The third day of the #SnakemakeHackathon2026 at #TUM is about to end. We were very productive and I have merged over 20 pull requests that fix various bugs, clean up code, add new functionality and improvide user as well as developer experience. Thanks a lot to all the participants!
Well timed question. Indeed a student assistant will start on the preparation for being able to have #rust modules in the #Snakemake codebase via pyo3. We will start with the output file index. There might be the first #rust rewrite work already during hackathon in case somebody is interested.
I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...
The new #Snakemake releases in the last weeks (9.14.*-9.16) have massively improved the way Snakemake handles source files from github (wrappers, modules, scripts, envs), avoiding the github API entirely and caching (bare) git repos instead. This increases performance and avoid hitting API limits.
Ah - a friend told me! Use -noai after your search term
bsky.app/profile/zami...
We have released multiple new #Varlociraptor versions in the last weeks, providing various model improvements that further reduce false positives, improve the performance, and fix bugs with the log2fc operator of Varlcoriaptor's calling grammar.
varlociraptor.github.io
🚀 Our new paper on Alignoth just published in Bioinformatics!
Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows.
📄 doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
#Snakemake 9.14 is released. It integrates with yet another scripting language ( #hy, adding to the already existing #python, #r, #rust, #bash, and #julia support). Further it offers a massively improved local storage footprint. Many thanks to our awesome community! snakemake.github.io
The official Datavzrd documentation now includes an AI (trained on docs, code and our paper) to answer all your questions: datavzrd.github.io/docs/index.h...
Huge thanks to @gurubase.bsky.social for supporting Open-Source software and making this possible! @johanneskoester.bsky.social
Check out our demo hosted on GitHub pages: alignoth.github.io/alignoth-exa...
Props to my colleague Felix who worked with me on this over the last few weeks in the @johanneskoester.bsky.social lab.
We’ve added a new Snakemake meta-wrapper for creating standalone variant reports:
🔗 snakemake-wrappers.readthedocs.io/en/stable/me...
It combines Datavzrd for an interactive overview table with Alignoth for read pileup plots — all linked together in one portable HTML report.
This is really a worrying trend. Not even that extreme, but I am also worried about people using AI as writing assistant. I think the process of having to find concise and sane words describing the work is an important step, sometimes even leading to new insights or rethinking your own work.
Super happy to announce a major update of our portable and interactive alignment viewer #alignoth written in #rust. The new version provides improved highlighting of specific genomic sites or regions via VCF or BED inputs and also updates the coverage plot with variants! @johanneskoester.bsky.social
I have indeed plans to rewrite performance critical inner parts of snakemake in rust. Might be also something for the hackathon.
The #Snakemake wrapper repository and #Snakedeploy have received a major update: each wrapper now reports the latest version with changes, and #Snakedeploy can automatically upgrade all wrappers in your workflow to those versions. snakemake-wrappers.readthedocs.io
#Snakemake has a novel feature for generalizing rules and modules: pathvars! snakemake.readthedocs.io/en/stable/sn...
Pathvars are particularly useful to make modules parameterizable and more generic. Further, they reduce boilerplate code commonly used for defining output folders.
Cool, thanks!
Want to help shaping the future of #Snakemake? Then participate in the Snakemake hackathon 2026 in Munich! There's still room as the maximum number of participants is not yet reached. You can register here: indico.cern.ch/e/snakemake-...
#sciworkflows #reproducibility
Version 3 of the Snakemake rolling paper is now pulbished on @f1000publishing.bsky.social: f1000research.com/articles/10-...
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
#rustbio 3.0 is released, providing BEDPE support and an improved API for Myers bitparallel pattern matching. github.com/rust-bio/rus...
Our tool #vembrane has a new homepage, providing a high level summary of all the things you can do with it to transform VCF/BCF files via simple Python expressions: vembrane.github.io
Filter, tag, annotate, sort, and flexibly convert to CSV/TSV, JSON, JSONL, YAML and FHIR via a unified syntax.
Open postdoc position in my former lab at @danafarber.bsky.social and @harvard.edu Medical School (CFCE). A working environment full of nice and smart people! careers.dana-farber.org/job/12169/po...
Happy to share our invited article “Komplexe Tabellen verständlich machen” just published in BIOspektrum: doi.org/10.1007/s122... about our tool #datavzrd @johanneskoester.bsky.social
⚠️ Disclaimer: The article is in German.
#Varlociraptor 8.7.4 is released. It provides a major performance improvement, leading to potentially dramatically decreased computational complexity for certain event definitions containing fold changes. github.com/varlocirapto...
#variant_calling #genomics
#Snakemake 9.10 has been released. The major change is that it now supports scheduling plugins. By that your scheduling algorithm research becomes immediately usable with thousands of workflows by thousands of users. snakemake.github.io
Next year in march, the 2nd #Snakemake hackathon, this time at the #TUMunich in Germany, will take place. If you are interested in participating, follow the link on snakemake.github.io and check out the details!
Our paper on Datavzrd has been published in @plosone.org! 🥳
Datavzrd is a new tool written in Rust for creating interactive, shareable HTML reports from tabular data — no server needed.
Check it out here:
🔗 journals.plos.org/plosone/arti...
@johanneskoester.bsky.social
#vembrane, our CLI tool for manipulating VCF/BCF files via Python expressions has gained a new subcommand for sorting. Use it to sort by impact, pathogenicity, frequencies, or any complex Python logic, e.g. for variant prioritization.
github.com/vembrane/vem...
#genomics #bioinformatics
There have been 7 new #Snakemake releases since my last post in May. The most important new feature is --omit-flags, which allows you to deactivate individual input/output flags like "pipe" for the entire workflow (e.g. for debugging). Apart from that, many bugs have been fixed.
snakemake.github.io
Tip of the day: I have extended the auto-rendered docs of all snakemake executor plugins to give more information on how to best use them. Example: snakemake.github.io/snakemake-pl..., see the usage section.
