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danilomonge
danilomongeCOMMUNITY
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createpanelrefs

Generate validated run metadata and parameter guidance for nf-core/createpanelrefs pipelines.

1|Updated Jun 19, 2026
Search Tags:#bioinformatics#nf-core#nextflow#cnv#samplesheet#createpanelrefs#panel-of-normals
One-click install
npx skills add https://github.com/danilomonge/nf-claw --skill createpanelrefs
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: createpanelrefs
Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/createpanelrefs
Command: npx skills add https://github.com/danilomonge/nf-claw --skill createpanelrefs

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill turns the complexity of nf-core/createpanelrefs into a safe, repeatable run guide, so you can build panels of normals and related models without guessing parameters or release details.

Core Features & Use Cases

  • Release-aware guidance for createpanelrefs runs, including the pinned latest version and alternate pipeline versions.
  • Samplesheet and parameter validation for required inputs, tool selection, reference genome settings, and output locations.
  • Practical for creating panel-of-normals references or similar models from many samples while keeping runs deterministic and reproducible.
  • Useful when you need to inspect supported inputs, required flags, allowed values, and output expectations before launching a Nextflow job.

Quick Start

Ask the Skill to prepare a valid nf-core/createpanelrefs run plan from your samplesheet, chosen tools, and output directory.

Frequently Asked Questions about createpanelrefs

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

FAQPage Schema
How do I build a panel of normals for CNVkit or Mutect2 using Nextflow?▼

To build a panel of normals, this Skill generates validated run metadata, enforces required samplesheet inputs, and provides parameter guidance for deterministic nf-core/createpanelrefs execution across CNVkit, GATK GENS, GermlineCNVCaller, and Mutect2.

What is a panel of normals and when do I need it for CNV calling?▼

A panel of normals is a reference model built from many normal samples to filter false positives during CNV calling. You need it when running tools like GermlineCNVCaller or Mutect2 to ensure accurate, reproducible variant detection.

How do I validate a samplesheet for the nf-core createpanelrefs pipeline?▼

You validate a samplesheet by checking required inputs, tool selection, and reference genome settings against schema constraints. This Skill enforces allowed parameter values and output expectations to ensure your Nextflow run is deterministic.

Can I use nf-core createpanelrefs with different pipeline release versions?▼

Yes, this Skill provides release-aware guidance for createpanelrefs runs, including the pinned latest version and alternate pipeline versions, ensuring you apply the correct release-specific documentation and parameter constraints.

What parameters are required to create a panel of normals with GATK GENS?▼

Required parameters include valid samplesheet inputs, selected tools, reference genome settings, and output locations. This Skill enforces schema constraints and allowed values for deterministic Nextflow execution when building GENS models.

Why does my nf-core createpanelrefs run fail parameter validation?▼

Runs fail when required inputs, tool selection, or reference genome settings violate schema constraints. This Skill enforces allowed parameter values and output expectations to prevent validation errors before launching your Nextflow job.

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