add support for long reads (PacBio and/or ONT)

[FranBonath]

[FranBonath]

need to figure out good QC tools (nanoplot (ONT, Minknow report), [longQC, currently doesn't work] , lima [for Pacbio, requires barcodes])

[TMAdams]

Been looking at possible tools for this. Mostly seem to have not been updated in years, though RabbitQCPlus claims to be usable on long read data. I'll test it locally and see how it goes.

Other options that look to be abandoned:
LongQC
SequelTools

[kedhammar]

I've implemented ToulligQC for our ONT runs, I've been happy with it :) It is already available as an nf-core module I believe.

Edit: I was wrong about the MultiQC integration

[TMAdams]

Been looking at possible tools for this. Mostly seem to have not been updated in years, though RabbitQCPlus claims to be usable on long read data. I'll test it locally and see how it goes.

Other options that look to be abandoned: LongQC SequelTools

RabbitQCPlus works on my system for HiFi data, it produces stats on read lengths and read quality as an html report, depends what we're looking for as output really.

[pontushojer]

I think Sequali would be a great option here. It has both a nf-core module and a MultiQC module, unlike e.g. TouliQC.

It is designed with both long and short reads in mind, so it would be more useful overall. I have used it on PacBio data, but there are example reports for both ONT and Illumina in the sequali documentation.