Latest medaka models not available - update artic module

[tavareshugo]

Description of the bug

The latest medaka models cannot be used at the moment, since they are not available through artic 1.2.2.
I have made a pull request on the core modules to update the version to 1.2.3, if it gets accepted then the pipeline here would need to have its modules updated also.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[maxulysse]

I approved and the tests are now running (it was your first PR, so tests were not running).
I'll watch out and comment on your PR if needed

[maxulysse]

nf-core/modules#2557 is now merged, do you need help @tavareshugo on making the PR to update the medaka modules?

[tavareshugo]

@maxulysse some guidelines would be great, if you don't mind (but I'd like to learn what the workflow is!). Here's what I've done:

• Forked this repo
• Made a new (for now local) branch to bump artic version
• Ran nf-core update modules locally on that branch

But besides updating modules.json, this command also moved all these modules:

Moved viralrecon/modules/nf-core/modules/bcftools/sort to viralrecon/modules/nf-core/bcftools/sort.

For basically every nf-core module.

I guess this is not the way to do it?

[maxulysse]

I'll have a look first things tomorrow

[maxulysse]

ok, so main issue is that we need to merge the TEMPLATE sync (#331)
Can you pause your this PR for now?
I'll have a look at this #331 PR

[maxulysse]

@tavareshugo TEMPLATE has been synced and merged, you can now have a look at updating modules.
with nf-core tools (cf https://nf-co.re/tools/#installation), command should be simply:

nf-core modules update artic/guppyplex
nf-core modules update artic/minion

[tavareshugo]

@maxulysse submitted a pull request -- hope it's all good.

And thanks so much for guiding me in the procedure to make small contributions to these fantastic pipelines!

[maxulysse]

I saw, and it looks perfect <3