DPL-050 Automated processing on Beckmans: New LH lab Newcastle [Heron]

[rl15]

User story
DPL-050 | As representative fo LH labs (Alan K) I would like to begin receiving covid samples from new LH lab; Newcastle to support automated picking on robotics.

Who are the primary contacts for this story
Alan K (PAM)
Sonia G (PAM)
Cristina A (PAM)

Acceptance criteria
To be considered successful the solution must allow:

• Plate maps standard distributed by Alan to Newcastle lab lead
• Expected file name (individual files per plate): ICHNEnnnnnc.csv
• Enable read from SFTP share /project-heron_newc (Share is there, not checked psd-lims has read access)
• Create lab_id: NCL
• Support creating a plate with barcode ICHNEnnnnnc (where n = character and c = letter) in Sequencescape
• New COG-UK prefix: NEWC
• biomek_labware_class: kingfisher DWP

Assumptions

    No unconsolidated plate map file type expected

Additional context
Change: Expected on line from 19th July

[KatyTaylor]

Created draft branches in crawler, baracoda and sequencescape while sftp access is granted and some more information is confirmed.

[KatyTaylor]

Pull requests:
#400
sanger/baracoda#166
sanger/sequencescape#3267

[KatyTaylor]

Tested this in our UAT environment today, using the file that’s on the SFTP - ICHNE00014W.csv

It didn’t process successfully (see entry at 26/07/2021, 14:31:05 in Lighthouse UI) – the main issue seems to be that their CT targets use a different capitalisation to the plate map standard.

Plate map standard	Newcastle file	Difference
ORF1ab	Orf1ab	Capitalisation
S gene	S Gene	Capitalisation
N gene	N Gene	Capitalisation
MS2	MS2	No difference