Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

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

Preview of an important slide:

snkmt 0.2.0 is out! New features:

1. Multi-database support - switch between dbs via ctrl+p (like VSCode)
2. Workflow filtering - hide/filter by snakefile, status, or date for cleaner navigation

github.com/cademirch/sn...
#snakemake #bioinformatics #workflow #opensource #python #cli #tui

Recording of the tutorial now up on the @scipyconf.bsky.social YouTube channel: www.youtube.com/watch?v=8AYp...

Link to the new documentation pages:

- conda-forge.org/docs/mainta...
- conda-forge.org/docs/mainta...

Some great tips on making better #dataviz 👇 In my experience, the final point—feedback—is invaluable

Funny how another person might focus on something completely different to what you intended 🙃 Adjusting from this feedback always makes for a clearer visual message📊🧪

www.nature.com/articles/s41...

This is awesome Gregg! @rupdecat.fediscience.org.ap.brid.gy something like this this would be a cool addition the the slurm plugin. Perhaps users could supply their cluster’s partition limits via a yaml file?

I forgot to include snkmt as a dependency for the logger plugin 😅, so if you've already installed as above, either grab the latest plugin version, or pip install snkmt!

Setup is super easy:
1. Install the logger plugin:
pip install snakemake-logger-plugin-snkmt
2. Use the --logger option in Snakemake:
snakemake --logger snkmt
3. Pull up the dashboard:
snkmt console

Give it a try and let me know what you think!
github.com/cademirch/sn...
3/3

snkmt provides a clean terminal ui built with #textual, meaning you can use it on servers. Some key features:

- View all workflows, and their progress
- Per-rule progress for selected workflow
- View failed job log files for quick debugging 2/3

Excited to share the #Snakemake monitoring tool I've been working on:
snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics #workflow #opensource 1/3

Could you expand on this? Not sure I understand mapping a tool's arguments to wildcards, is this something that another workflow manager does? I like the idea, and think that wildcards could use improvement