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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.

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CodingKaiser
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CodingKaiser
Updated 1/19/2026
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quick start

Installation and usage

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.

Installation
$ install --globalskills.sh
Usage

Once installed, you can use this skill by running the following command in your terminal:

skills use mixed-r-python-pipeline