Stan1520
commented
3 weeks ago Refined User Story after meeting with Scott, the primary contact.
New Pipeline Automation for Submissions
Description of the Problem: To Create an automated method to generate “Limber-Htp – GBS” library preparation submissions for “LANS-96 Lysate” plates generated by the “Limber-Htp – ANOSPP Lysate Prep” extraction pipeline
Currently, the process of submissions involves a manifest submission followed by a non-destructive extraction submission. This workflow has inefficiencies, particularly regarding the lack of automation in the second submission. This results in unnecessary back-and-forth communication between teams, leading to time wastage and potential delays in processing.
Contact Person: Scott Thurston
User Story: As R&D (Scott T) I would like an automated method to generate “Limber-Htp – GBS” library preparation submissions for “LANS-96 Lysate” plates generated by the “Limber-Htp – ANOSPP Lysate Prep” extraction pipeline, in order to simplify and speed up the ANOSPP GBS submission process, as well as reduce the burden on the SSRs.
Acceptance Criteria:
- Remove the requirement for a separate “Limber-Htp – GBS” submission template to be completed for LANS-96 Lysate plates created by the “Limber-Htp – ANOSPP Lysate Prep” extraction process.
- Assign the correct primer panel to the LANS-96 Lysate plate.
- LANS-96 Lysate plates containing samples from the ANOSPP study will require primer panel “ANO_SPP_v1.0”.
- Allow some method to change the primer panel associated with this automated request in the event that the ANOSPP panel gets an updated version in the future.
- The system automatically triggers the second submission upon the completion of the non-destructive extraction.
- Back-and-forth communication requirements between teams are minimized, allowing for faster processing times.
- The automation must be tested with existing submissions to ensure compatibility and correctness.
Dependencies: We are currently aiming for 24 plates per week to be submitted for the ANOSPP project through the “Limber-Htp – ANOSPP Lysate Prep” extraction pipeline. This story would halve the number of submissions for the SSR and enable the process to scale up throughput in the future.
This feature should bring the submission approach in line with other Non-Destructive Extraction pipelines (e.g. “Limber-Htp – Bioscan Lysate Prep” DPL-903)
No well-level fails are required.
Process maps for the “Limber-Htp – ANOSPP Lysate Prep” extraction pipeline are attached.
One for the pipeline itself, one to indicate how the Lysate Prep pipeline interacts with the start of GBS. The second process map also includes Faculty’s later, separate submission of samples for WGS based on GBS sequencing results, which is not relevant to this story, but gives wider context.
Out of Scope (To be considered later)
- Notifications are sent to relevant teams when the second submission is initiated.
- A confirmation log is generated for each automated submission for tracking and auditing purposes.
User Story
As R&D (Scott T) I would like an automated method to generate “Limber-Htp – GBS” library preparation submissions for “LANS-96 Lysate” plates generated by the “Limber-Htp – ANOSPP Lysate Prep” extraction pipeline, in order to simplify and speed up the ANOSPP GBS submission process, as well as reduce the burden on the SSRs.
RT Ticket - https://rt.sanger.ac.uk/Ticket/Display.html?id=811574
Who are the primary contacts for this story Scott T (R&D)
Knowledge or Stake holders Lena H-H (SSR) Liz H (SSR)
Lynda D (Sample Prep)
Acceptance Criteria In order to be successful, this story should:
Remove the requirement for a separate “Limber-Htp – GBS” submission template to be completed for LANS-96 Lysate plates created by the “Limber-Htp – ANOSPP Lysate Prep” extraction process. Assign the correct primer panel to the LANS-96 Lysate plate. LANS-96 Lysate plates containing samples from the ANOSPP study will require primer panel “ANO_SPP_v1.0”. Allow some method to change the primer panel associated with this automated request in the event that the ANOSPP panel gets an updated version in the future.
Additional context or information
For the LANS-96-Stock plates, two sequencescape submissions are required in total. One submission is required for the extraction process (where a LANS-96-Stock plate generates a LANS-96 Lysate plate), and a separate submission is required for the LANS-96 Lysate plate to proceed to GBS library preparation.
We are currently aiming for 24 plates per week to be submitted for the ANOSPP project through the “Limber-Htp – ANOSPP Lysate Prep” extraction pipeline.
This story would halve the number of submissions for the SSR and enable the process to scale up throughput in the future.
This feature should bring the submission approach in line with other Non-Destructive Extraction pipelines (e.g. “Limber-Htp – Bioscan Lysate Prep” DPL-903)
No well-level fails are required.
Process maps for the “Limber-Htp – ANOSPP Lysate Prep” extraction pipeline are attached.
One for the pipeline itself, one to indicate how the Lysate Prep pipeline interacts with the start of GBS.
The second process map also includes Faculty’s later, separate submission of samples for WGS based on GBS sequencing results, which is not relevant to this story, but gives wider context.