Hello, We have developed a QC tool named ToulligQC (https://nf-co.re/modules/toulligqc), dedicated to nanopore reads and it has recently been added to the nf-core modules library. Looking at your pipeline, our tool would be a good addition to do the raw read and post-extraction QC steps. The advantages of our tool are the following: - summary of runs presented as HTML report, with information about the sequencing run, basecalling and demultiplexing steps => read count and length distributions, homogeneity of the run, location of potential flow cell spatial biases, statistics about pass and fail reads - option to split QC by barcoded samples I have also observed when running your pipeline that when given mutliple fastq files, Nanoplot and NanoComp overwrite their own report and therefore only provides one report whilst ToulligQC will write and save a report for each file. Here is an example of a ToulligQC report. I am happy to work on the implementation of ToulligQC and submit a PR, but I wanted to confirm your interest first. Please feel free to reach out if you have any questions or require further information! 🙂

@Salomé Brunon: Fantastic! Thanks for letting us know. We will certainly be implementing this, it looks great - I will open up an issue in the repo to ensure we don’t lose track of it. As for the NanoComp issue - we will also look into this, we likely need to modify some of the outputs to prevent the overwrite, so thanks for reporting it as well!

@Lara Ianov Amazing, that's great news! Just to confirm, should I go ahead and work on adding the module to your pipeline or do you prefer to do it yourself?

Hi @Salomé Brunon - feel free to go ahead and do it yourself and submit a PR for us. If don’t see anything by sometime mid-late next week, I can add it myself (this will be my next window of opportunity to work on it). Thanks so much!

@Lara Ianov Perfect, I'll give it a go this coming week then 🙂

@Salomé Brunon: awesome, thanks for all the updates and great to see that there is no issue on Nanoplot/NanoComp (I was wondering what else it could be going on there, so glad it is working fine). And sounds good on the PR - I will keep an eye out for it and perform our tests on it as well once I get the notification!

@Lara Ianov - shout if you need any help with the overwritten outputs. Likely just need to make the filename variable during publishing.

Thanks @Phil Ewels: we got it all figured out. Should be all there in the dev branch ready for review 🙂

Great!