Updating tools/tb-profiler from version 4.4.1 to 6.5.0

[planemo-autoupdate]

Hello! This is an automated update of the following tool: tools/tb-profiler. I created this PR because I think the tool's main dependency is out of date, i.e. there is a newer version available through conda.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/tb-profiler from version 4.4.1 to 4.4.2.

Project home page: https://github.com/jodyphelan/TBProfiler/releases

For any comments, queries or criticism about the bot, not related to the tool being updated in this PR, please create an issue here.

[bgruening]

--kmer_counter might be relevant

[bgruening]

ping @pvanheus

[pvanheus]

Thanks for the ping @bgruening - really cool to see that this passes all tests. As to the --kmer_counter - I see the upstream author has added the option for using dsk as an alternative to kmc. I've asked why... because dsk seems rather old and not well maintained.

I don't think that adding the --kmer_counter option is a priority, but before it is added the upstream bioconda package would need to add dsk as a dependency.

Since this is not a time-critical update, I'll review this update after getting a response from Jody on the dsk issue.

[apetkau]

I've noticed this PR is a bit out-of-date and there have been later PRs that have been made to update tb-profiler. Should updating to 6.3.0 be made in this PR, or in another PR?

[bgruening]

Please feel free to start a new PR. Whatever is easier for you.

[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.

[apetkau]

We are going to start working on fixing this up next week.

[bgruening]

thanks @apetkau!

[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.