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Y24-267 - LCM Triomics Pipeline configuration and integration test for WGS branch #4289

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1 of 4 tasks
Tracked by #4199
yoldas opened this issue Aug 19, 2024 · 1 comment · Fixed by #4414 · May be fixed by sanger/limber#1991
Closed
1 of 4 tasks
Tracked by #4199

Y24-267 - LCM Triomics Pipeline configuration and integration test for WGS branch #4289

yoldas opened this issue Aug 19, 2024 · 1 comment · Fixed by #4414 · May be fixed by sanger/limber#1991
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EMSeq emSEQ Size: M Medium - medium effort & risk

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@yoldas
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yoldas commented Aug 19, 2024

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 WGS branch of the pipeline, upper 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 WGS branch
  • Integration Suite test with placeholder manual transfers where the bed verifications will go (separate story)

Dependencies

References
This story is part of the parent story:

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 do an automated submission on Adp Lig plate for the WGS branch when the plate is in passed state. We will enable a button to do the one-click submission when the plate is passed. This will allow the creation of the first plate of the branch (DNA Lib PCR).

@psd-issuer psd-issuer bot changed the title LCM Triomics Pipeline configuration and integration test for WGS branch Y24-267 - LCM Triomics Pipeline configuration and integration test for WGS branch Aug 19, 2024
@yoldas yoldas added the EMSeq emSEQ label Aug 19, 2024
@TWJW-SANGER TWJW-SANGER added the Size: M Medium - medium effort & risk label Aug 29, 2024
@SHIV5T3R SHIV5T3R self-assigned this Aug 29, 2024
@yoldas yoldas self-assigned this Oct 9, 2024
@yoldas
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yoldas commented Oct 9, 2024

Created branches:

Sequencescape: 4289-y24-267-lcm-triomics-pipeline-configuration-and-integration-test-for-wgs-branch
Limber: y24-267-lcm-triomics-pipeline-configuration-and-integration-test-for-wgs-branch
Integration Suite: y24-267-lcm-triomics-pipeline-configuration-and-integration-test-for-wgs-branch

I will be merging bed verification branches into these to continue.
Bed verifications for WGS path are already coded up in the bed verification story.
We have an idea about how Adp Lig behaviour looks like, integration suite can be made ready based on that.

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EMSeq emSEQ Size: M Medium - medium effort & risk
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