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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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Artic V5.3.2 primer scheme #80

Closed VLeducq closed 1 year ago

VLeducq commented 1 year ago

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 commented 1 year ago

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 https://github.com/epi2me-labs/wf-artic/blob/428300f74d76e4af18048799db37beb754ec6475/nextflow_schema.json#L69-L91

mattdmem commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Hello,

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

Thanks

Matt

CONFIDENTIAL

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

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mattdmem commented 1 year ago

Added custom scheme instructions to README in v0.3.30