Cade Mirchandani
cademirch.bsky.social
Cade Mirchandani
@cademirch.bsky.social
bioinformatics phd candidate @ ucsc

https://github.com/cademirch
Obsidian is great! I found this video helpful for getting started. www.youtube.com/watch?v=B0yA...
October 29, 2025 at 4:30 PM
Reposted by Cade Mirchandani
Recording of the tutorial now up on the @scipyconf.bsky.social YouTube channel: www.youtube.com/watch?v=8AYp...
Arts, Feickert, & Kirkham - Reproducible Machine Learning Workflows for Scientists with pixi
YouTube video by SciPy
www.youtube.com
September 10, 2025 at 2:50 PM
Reposted by Cade Mirchandani
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?
June 5, 2025 at 4:59 AM
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!
June 3, 2025 at 9:45 PM
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
GitHub - cademirch/snkmt
Contribute to cademirch/snkmt development by creating an account on GitHub.
github.com
June 3, 2025 at 2:52 PM
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
June 3, 2025 at 2:52 PM
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
January 25, 2025 at 10:25 PM