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Y25-071 - As a SSR (Liz C) I would like to be able to use the Bulk Sequencing Request page with the Element Aviti sequencer so that we can use the new sequencer. #4649

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TWJW-SANGER opened this issue Jan 30, 2025 · 0 comments

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TWJW-SANGER commented Jan 30, 2025

User story
As a TL (Tris) I would like to be able to use the Bulk Sequencing Request page with the Element Aviti sequencer so that we can use the new sequencer.

Who are the primary contacts for this story
Tris B
Mike Q
Liz C
See our Confluence project page for "Element Aviti"

Who is the nominated tester for UAT
Liz C

Acceptance criteria

Consider if these features can be featured flagged to decouple testing and deployment.
To be considered successful the solution must allow:

  • For every entry in the Submission template combobox that currently ends "MiSeq sequencing" or "NovaSeq 6000 paired end sequencing" we want an additional option but ending with "Element Aviti sequencing". Following the existing pattern with sequencing platform at the end of the template name.
  • The user can select from 3 Flowcell Kit Types - LO (Low Output), MO (Medium Output), HO (High Output)
  • For the LO (Low Output) flowcell kit the user can select a Read Length of 150.
  • For the MO (Medium Output) flowcell kit the user can select a Read Length of 75,150 or 300.
  • For the HO (High Output) flowcell kit the user can select a Read Length of 75, 150, or 300.
  • The user must enter the "% Element PhiX needed" as a number between 0-100 inclusice.
  • The user can enter the "Fragment size required (from)" as an integer number using a spinbox (as per NovaSeq)
  • The user can enter the "Fragment size required (to)" as an integer using a spinbox (as per NovaSeq).
  • The user can select the Library Type from a dropdown as appropriate for the pipeline.
  • The user can select the number of PCR Cycles using a spinbox as appropriate for the pipeline.
  • Submissions to this pipeline will have an additional option field of "Low Diversity" which can have the values "Yes" or "No".
  • The user must explicitly select a value for "Low Diversity" for the submission to be valid - it cannot be left blank.
  • Batches created will belong to a new sequencing pipeline "Element Aviti"
  • The submissions created will appear on the /submissions page.
  • Excel templates generated for Element Aviti bulk submissions can be completed and uploaded to create bulk submissions.
  • Error validations and messages are extended to cover incorrect data entry for Aviti fields and options.
  • Update the Guidance text on the right hand of the page to include new Aviti Element fields and information

Additional context
The bulk submission page can be found at /bulk_submissions/new

Add any other context or screenshots about the feature request here.

@psd-issuer psd-issuer bot changed the title As a SSR (Liz C) I would like to be able to use the Bulk Sequencing Request page with the Element Aviti sequencer so that we can use the new sequencer. Y25-071 - As a SSR (Liz C) I would like to be able to use the Bulk Sequencing Request page with the Element Aviti sequencer so that we can use the new sequencer. Jan 30, 2025
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