epitopeprediction

Run nf-core epitopeprediction pipelines with schema-validated samplesheets and pinned versions.

1|Updated Jun 19, 2026

Search Tags:#bioinformatics #reproducibility #nf-core #nextflow #samplesheet #epitope prediction #mhc binding

Ready to run

npx skills add https://github.com/danilomonge/nf-claw --skill epitopeprediction

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: epitopeprediction
Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/epitopeprediction
Command: npx skills add https://github.com/danilomonge/nf-claw --skill epitopeprediction

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill helps you run the nf-core epitopeprediction workflow without having to memorize release-specific flags, required inputs, or tool-specific settings. It turns a complex immunology analysis pipeline into a guided, reproducible run.

Core Features & Use Cases

Variant-driven epitope discovery: Predict candidate epitopes from variants, proteins, or peptides for downstream analysis.
Release-aware execution: Use the pinned pipeline version or select a specific historical release when reproducibility matters.
Validated parameters and outputs: Work from a schema-checked samplesheet, required input and output paths, and a documented parameter reference.
Research scenarios: Support neo-epitope generation, binding hotspot scans, and immunopeptidomics-style peptide prediction.

Quick Start

Ask the assistant to run the epitopeprediction Skill on my samplesheet and save the results to my chosen output directory.

Frequently Asked Questions about epitopeprediction

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

FAQPage Schema

How do I run nf-core epitopeprediction for variant neo-epitope discovery?▼

Run neo-epitope discovery by providing a schema-validated samplesheet and an output directory to the epitopeprediction workflow. The pipeline manages variant input processing and candidate epitope prediction automatically without manual parameter hunting.

What is a schema-validated samplesheet for reproducible epitope prediction?▼

A schema-validated samplesheet is a structured input file defining samples and metadata for the epitopeprediction pipeline. It enforces correct formatting and required fields to ensure reproducible execution and prevent input errors.

Can I use a specific historical release of the epitopeprediction pipeline for reproducibility?▼

Yes, you can pin a specific historical nf-core epitopeprediction release for reproducibility. The workflow supports release-aware execution, allowing you to lock a specific pipeline version when consistent results matter.

What's the best way to predict MHC binding hotspots from protein sequences?▼

Use the epitopeprediction workflow's protein scanning mode to predict MHC binding hotspots. It processes protein sequences through the pipeline with validated parameters, generating binding prediction outputs in your designated output directory.

Does the epitopeprediction pipeline support immunopeptidomics peptide analysis?▼

Yes, the epitopeprediction pipeline supports immunopeptidomics-style peptide prediction. It processes peptide inputs through the same schema-validated samplesheet approach, generating binding predictions while maintaining reproducible execution standards.

Why do I need to pin pipeline versions for reproducible Nextflow workflow execution?▼

Pinning pipeline versions locks the exact code and parameters used, which is required for reproducible Nextflow execution. The epitopeprediction workflow enforces version pinning and output-directory management to guarantee consistent results across runs.