immunopipe-config

Generate end-to-end immunopipe TOML configurations for RNA and TCR/BCR analyses.

22|4|Updated May 18, 2021

Search Tags:#routing #config #pipeline #generate #rna-seq #immunopipe #data-type

Ready to run

npx skills add https://github.com/pwwang/immunopipe --skill immunopipe-config

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: immunopipe-config
Source: https://github.com/pwwang/immunopipe/tree/main/skills/immunopipe-config
Command: npx skills add https://github.com/pwwang/immunopipe --skill immunopipe-config

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Generates end-to-end immunopipe pipeline configurations by assessing data type (RNA with or without TCR/BCR) and analysis goals, routing to the appropriate process skills for detailed configuration.

Core Features & Use Cases

Generates a complete pipeline configuration skeleton tailored to RNA-only or RNA+TCR/BCR analyses.
Routes to specific process configuration skills and configures pipeline-level options (name, outdir, scheduler).
Supports quick-start workflows and validation guidance for immediate execution.

Quick Start

Start by running the immunopipe-config skill to generate a new TOML config and route to the appropriate process skills.

Frequently Asked Questions about immunopipe-config

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

FAQPage Schema

How do I generate a configuration file for an immunopipe pipeline?▼

You generate an immunopipe configuration by using a routing skill that assesses your RNA-seq data type and analysis goals to produce a complete TOML skeleton. It determines essential and optional processes, then configures pipeline-level options for immediate execution.

Can I configure an immunopipe pipeline for RNA-seq data without TCR or BCR sequences?▼

Yes, you can configure pipelines for RNA-only analyses. The skill evaluates your specific data type, routing RNA-only inputs to generate a tailored configuration skeleton that excludes unnecessary TCR/BCR processes while validating the resulting TOML.

What is the best way to set up pipeline-level options like scheduler and outdir for immunopipe?▼

The best way to set up pipeline-level options is through automated configuration generation. The skill configures options like name, outdir, and scheduler based on your analysis goals, ensuring the TOML is valid and ready for the immunopipe pipeline run.

How does pipeline configuration routing work for RNA-seq with TCR/BCR data?▼

Pipeline configuration routing works by evaluating your data type and directing RNA+TCR/BCR inputs to specific process configuration skills. This generates a detailed TOML file that includes all essential and optional processes required for your combined analysis goals.

Do I need to manually validate the TOML configuration generated for my immunopipe pipeline?▼

No, manual validation is unnecessary. The configuration skill automatically validates the generated TOML file after routing to the appropriate process skills, providing guidance so you can immediately execute the immunopipe pipeline without configuration errors.