Y24-194 - LCM WGS/EM-Seq - Pipeline configuration and integration test

[andrewsparkes]

User story
As Scott and Sara we would like tracking developed for the new LCM WGS/EM-Seq pipeline. A process map and associated documentation contain the details required.

Who are the primary contacts for this story
Scott G (R&D)
Sara W (Lab ops)

Who is the nominated tester for UAT
TBC

Acceptance criteria
Sub-stories have been created that should cover this story. The following acceptance criteria are for checking everything is joined up and tested:

• Integration Suite test for whole pipeline, including the same samples going down both the EM-Seq and WGS branches.
• Confirm Submission names, request type and library type names with stakeholders

Dependencies
This story is divided into two stories for EMSeq and WGS branches and a common initial part up to the Adp Lig plate. Transitive dependencies have been added here as well to find them easier.

• Y24-271 - Configuration and integration test for the start of LCM Triomics Pipeline
• Y24-266 - LCM Triomics Pipeline configuration and integration test for EMSeq branch
• Y24-267 - LCM Triomics Pipeline configuration and integration test for WGS branch
• Y24-268 - Create a presenter for automated submission for WGS branch on Adp Lig plate
• Y24-460 - Confirm and update fragment sizes for WGS Branch - Automated Submission

References
This story has a non-blocking relationship with:

• Y24-196 - LCM WGS/EM-Seq - Research - Test pipeline configuration This is the research story about the branch point.
• LCM WGS/EM-Seq Bed verifications This is the following story for bed verifications.

Additional context
See the following documents for detailed information (e.g. steps and plate purposes):
LucidChart Process Diagram
Overview document
CLCM Multiomics document

Mostly this story is standard SS and Limber configuration.
These are the tricky bits I can see (also see docs above):

1. Submissions - Initial submission is on the Lysate plate at the start, for DNA prep (RNA branch may be added later). Then part way along this brnaches into WGS and EM paths. Both branches will always happen, in parallel. You cannot use one submission all the way through because of this later branch. But as both will always happen for all samples then you don't want to have to wait on the SSR to manually create submissions at the branch point. Possibly create an automatic submission to branch off the EM path? Have to try out some options and see what works best.
2. There are several places where they have annotated bed verifications that want to check multiple plates in advance. We can't do bed verifications that involve transfers that go A->B->C, but we should be able to do verifying ones that check plates are in specific positions. But only if LIMS already knows about the barcodes of those plates, so they'd have to be set up in advance. Includes crossing the branching point.
3. They would like to print out labels in advance for these steps that include the branching. I'm not sure we can do that.

The research story for the branching point is Y24-196 - LCM WGS/EM-Seq - Research - Test pipeline configuration

[yoldas]

Library Types (Email)

WGS:

"For the WGS libraries that have recently been submitted for sequencing after manual EMseq library preparation they have been using:
o Library Type: LCMB
o Fragment size required (from): 450
o Fragment size required (to): 450"

However please let me confirm this with the SSRs, because using 450 for both the to & from library sizes is not what I was expecting to see.

EMSeq:

"For the EMseq libraries, there is a pre-existing library type ‘emSEQ’ which can be used to maintain consistency with the manual EMseq work done up to now."

[yoldas]

We have updated the library types based on the feedback by email on 27 November:
Y24-194 PR [Sequencescape] UAT Updates 3 LCM WGS EMSeq pipeline configuration and integration test
Y24-194 PR [Limber] UAT Updates 3 LCM WGS EMSeq pipeline configuration and integration test
Y24-194 PR [Integration] UAT Updates 3 LCM WGS EMSeq pipeline configuration and integration test

However, we still need to confirm the WGS submission options, which will be finalised by the story
Y24-460 - Confirm and update fragment sizes for WGS Branch - Automated Submission

We have also created the following stories as enhancements for later.
Y24-463 - Custom text for robot start buttons
Y24-464 - Create multiple plates in pending state at once
Y24-489 - Show the robot button Bravo LCMT DNA Adp Lig => LCMT DNA Lib PCR after the WGS branch submission

[yoldas]

I have set superseded_by on the old submission: Limber-Htp - LCM Triomics EMSeq in UAT; the replacement is Limber-Htp - LCM Triomics .

Note that the request type for the Limber-Htp - LCM Triomics submission is still 'LCM Triomics EMSeq' . This is because the pipeline starts with EMSeq and branches off for WGS later and (RNASeq in the future).