Ok let's call this week's meeting off then. I'll try to work on the project on the side during summer a bit. And resume our meetings 2nd Thursday September!

If anything pops-up, just message here 😉

Hi all, if its ok I'm going to cross post this here, since this is a frequent situation in our meta-omics world. Any thoughts on process substitution vs separate processes for concatenation? https://nfcore.slack.com/archives/CE6SDBX2A/p1785765681829679 Would be applicable for any of the tools that support merging files from the same sample across sequencing runs.

Quick update for the nf-core meta-omics pipeline flow use case: I started playing with some of the datasets in the study that @Daniel Lundin suggested (Brackish surface water), that contain MT, MG and Amplicon samples, which is exactly what we want. Already ran

fetchngs

for the pilot use-case, and currently running

metatdenovo

on our cluster. It doesn't make sense to run

detaxizer

since there is no host in this environment. I made my use-case repo public, so feel free to have a look and make any PRs with suggestions/corrections etc: github.com/vagkaratzas/meta-omics-sig Something that you might find insightful, and gives flavour to the project: vagkaratzas.github.io/meta-omics-sig I made a github page for the repo, that can act as both project tracking resource, as well as educational material, since users can click on a pipeline and see a couple of sentences as info, expected inputs/outputs (chained pipelines), and links to each nf-core site

new meta-omics pipeline map PR for the website: github.com/nf-core/website/pull/4348 Care to have a look? Added seqsubmit, compressed size, removed old unused ones

@Julian Flesch like my converters here? 😛 github.com/vagkaratzas/meta-omics-sig/…/converters vagkaratzas.github.io/meta-omics-sig evolving with the runs..metatdenovo (198252 proteins) and proteinfamilies (405 families) executed for the pilot LMO study

Ran detaxizer (for phiX174) and proteinfamilies for the pilot dataset: vagkaratzas.github.io/meta-omics-sig detaxizer found minimal cases, that hadnt made it into metatdenovo's results anyway - so no need to rerun metatdenovo (198,252 proteins) and proteinfamilies (405 families) so far. Deciding next run for the pilot LMO dataset: 1. viralmetagenome: bots say NO:

1. Wrong size fraction

ERR13967264  LMO metagenome 2016-03-15 2 m depth, filter fraction: 0.2, replicate a
             WGS | METAGENOMIC | RANDOM

The LMO metagenome is material collected on a 0.2 µm filter, library_selection: RANDOM — no viral enrichment, no hybrid capture. Free virions are 20–200 nm; they pass through 0.2 µm into the filtrate, which is discarded. What you'd actually be looking at is prophage in bacterial genomes, intracellular replicating phage, and whatever NCLDV is big enough to be retained. That's a real signal, but it's not a virome, and it's not what the pipeline expects.

2. Wrong pipeline purpose — the defaults give it away

viralmetagenome is "reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture." Then: scaffold to centroid → iVar consensus → intra-host variants. This is the pipeline you run when you have a known-ish virus in a sample and want its consensus genome plus within-host diversity. "Intra-host variants" has no meaning for a Baltic Sea community, and RVDB/Virosaurus are the wrong references for marine phage — most contigs would simply not hit the reference pool, which is the step the whole workflow pivots on.

2. MAG: bots go YES:

1. It closes the loop on issue #100. Patch group and short_reads_platform into detaxizer's sheet, feed it to mag, and you have evidence the proposed fix is correct — not just that the current output is broken.
2. It unblocks mag → proteinfamilies, the route the metro map has always drawn and this project has never been able to test, because mag emits no protein FASTA. You'd add the ORF-calling step the table keeps flagging — and you already have run 03's 405 families from the metatdenovo route as the comparison. MAG-derived vs MT-derived proteins into the same pipeline is a genuine methods result, not just an edge tick.
3. It's the prerequisite for seqsubmit, the chain's only exit back to the archive.

they keep saying that mag cannot produce proteins, when it can though. @Joon Klaps @James Fellows Yates if you disagree with the above, poke me

No monthly meeting this month either because of vacations. Next meeting scheduled for 10 September.

Not related to meta-omics, but to pipeline-chaining. I assume you have solved this: how do you generate a samplesheet for a downstream pipeline that contains the published output?

Hey all! Can we move this month's meeting to the 17th (instead of 10th)?

Thanks for the vote, let's move it for the 17th then 😄

Hello, I was wondering if it has ever been discuss the development of a pipeline focused on identifying mobile genetic elements within metagenomes or MAGs?

Hi all! Just a reminder that we will hold our meta'omics monthly meeting this Thursday at 1500 1600 CEST, through WorkAdventure: play.workadventu.re/@/nf-core/nf-core/office Feel free to add any points for discussion under

Specific

in hackmd.io/…?… See you on Thursday!

Project Board for reference: github.com/orgs/nf-core/…/1 drop quick ideas there or on Slack

pipeline chaining caught another bug, this time in mag 5.5.0: github.com/nf-core/mag/issues/1115

^BUSCO batch mode leaks lineage state between bins: bin_summary.tsv mixes odb10/odb12.2, mislabels domains and misaligns columns

The problem is within BUSCO 6.1.0 though

I've been cooking on something this week to solve various pain points that I have found while working on my metagenomics pipeline. What was originally meant to be a little swiss-army knife toolset for dealing with bin FASTA files turned into a little tool suite for importing, collating and filtering data (sequences, annotations, coverage, taxonomy) across a whole set of binners, and to generate MiMAG scores when data is available. It reads in data into a custom JSON format, and can then re-export it in per-bin FASTA, GFF (if annotations are loaded), or contig2bin format. It's designed to be composable via piping between commands. Forgive the LLM-generated README, but I wanted to share early and see if this is something others would find useful/would be interested in contributing? github.com/prototaxites/bintools

New location, I had to rename the package due to a PyPI conflict: github.com/sanger-tol/metabintools

Another issue while running the pipelines, this time for #CEA7TBJGJ , so check this one before next release @Daniel Straub: github.com/nf-core/ampliseq/issues/1081 Simple fix

either the suggested one, or create an updated container for it

I finally made a metro map for nf-core/ampliseq. Its simplified regarding modules and connections to rather highlight options and capabilities but also attempting to advance understanding of the pipeline concept. Not sure if I made the right choices, so I would appreciate feedback. Potential issues that I saw but accepted as simplification: • ONT & Illumina both default • crossover ONT to Illumina (theoretically, someone could set for Illumina data Savont, or for ONT data DADA2, but would need explicit overwriting) • DADA2 steps heavily simplified • every single step is optional. One of DADA2 and Savont must run when raw reads are input. With ASV intermediate input, even those are omitted. However, ASV input isnt shown because most downstream stuff isnt compatible then (no abundance profile!). So I opted not to loop around optional steps.

Hey all! just a reminder for this month's meta'omics meeting for Thursday 8th at 1500 1600 CEST, through WorkAdventure: play.workadventu.re/@/nf-core/nf-core/office as per usual. Vote thumbs up/down if can/can't make it.

Feel free to already drop items for discussion in the agenda under

#### Specific

: hackmd.io/…?…

^Mooorning! Just a reminder for today's meeting at 15:00 CEST

Happening now!

Hi! I have a question about bwa-mem2+samtools usage I’m wondering are there any good solutions from nf-core not just install each module separately

bwa index, bwa mem, samtools view, samtools sort, samtools index

but use pipes in one module like

bwa index | bwa mem | samtools view | samtools sort | samtools index

because it saves space and basically works very good and quick with piping outputs between those tools? maybe not the best place to ask but I feel people here should have enough knowledge using bwa + samtools…

The first release of nf-core/bacmodel is out! 🎉🎉 You can now try it out and use it for your bacterial modelling workflows! 🦠 I’d be very happy to hear your feedback — whether it’s about the workflow, the outputs, documentation, or anything that could be improved. If you give it a try, please let me know what works well and what doesn’t! Thanks, and happy hackathon 😊

a question to the sig group, is Seqera platform necessary requirement to run chained pipelines for the meta-omics project? @Evangelos Karatzas