Lot's of new #snakemake and #snakemake plugin releases in the last days, with a plethora of bug fixes and small feature improvements. snakemake.github.io #sciworkflows #reproducibility

If I remember correctly there is a book with a printout of the initial human genome assembly of chromosome 1 at the Hinxton campus in GB. Does by chance somebody have a picture that they can share here or per PM?

New #snakemake_wrappers release with 17 updates and 1 new wrapper! snakemake-wrappers.readthedocs.io #sciworkflows #reproducibility

#Snakemake 8.20.4 has been released. It provides a massive speedup of job processing, most notable during dry-run. #sciworkflows #reproducibility snakemake.github.io

I just discovered that CodeRabbit is also able to find bugs in #Snakemake workflows:

Our manuscript on continuous benchmarking of genomic variant calling pipelines using a combination of simple public services has passed the review process on F1000: doi.org/10.12688/f1000…

The resulting continuously updated reports nicely illustrate the power of combining #snakemake with #datavzrd: ncbench.github.io/report/report.…

It feels like a dedicated web server with a database, but it is just a bunch of rules and YAML config files for the datavzrd tables.

If you are interested in shaping the future of #Snakemake, implement new features or plugins, or fix bugs, join us at the CERN in March 2025 for our Snakemake hackathon: indico.cern.ch/event/snakemak… This includes the ability to take a super exciting tour on the LHC!

Lodging is for free, generously sponsored by the FAIROS-HEP initiative. The hackathon is open to all scientific fields and we focus on improving #Snakemake for all fields at the same time.

The recent #Snakemake releases (last one yesterday) have introduced several fixes to software deployment with conda. In the latest, mamba support has been dropped in favor of conda >=24.7. Since conda uses libmamba internally, it should be equally fast nowadays.

The impact should be minimal, since any mamba installation also comes with conda. You can simply update to the latest conda to make #Snakemake happy.

In the future, we will move the conda support into a new to be written deployment plugin which will then at some point internally use py-rattler instead of the conda cli for deployment and solving. prefix.dev/blog/introduci…

So far, I thought that there is no reasonable way to observe a read alignment CIGAR with a leading deletion. We have recently seen this though. Is that reasonable? How could the aligner know without matching bases in the read before the deleted ones? (BAM comes from giraffe)

We already have many fantastic registrations for the Snakemake hackathon 2025 at CERN! But there are still some free seats left. Make sure to apply/register soon if you want to shape the future of Snakemake! indico.cern.ch/event/snakemak…

There were several new #Snakemake releases in the last weeks. Most importantly, the scheduler performance has been improved and there is a new CLI option to mark certain files as "ancient" at runtime (overriding mtime based rerun triggers). snakemake.github.io

There is a new #Snakemake tutorial that complements the general tutorial by specifically introducing how to use #Snakemake for plotting and interactive reporting, including how to combine #Snakemake with #Datavzrd: snakemake.readthedocs.io/en/stable/tuto…

#Datavzrd, our tool for rapid and server-free visualization of tabular data now supports spells, which enable to share and collaborate on column visualizations and thereby extend Datavzrd further: datavzrd.github.io/docs/spells.ht…

Given all the issues with fake news, hatespeech, the now even more problematic ownership situation of X, I wonder why we as scientific community haven't managed yet to move entirely to mastodon? Can that be justified? Can we somehow heal X? Or do we just support a doomed system?

#schalke gelb war schon unnötig von Katic, aber rot hat das medizinische Personal mitzuverantworten. Der darf doch niemals wieder auf den Platz.