mixed-r-python-pipeline

Expert guidance for turning existing Snakemake analysis projects (with Snakefile + src/) into pip-installable CLI tools that can deploy the workflow to new projects. Use when the user has a working analysis project with Snakemake and R/Python scripts and wants to make it reusable/deployable. Creates CLI with init, validate, update, clean, info commands. Reference implementation at /Users/wolski/projects/ptm-pipeline.