🐍 For all ye #snakemake users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳
The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.).
See github.com/snakemake/sn... for more
The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.).
See github.com/snakemake/sn... for more
GitHub - snakemake/snakefmt: The uncompromising Snakemake code formatter
The uncompromising Snakemake code formatter. Contribute to snakemake/snakefmt development by creating an account on GitHub.
github.com
March 24, 2026 at 2:10 AM
🐍 For all ye #snakemake users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳
The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.).
See github.com/snakemake/sn... for more
The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.).
See github.com/snakemake/sn... for more
Go little snakemake, go! Cotton genomes almost there!
February 13, 2026 at 4:20 AM
Go little snakemake, go! Cotton genomes almost there!
Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!
GitHub - RILAB/argprep: Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files.
Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files. - RILAB/argprep
github.com
March 3, 2026 at 5:41 PM
Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!
I’m excited to share noHiC-Snakemake, a pangenome-enhanced, reference-guided contig genome scaffolding pipeline.
If you work on plant genome assembly, I'd love for you to give it a try 😄.
GitHub repo: github.com/andyngh/noHi...
If you work on plant genome assembly, I'd love for you to give it a try 😄.
GitHub repo: github.com/andyngh/noHi...
GitHub - andyngh/noHiC-Snakemake: A Snakemake reimplementation of noHiC - the personalized reference-guided contig scaffolding pipeline
A Snakemake reimplementation of noHiC - the personalized reference-guided contig scaffolding pipeline - andyngh/noHiC-Snakemake
github.com
September 25, 2026 at 9:35 AM
I’m excited to share noHiC-Snakemake, a pangenome-enhanced, reference-guided contig genome scaffolding pipeline.
If you work on plant genome assembly, I'd love for you to give it a try 😄.
GitHub repo: github.com/andyngh/noHi...
If you work on plant genome assembly, I'd love for you to give it a try 😄.
GitHub repo: github.com/andyngh/noHi...
Today, the #SnakemakeHackathon2025 at @cern.bsky.social has ended with the release of Snakemake 9.0! Huge thanks to the amazing participants and all organizers! In total there were 19 new releases within the ecosystem, including hundreds of new features and bug fixes for Snakemake and its plugins!
March 14, 2025 at 10:11 PM
Today, the #SnakemakeHackathon2025 at @cern.bsky.social has ended with the release of Snakemake 9.0! Huge thanks to the amazing participants and all organizers! In total there were 19 new releases within the ecosystem, including hundreds of new features and bug fixes for Snakemake and its plugins!
January 13, 2025 at 5:07 PM
Once more unto the breach:
A fast introduction to snakemake, in 5 examples.
A fast introduction to snakemake, in 5 examples.
A fast introduction to snakemake (in 5 examples) - HackMD
# A rapid introduction to snakemake (in 5 examples) See github repo: [ctb/2026-rapid-snakemake-intr
hackmd.io
January 14, 2026 at 7:25 PM
Once more unto the breach:
A fast introduction to snakemake, in 5 examples.
A fast introduction to snakemake, in 5 examples.
PopGLen—A Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods. #Snakemake #PopulationGenomics #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
PopGLen—A Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods
AbstractSummary. PopGLen is a Snakemake workflow for performing population genomic analyses within a genotype-likelihood framework, integrating steps for r
academic.oup.com
March 12, 2025 at 12:00 AM
PopGLen—A Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods. #Snakemake #PopulationGenomics #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....
GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.
A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt
github.com
March 16, 2026 at 9:14 AM
Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....
Workflow management using Snakemake
russpoldrack.substack.com/p/workflow-m... - the latest in my Better Code, Better Science series.
russpoldrack.substack.com/p/workflow-m... - the latest in my Better Code, Better Science series.
Workflow management using Snakemake
Better Code, Better Science: Chapter 8, Part 5
russpoldrack.substack.com
March 31, 2026 at 3:09 PM
Workflow management using Snakemake
russpoldrack.substack.com/p/workflow-m... - the latest in my Better Code, Better Science series.
russpoldrack.substack.com/p/workflow-m... - the latest in my Better Code, Better Science series.
I'm deliberately not importing my old tweets, but I do want to re-share a tutorial I made a couple of years ago -- check it out if you're an R user interested in leveling up your Python & Snakemake skills! sovacool.dev/posts/just-e...
#rstats #python #snakemake #bioinformatics
#rstats #python #snakemake #bioinformatics
Just enough Python for Snakemake – sovacool.dev
A tutorial for R users who want to write advanced Snakemake workflows
sovacool.dev
November 20, 2024 at 2:00 AM
I'm deliberately not importing my old tweets, but I do want to re-share a tutorial I made a couple of years ago -- check it out if you're an R user interested in leveling up your Python & Snakemake skills! sovacool.dev/posts/just-e...
#rstats #python #snakemake #bioinformatics
#rstats #python #snakemake #bioinformatics
Snk: A Snakemake CLI and Workflow Management System joss.theoj.org/papers/10.21...
December 3, 2024 at 3:00 AM
Snk: A Snakemake CLI and Workflow Management System joss.theoj.org/papers/10.21...
I just discovered #snakesee from Nils Homer: github.com/nh13/snakesee. This is a nice approach to monitor all running snakemake workflows.
GitHub - nh13/snakesee: A terminal UI for monitoring Snakemake workflows
A terminal UI for monitoring Snakemake workflows. Contribute to nh13/snakesee development by creating an account on GitHub.
github.com
March 16, 2026 at 9:10 AM
I just discovered #snakesee from Nils Homer: github.com/nh13/snakesee. This is a nice approach to monitor all running snakemake workflows.
The #snakemake workflow catalog has since recently >300 registered workflows with standardized and unified usage instructions . Furthermore, Michael Jahn from Emmanuelle Charpentier's lab is now the new maintainer of the catalog: snakemake.github.io/snakemake-wo...
Snakemake workflow catalog
snakemake.github.io
January 26, 2025 at 12:04 PM
The #snakemake workflow catalog has since recently >300 registered workflows with standardized and unified usage instructions . Furthermore, Michael Jahn from Emmanuelle Charpentier's lab is now the new maintainer of the catalog: snakemake.github.io/snakemake-wo...
Interesting project: Snk: A Snakemake CLI and Workflow Management System https://joss.theoj.org/papers/10.21105/joss.07410 🧬🖥️🧪 https://github.com/Wytamma/snk
November 26, 2024 at 4:30 PM
Interesting project: Snk: A Snakemake CLI and Workflow Management System https://joss.theoj.org/papers/10.21105/joss.07410 🧬🖥️🧪 https://github.com/Wytamma/snk
Excited to share my first JOSS publication 🎉 Snk: A #Snakemake CLI and Workflow Management System joss.theoj.org/papers/10.21...
Snk: A Snakemake CLI and Workflow Management System
Wirth et al., (2024). Snk: A Snakemake CLI and Workflow Management System. Journal of Open Source Software, 9(103), 7410, https://doi.org/10.21105/joss.07410
joss.theoj.org
November 26, 2024 at 1:07 AM
Excited to share my first JOSS publication 🎉 Snk: A #Snakemake CLI and Workflow Management System joss.theoj.org/papers/10.21...
At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa....
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
March 14, 2026 at 5:32 PM
At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa....
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
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
#sciworkflows #reproducibility
Snakemake Hackathon March 2026
We are excited to announce the Snakemake Hackathon 2026, to be held 9-13 March, 2026 at the Technical University Munich. This event will bring together passionate developers and data scientists to col...
indico.cern.ch
October 17, 2025 at 4:49 PM
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
#sciworkflows #reproducibility
#Snakemake has an update best practices guide: snakemake.readthedocs.io/en/stable/sn...
Best practices | Snakemake 8.29.0 documentation
snakemake.readthedocs.io
February 28, 2025 at 2:52 PM
#Snakemake has an update best practices guide: snakemake.readthedocs.io/en/stable/sn...
Monthly Snakemake developer meeting: Tuesday, Sept 30th at 6am PST!
Open to all - developers & users. We discuss issues/PRs and cowork on Snakemake projects.
DM me to join!
#snakemake #workflows #opensource #bioinformatics #oss
Open to all - developers & users. We discuss issues/PRs and cowork on Snakemake projects.
DM me to join!
#snakemake #workflows #opensource #bioinformatics #oss
September 29, 2025 at 5:33 PM
Monthly Snakemake developer meeting: Tuesday, Sept 30th at 6am PST!
Open to all - developers & users. We discuss issues/PRs and cowork on Snakemake projects.
DM me to join!
#snakemake #workflows #opensource #bioinformatics #oss
Open to all - developers & users. We discuss issues/PRs and cowork on Snakemake projects.
DM me to join!
#snakemake #workflows #opensource #bioinformatics #oss
#Snakemake 8.29 has been released. It provides various improvements to the integrated reporting, as well as many small bug fixes: snakemake.readthedocs.io/en/stable/pr...
Changelog | Snakemake 8.29.0 documentation
snakemake.readthedocs.io
February 28, 2025 at 2:52 PM
#Snakemake 8.29 has been released. It provides various improvements to the integrated reporting, as well as many small bug fixes: snakemake.readthedocs.io/en/stable/pr...
Preview of an important slide:
September 24, 2025 at 4:02 PM
Preview of an important slide:
We have found the workflow manager 'Snakemake' to be very useful for fMRI data processing and analysis. In this paper, we describe how Snakemake can be applied in a neuroimaging context.
Orchestrating neuroimaging data processing using the 'Snakemake' workflow manager: https://osf.io/fmdvn
February 17, 2026 at 2:45 AM
We have found the workflow manager 'Snakemake' to be very useful for fMRI data processing and analysis. In this paper, we describe how Snakemake can be applied in a neuroimaging context.
🧵 Why are workflow languages like Snakemake essential for bioinformatics? Let’s explore their power in streamlining genomic data analysis.
February 8, 2025 at 2:45 PM
🧵 Why are workflow languages like Snakemake essential for bioinformatics? Let’s explore their power in streamlining genomic data analysis.
What even is truth? Seems like it should be the purview of philosophers and poets — clearly not people (me) designing snakemake workflows.
February 26, 2026 at 1:36 AM
What even is truth? Seems like it should be the purview of philosophers and poets — clearly not people (me) designing snakemake workflows.