Y24-266 - LCM Triomics Pipeline configuration and integration test for EMSeq branch

[yoldas]

User story
As PSD, we would like to create configuration and integration test for the EMSeq branch of the LCM Triomics WGS/EMSeq pipeline to enable parallel development of the EMSeq branch of the pipeline, lower path of the Process Diagram.

Who are the primary contacts for this story
Abdullah (PSD)
Andrew (PSD)
Katy (PSD)
Shiv (PSD)
Scott G (R&D)
Sara W (Lab ops)

Who is the nominated tester for UAT
TBC

Acceptance criteria
To be considered successful the solution must allow:

• Sequencescape and Limber configuration of the EMSeq branch
• Integration Suite test with placeholder manual transfers where the bed verifications will go (separate story)

Dependencies
This story is blocked by the following dependencies:

• Y24-271 - Configuration and integration test for the start of LCM Triomics Pipeline

References
This story is part of the parent story:

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

Additional context
We do a common initial submission for WGS and EMSeq branches.

The initial part up to and including Adp Lig plate is common for WGS and EMSeq branches.

We allow pre-creation of the following plates using Permissive presenter: LCMT DNA frag, LCMT DNA end prep, LCMT DNA adp lig, LCMT EM ox and LCMT EM ox stop

[yoldas]

Current WIP names

WIP=013_lcm_triomics_plate_purposes,013_lcm_triomics_catalogue,018_limber_lcm_triomics_request_types,014_lcm_triomics_submission_templates

[yoldas]

GitLab Integration suite merge request: Y24 266 lcm triomics pipeline configuration and integration test for emseq branch

The branch name is y24-266---lcm-triomics-pipeline-configuration-and-integration-test-for-emseq-branch

The test for EMSeq is spec/limber/lcm_triomics_spec.rb .

[yoldas]

Tag Layout Template Names are common for both branches; received by email. I have added them to the LCMT EM LibPCR purpose config and updated the integration suite to use the dual index TS_pWGSB_UDI96 template.

TS_pWGSA_UDI96v2 (also known as pWGSA_UDI_tempi7s and pWGSA_UDI_tempi5s)
TS_pWGSB_UDI96
TS_pWGSC_UDI96
TS_pWGSC_UDI_tag60_61_swap
TS_pWGSD_UDI96

pWGSA_UDI_tempi7s and pWGSA_UDI_tempi5s refer to the tag groups for the first one. See the query in the screenshot.

[yoldas]

For UAT Testing:

We have deployed the EMSeq branch of the LCM Triomics Pipeline (Y24-271 and Y24-266) into the UAT environment.

There is no bed verification in this story, which will be implemented by Y24-198.

EMSeq branch is the lower path in the process map. Note that there will be another branch off Adp Lig plate but it is a separate story (Y24-267)

• The EMSeq branch starts with the submission Limber-Htp - LCM Triomics EMSeq on LCMT Lysate plate.
• The request type for this submission is LCM Triomics EMSeq. Note that this is a library request which is used until the end of the EMSeq branch. We could not have a separate DNA Prep request for the common part with WGS because of pre-creating plates across the branch point.
• The library type is set to LCM Triomics EMSeq for the branch.
• The EMSeq branch allows creation of the following plates without any transfers: LCMT DNA Frag, LCMT DNA End Prep, LCMT DNA Adp Lig, LCMT EM TET2 Ox, and LCMT EM TET2 Stop .
• Once they are created, manual transfers into them can happen in that order (no bed verification in this story)
• Concentrations for LCMT EM PCR XP plate can be added by "Generate concentrations for a plate" UAT action for the test. (Quanthub upload of concentrations)
• A tag plate is coming into the LCMT EM Lib PCR plate.
• The LCMT EM Pool XP tube needs a custom pooling file.
• The pipeline continues until the end to create the LCMT EM Pool XP Norm tube.

UAT environment:
Sequencescape: https://uat.sequencescape.psd.sanger.ac.uk/
Limber: https://uat.limber.psd.sanger.ac.uk/