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danilomonge
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genomeassembler

Translate samplesheets and analysis goals into validated nf-core/genomeassembler pipeline executions.

1|Updated Jun 19, 2026
Search Tags:#scaffolding#bioinformatics#nf-core#nextflow#polishing#genome assembly#long reads
One-click install
npx skills add https://github.com/danilomonge/nf-claw --skill genomeassembler
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: genomeassembler
Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/genomeassembler
Command: npx skills add https://github.com/danilomonge/nf-claw --skill genomeassembler

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

nf-core/genomeassembler is powerful but complex, with many interdependent options, release-specific behaviors, and strict input requirements. This Skill turns that complexity into a reliable guided workflow so you can launch genome assembly runs without guessing flags or parameter values.

Core Features & Use Cases

  • Long-read genome assembly: Supports assembly workflows for ONT and PacBio HiFi datasets.
  • Polishing and scaffolding: Helps choose and configure polishing with Medaka or Pilon, and scaffolding with LINKS, Longstitch, or RagTag when applicable.
  • Validated execution: Uses the correct samplesheet structure, required inputs, and release-pinned configuration for reproducible runs.
  • Practical use cases: Ideal for starting a new assembly, rerunning a specific pipeline release, or preparing a safe demo execution with the right profile and inputs.

Quick Start

Ask the assistant to run the genomeassembler skill on your samplesheet and output directory, then select the needed profile and optional parameters from the skill reference.

Frequently Asked Questions about genomeassembler

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

FAQPage Schema
How do I run a long-read genome assembly with Nextflow without guessing parameters?▼

Run genome assembly by translating a samplesheet and analysis goals into validated Nextflow execution instructions, enforcing strict parameter validation and release pinning for safe, reproducible runs without guessing flags.

Can I use ONT and PacBio HiFi datasets for polishing and scaffolding in nf-core pipelines?▼

ONT and PacBio HiFi datasets are supported for assembly workflows, including polishing with Medaka or Pilon and scaffolding with LINKS, Longstitch, or RagTag, plus optional reference-guided steps and short-read support.

What's the best way to configure a validated samplesheet for genome assembly?▼

Configure a validated samplesheet by matching the correct input schema structure, required inputs, and release-pinned configuration to ensure reproducible genome assembly runs.

Does the genomeassembler workflow support reference-guided assembly steps?▼

Reference-guided steps are supported as optional components within the genome assembly workflow, alongside long-read assembly, polishing, scaffolding, and quality control for ONT and PacBio HiFi datasets.

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

Parameter validation fails when interdependent options, release-specific behaviors, or strict input schema constraints are not met, requiring validated pipeline execution instructions to ensure safe Nextflow runs.

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