metapep

Orchestrate nf-core/metapep pipeline runs for reproducible epitope predictions from metagenomic samples.

1|Updated Jun 19, 2026

Search Tags:#bioinformatics #nf-core #nextflow #metagenomics #samplesheet #metapep #epitope prediction

Ready to run

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

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill removes the guesswork from running nf-core/metapep by turning metagenomic inputs into a reproducible epitope-prediction workflow with the right release, parameters, and outputs.

Core Features & Use Cases

Reproducible pipeline execution: Runs the pinned metapep release with validated inputs and version-aware command generation.
Samplesheet and parameter guidance: Helps users provide the required samplesheet columns, choose supported prediction modes, and avoid invalid flags.
Research workflow support: Useful for metagenomic studies that need peptide generation, MHC/HLA affinity prediction, and standard run provenance for later review.

Quick Start

Ask the Skill to prepare and run metapep on your samplesheet, output path, and preferred profile so it can generate a validated nfclaw command for the correct release.

Frequently Asked Questions about metapep

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

FAQPage Schema

How do I predict metagenomic epitopes from sequencing samples without manual parameter hunting?▼

Metagenomic epitope prediction is simplified by orchestrating the nf-core/metapep pipeline to produce peptide and MHC/HLA affinity predictions from your samples without manual parameter hunting. The workflow enforces schema-validated inputs and version pinning for reproducible runs.

How do I format a samplesheet for nf-core metapep metagenomic workflows?▼

To format a samplesheet for nf-core metapep, you must include required samplesheet fields and output directory parameters. The workflow enforces schema-validated inputs to ensure your assemblies, bins, taxa, and protein inputs are correctly structured before running the pipeline.

Can I run reproducible metagenomic analyses across assemblies, bins, and taxa using Nextflow?▼

Yes, you can run reproducible metagenomic analyses across assemblies, bins, and taxa using Nextflow. The workflow orchestrates the pinned metapep release with validated inputs and version-aware command generation to capture full run provenance for later review.

What is the best way to avoid invalid flags when running nf-core metapep for epitope prediction?▼

The best way to avoid invalid flags during epitope prediction is to use a workflow that enforces runtime-safe parameter constraints and schema validation. This ensures you choose supported prediction modes and prevents invalid flags from disrupting your metagenomic analysis.

Why does my metagenomic pipeline fail when I omit the required outdir and samplesheet fields?▼

Metagenomic pipeline execution fails without required outdir and samplesheet fields because the workflow enforces strict schema-validated inputs. Omitting these required parameters violates runtime-safe constraints, preventing the pinned metapep release from generating a valid command.

Do I need Nextflow installed to run metagenomic epitope prediction with this workflow?▼

Yes, you need Nextflow installed to run metagenomic epitope prediction, as the workflow orchestrates the nf-core/metapep pipeline. It generates a validated Nextflow command for your preferred profile, output path, and pinned release version to ensure reproducible analysis.