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CodingKaiser
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mixed-r-python-pipeline

Convert Snakemake workflows into a pip-installable CLI with init, validate, update, clean, and info commands.

6|1|Updated Nov 26, 2025
Search Tags:#automation#workflow#python#cli#packaging#snakemake
One-click install
npx skills add https://github.com/CodingKaiser/kaiser-skills --skill mixed-r-python-pipeline
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: mixed-r-python-pipeline
Source: https://github.com/CodingKaiser/kaiser-skills/tree/main/mixed-r-python-pipeline
Command: npx skills add https://github.com/CodingKaiser/kaiser-skills --skill mixed-r-python-pipeline

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Turn Snakemake projects into reusable, pip-installable CLI tools so teams can deploy workflows to new projects without manual setup.

Core Features & Use Cases

  • Converts a working Snakemake project (Snakefile + src/) into a distributable CLI tool.
  • Provides init, validate, update, clean, and info commands to manage deployment and lifecycle.
  • Supports template copying, config generation, and deployment to new projects in a repeatable way.

Quick Start

Use the mixed-r-python-pipeline CLI to initialize a new project at /path/to/new/project and deploy Snakefile + src/.

Frequently Asked Questions about mixed-r-python-pipeline

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I convert a Snakemake workflow into a reusable CLI tool?▼

To convert a Snakemake workflow into a reusable CLI tool, you wrap the existing Snakefile and src/ directory into a pip-installable package using template generation and packaging tooling.

What are the prerequisites for packaging a Snakemake project into a CLI?▼

Packaging a Snakemake project into a CLI requires a Python runtime with Snakemake installed, a working Snakefile, a src/ directory, and standard Python packaging tooling.

How do I deploy a Snakemake workflow to a new project without manual setup?▼

To deploy a Snakemake workflow to a new project without manual setup, use the init CLI command to initialize the target path and copy the Snakefile and src/ templates.

What commands are available for managing a packaged Snakemake CLI lifecycle?▼

The packaged Snakemake CLI provides init, validate, update, clean, and info commands to manage deployment, generate configs, and maintain the workflow lifecycle.

Can I use standard Python packaging to distribute Snakemake automation workflows?▼

Yes, you can use standard Python packaging to distribute Snakemake automation workflows by generating a pip-installable CLI that supports repeatable deployments to new projects.

When should I not use a CLI wrapper for my Snakemake pipeline?▼

You should not use a CLI wrapper for your Snakemake pipeline if your project lacks a working Snakefile or a src/ directory, as the conversion relies on these specific structural inputs.

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