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run-cso

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Run CSO caller pipeline

Data & Analytics#genomics#pipeline#cso#slurm#cancer signal origin#clinical samples
Authorgh-hazhang
Version1.0.0
Installs0

System Documentation

What problem does it solve?

This skill automates the execution of the Cancer Signal Origin (CSO) caller pipeline, simplifying the analysis of clinical samples.

Core Features & Use Cases

  • Automated Pipeline Execution: Runs the full CSO caller pipeline with SLURM job management.
  • Sample Handling: Manages both local and archived clinical samples, including automatic retrieval.
  • Progress Monitoring: Provides real-time updates and handles timeouts gracefully.
  • Use Case: Analyze clinical samples for cancer signal origins by providing a report file and output directory, letting the skill manage the complex execution and monitoring.

Quick Start

Run the CSO caller pipeline using your clinical report and specify an output directory.

Dependency Matrix

Required Modules

None required

Components

scriptsreferences

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: run-cso
Download link: https://github.com/gh-hazhang/scripts/archive/main.zip#run-cso

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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