Updating tools/medaka from version 1.4.4 to 2.0.1

[planemo-autoupdate]

Hello! This is an automated update of the following tool: tools/medaka. I created this PR because I think the tool's main dependency is out of date, i.e. there is a newer version available through conda.

I have updated tools/medaka from version 1.4.4 to 1.5.0.

Project home page: https://github.com/nanoporetech/medaka/releases

[simonbray]

From the release notes:

Remove medaka_variant in deference of clair3.

No idea if wrapping this should be a priority: https://github.com/HKU-BAL/Clair3

Also, the documentation site is no longer accessible; I updated the links to point directly to the GitHub repo: https://nanoporetech.github.io/medaka/index.html

[simonbray]

in 1.6.0:

--qualities option for smolecule and stitch to output consensus fastq.

[pvanheus]

From the release notes:

Remove medaka_variant in deference of clair3.

No idea if wrapping this should be a priority: https://github.com/HKU-BAL/Clair3

There's an open issue on clair3: #4299

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.