Y24-460 - Confirm and update fragment sizes for WGS Branch - Automated Submission

[StephenHulme]

Description
The WGS Branch - Automated Submission created in #1982 requires fragment_size_required_from and fragment_size_required_to to be set to appropriate values - the current ones are copy-pasted from another submission and can be considered incorrect.

Acceptance Criteria
The following outputs from the research are produced:

• The correct values are discovered
• The values for fragment_size_required_from and fragment_size_required_to are replaced with the correct values
  • See:

    # config/purposes/lcm_triomics.wip.yml
    
    LCMT DNA Adp Lig:
     :submission_options:
       WGS Branch - Automated Submission:
         request_options:
    

Who the primary contacts are for this work

• @yoldas
• @andrewsparkes
• @KatyTaylor
• @StephenHulme

Knowledge or Stake holders

• Scott T

Additional context or information
Any other useful context or information that may be useful.

[StephenHulme]

Putting this into Todo since it is a component of the already prioritised sanger/sequencescape#4199 - please feel free to re-prioritise.

[yoldas]

Question: what would be the correct request options for the WGS branch automated submission?

We have used the following configuration for the WGS Branch - Automated Submission for testing:
Template Name: Limber-Htp - LCM Triomics WGS
Request Options:
Library Type: LCM Triomics WGS
Fragment size required (from): 200
Fragment size required (to): 800
PCR Cycles: Not specified

The answer received by email (27 November)

"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."

[KatyTaylor]

Update: this is 'on hold' because we're waiting for confirmation as to what the fragment sizes should be.

[TWJW-SANGER]

Moving to done.
The pipeline has been implemented with fragment sizes originally specified the only question is if these are correct.
Should they need to change we will change them but given the lack of response we can unwip the pipeline and remind the stakeholder that these values are somewhat suspect.