Artic V5.3.2 primer scheme

[VLeducq]

What happened?

Hi,
Would it be possible to update the available primers schemes to include the IDT ARTIC V5.3.2 primers ?

Thanks

Operating System

ubuntu 20.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - CLI Execution Profile

Singularity

Workflow Version

v0.3.25

Relevant log output

none

[ammaraziz]

This is an issue for us as well except for Midnight V5 primers.

I've forked the repo, added V5 primers but I get this error:

• --scheme_version: Midnight-ONT/V5 is not a valid enum value (Midnight-ONT/V5)

I needed to add Midnight-ONT/V5 here

wf-artic/nextflow_schema.json

Lines 69 to 91 in 428300f

	"scheme_version": {
	"type": "string",
	"default": "ARTIC/V3",
	"description": "Primer scheme version.",
	"help_text": "This is the version of the primer scheme to use, more details about primer shemes can be found [here](https://labs.epi2me.io/ont-midnight-scheme-update/).",
	"enum": [
	"ARTIC/V1",
	"ARTIC/V2",
	"ARTIC/V3",
	"ARTIC/V4",
	"ARTIC/V4.1",
	"Midnight-ONT/V1",
	"Midnight-ONT/V2",
	"Midnight-ONT/V3",
	"NEB-VarSkip/v2b",
	"NEB-VarSkip/v1a-long",
	"NEB-VarSkip/v2",
	"NEB-VarSkip/v1a",
	"Midnight-IDT/V1",
	"ONT/V1",
	"ONT/V4.1"
	]
	},

[mattdmem]

Hi Both,

As far as I'm aware we do not have a version 5 of our primers (Midnight-ONT) - I guess you mean the Midnight-IDT scheme?

You can add custom schemes, instructions on how to do so can be found here: https://labs.epi2me.io/ont-midnight-scheme-update/#custom-primer-schemes

Thanks

Matt

[ammaraziz]

Hi Matt,

I might have gotten my wires crossed with which primer scheme we're using. I fumbled my way into adding a custom primer scheme.

It would be good to have the custom scheme instructions in a more prominent place on github repo. Even simply linking to it is sufficient enough.

Thanks,

Ammar

[mattdmem]

Hello, Yes, this is a good suggestion. We’ll add the instructions on how to use custom schemes to the README. Thanks Matt CONFIDENTIAL

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________________________________ From: Ammar Aziz ***@***.***> Sent: Wednesday, June 7, 2023 4:30:17 AM To: epi2me-labs/wf-artic ***@***.***> Cc: Matt Parker ***@***.***>; Comment ***@***.***> Subject: Re: [epi2me-labs/wf-artic] Artic V5.3.2 primer scheme (Issue #80) Hi Matt, I might have gotten my wires crossed with which primer scheme we're using. I fumbled my way into adding a custom primer scheme. It would be good to have the custom scheme instructions in a more prominent place on github repo. Even simply linking to it is sufficient enough. Thanks, Ammar — Reply to this email directly, view it on GitHub<#80 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AD3IA7XH67NKLQFFG7DR2LTXJ7YUTANCNFSM6AAAAAAYEZYLPA>. You are receiving this because you commented.Message ID: ***@***.***> IMPORTANT NOTICE: The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, re-transmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. Although we routinely screen for viruses, addressees should check this e-mail and any attachment for viruses. We make no warranty as to absence of viruses in this e-mail or any attachments. CONFIDENTIAL

[mattdmem]

Added custom scheme instructions to README in v0.3.30