Add chopper and nanoq options for longread preprocessing

[muabnezor]

closes #661

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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• Make sure your code lints (nf-core lint).
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• Output Documentation in docs/output.md is updated.
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[jfy133]

Code looking good so far!

Missing updates to citations.md and output.md though!

[jfy133]

Also don't worry about linting and checkm tests, the format I'm fixing now in the template merge in #689 , and for checkM the database server is done

[muabnezor]

I realized that allowing the user to choose filtering tools other than filtlong for long reads might introduce an issue. Since filtlong now uses preprocessed short reads to filter the long reads, this means that long reads will piggyback on the short reads and also undergo host removal, assuming the host is removed from the short reads.

If the user opts to use chopper for filtering long reads, we might need to implement a separate process for host removal from the long reads. However, it may be better to address this in a future PR. What do you think, @jfy133?

[jfy133]

Hmm, might need some discussion when I'm not so tired, that said the issue might be related to #691, is that correct? Maybe if we update the filtlong module this is less of a problem? What do you think?

[muabnezor]

Hmm, might need some discussion when I'm not so tired, that said the issue might be related to #691, is that correct? Maybe if we update the filtlong module this is less of a problem? What do you think?

#691 is kind of related to this, but I think it is reasonable to use when running in hybrid mode. Maybe we can talk more during dev-hours?

[jfy133]

Yes let's talk then!

I've almost finished the template merge too so can be more involved after that too 👍

[muabnezor]

This should be ready for review @jfy133

[jfy133]

Woohoo! I'm travelling rest of today and travelling again second half next week, I'll try and slip it in Mon/Tuesday if I can