submission code would need modification so it didn't appear and get in the way whilst you were still making the plate in from LILYS-96 Stock plate. Will need some experimentation to see how it can be done. We prefer not to have two versions of the LBSN-96 Stock plates for the two different routes. As part of this story we should also consider what Library type we should be applying at the submission here, as we're currently using an inappropriate short-read type.

andrewsparkes commented 2 months ago

This could be done as part of a refactor of the Bioscan pipeline configuration to simplify it after the ANOSPP pipeline goes live. Originally it was going to branch off into ANOSPP at the lysate plate which is why that library prep submission is there in Bioscan. But ANOSPP is now a separate pipeline so we could simplify Bioscan and remove the need for that separate library submission (or do it automatically if needed as the ANOSPP option is now separated).

KatyTaylor commented 4 weeks ago

Updated SSR contact after request from Liz C