Longread only functionality

[muabnezor]

This PR adds long-read only functionality to mag.

closes #662, #659, #275

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
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• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

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[d4straub]

I only had a short look, sorry, but I just wanted to express my gratitude that you tackle long read assembly!

[muabnezor]

I only had a short look, sorry, but I just wanted to express my gratitude that you tackle long read assembly!

My pleasure hehe. Still WIP. I have to tidy up the code and run some validation on real data, but we're getting there!

[muabnezor]

So far in this PR I have

• changed the validation schema to allow for long read only input
• Added a host removal track for long reads using minimap2 as aligner
• Added Flye and metaMDBG as longread assemblers
• refactoring of code so that all the assembly code is moved to a subworkflow

Downstream from the assembly, except for the binning preparation, the long read and short read assemblies are treated the same.

[muabnezor]

Me and some colleagues are running some tests on ont data, and I think this works as expected. We will continue testing and play around with the parameters, but if anyone wants to have a look through the code and suggest improvements, that would be awesome!