A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

*Hackathon thread / brainstorm!* 

Hi everyone! I'm a PhD student at Université de Sherbrooke :flag-ca: , working on multiple sequencing projects in microbial ecology, and a new contributor to nextflow/nf-core. I'll be attending the nf-core Barcelona hackathon :catalunya: in October. I'm curious to know if anyone else in /mag will be there?

The main reason for this thread: I'd like to gather ideas for a project submission, leveraging the hackathon to push improvements for /mag. Submitting a project ahead of the hackathon will help recruit participants to work on those ideas.

I identified and discussed a few roadblocks that became issues when processing large amounts of samples, but I have no idea of the scope of work we can tackle over two days (which will certainly depend on how many people hop on the mag train). For that reason I'd love to provide a list of potential projects/tasks/etc. that we collectively think could improve mag, and that might motivate more people to join the effort!

So far, we discussed :

• *QUAST alternative:* quast is overkill for what it's required for, quickly clutters work/ (~250 files per bin) causing inode quotas busts for larger projects (on most Canadian supercomputers at least; see <https://nfcore.slack.com/archives/CE9MS66BS/p1786628321715299|https://nfcore.slack.com/archives/CE9MS66BS/p1786628321715299>). Some suggested seqkit stats, seqfu, or creating one from scratch. If it can run multiple files in a single job, all the better.
• *Bin entry point :* add an additional entry point for the pipeline, by providing bins directly; would be useful for larger projects, allowing work/ cleanup post-binning, and increasing the overall modularity of /mag . 
That's it for now. Looking forward to hear your ideas and to know who will be there on October 15-16th !

I think the QUAST replacement is perfect doable in 2 days. It seems that <https://github.com/BioInfoTools/BBMap/blob/master/sh/statswrapper.sh|github.com/BioInfoTools/BBMap/blob/…/statswrapper.sh> could be a good replacement (have basically the same stats that QUAST, seqkit/seqfu not really). Will need a nf-core module, and integration with MultiQC too (either manual o with plugin).

The bin entry point  I think it requires more discussion. We can arrange a meeting or discuss it thoroughly here to address the design, because it will need a new samplesheet, adding tests, etc.

Another one could be adding myloasm. This should be a quick one too.

But I agree with QUAST replacement being the most feasible as you are touching less parts of the pipeline.

Bin entry point like Diego says might require more discussion and also you'll be touching many more files which might be harder if you're not very familiar with the whole code base.

<@UR949F5LG> was planning to implement de dereplication. Do you plan to do it during the hackathon or before that? :grin:

I think I can start before the hackathon but I'm a little uncertain if we have settled on all details. I won't be in Barcelona

yes bin entry is certainly out of my league at the moment. I'd be happy to join the discussion whenever it happens though!

I just saw the massive list of tools in <https://github.com/nf-core/mag/issues/1022|github.com/nf-core/mag/issues/1022> ! There's plenty :sweat_smile: