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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• Make sure your code lints (nf-core pipelines lint).
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• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• 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]

@jfy133 thanks for the review. I think I have addressed your suggested changes. I hope the tests go well!

[prototaxites]

FYI all - we have had a pretty catastrophic outage on our cluster and I'm not currently able to finish the test I was running - and it's unlikely I'll get a chance to finish it any time soon.

But I'm happy with the PR as-is - the long-read bits were working well after we fixed those wee bugs!

[jfy133]

Thanks for the heads up Jim!

@muabnezor I will check the changes later today or tomorrow. But our lab have just started getting our own nanopore data, so I'll test in that myself. It's only isolate data so shouldn't take too long

[jfy133]

@nf-core-bot fix linting

[jfy133]

@muabnezor From my test - and now looking at test_long output here too, the final bin_summary process doesn't get executed.

Is that to be expected? This is one of the critical output files...

[jfy133]

Code-wise I'm happy now!

I just want to explore the results a bit more (see comment above about missing bin_summary.tsv process

[jfy133]

@muabnezor is there any reason why you didn't set this?

[muabnezor]

@muabnezor From my test - and now looking at test_long output here too, the final bin_summary process doesn't get executed.

Is that to be expected? This is one of the critical output files...

no, this is not expected, are any of the channels from your test empty going into the process?

[jfy133]

@muabnezor From my test - and now looking at test_long output here too, the final bin_summary process doesn't get executed.
Is that to be expected? This is one of the critical output files...

no, this is not expected, are any of the channels from your test empty going into the process?

I'm running another long running test on my laptop at the moment so I can't check (unfortuantely)... any chance you could look? Otherwise I will do tomorrow

[muabnezor]

I'm running another long running test on my laptop at the moment so I can't check (unfortuantely)... any chance you could look? Otherwise I will do tomorrow

Sorry, can't get to that this week, I will have a look at it on monday

[muabnezor]

@jfy133
I'm looking into the bin_summary stuff, it ran fine a couple of commits ago, and I missed that it stopped running. good catch. I don't know if it is something I've done, or if the DEPTH process has had any changes recently, since I haven't touched anything after all the binning is done in this PR I think. I will try to get to what's wrong, but I'm currently having a lot of work to be done before summer vacations, so I don't know how much time I can spend on this.

[jfy133]

I did some exploration last night: https://nfcore.slack.com/archives/CE9MS66BS/p1749154196789889?thread_ts=1748503770.520549&cid=CE9MS66BS

Essentially for some reason there is an extra meta being added somewhere meaning the reeads and bins can't be combined in DEPTHS()

@dialvarezs as you are waiting for this to be able to continue with your stuff, any chance you could have a look?

[jfy133]

And to clarify @muabnezor it's not the DEPTHS subworkflow itself that is the issue, just the contents of the input channels :)

[muabnezor]

@jfy133, there, I think I fixed it in the last commit in how depth channel is returned from binning workflow. I think (and hope!) this will fix it. Thanks for helping with this!

[jfy133]

@muabnezor testing!

[jfy133]

Can confirm bin_summary.tsv now generated!

Everything else we can fix in post-production 😬

Thank you very very very much @muabnezor ! For the huge effort and your patience on this one, like I said before - many people are going to be very happy!

Hit that merge button!

[muabnezor]

@jfy133 just merged! Thanks for all the help with this PR!