createtaxdb

Run the nf-core/createtaxdb pipeline to build metagenomic classifier databases from a samplesheet.

1|Updated Jun 19, 2026

Search Tags:#provenance #bioinformatics #taxonomy #nf-core #nextflow #metagenomics #database building

Ready to run

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

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

It removes the manual trial-and-error involved in launching nf-core/createtaxdb runs, especially when you need the correct database inputs, required flags, and release-specific behavior to stay consistent.

Core Features & Use Cases

Builds metagenomic classifier databases from a samplesheet describing DNA and protein reference FASTAs.
Supports multiple classifier back ends such as Kraken2, Centrifuge, DIAMOND, Kaiju, MALT, sourmash, and others from one pipeline.
Fits research and lab automation workflows that need reproducible, version-pinned database generation and standardized MultiQC reporting.

Quick Start

Ask the skill to prepare and run createtaxdb from your samplesheet, output directory, and database name while preserving the pinned release and validated parameters.

Frequently Asked Questions about createtaxdb

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

FAQPage Schema

How do I build a metagenomic classifier database from a reference samplesheet?▼

To build a metagenomic classifier database, you provide a structured reference samplesheet describing DNA and protein FASTAs, an output directory, and a database name. The pipeline schema validates these parameters to generate the database.

What metagenomic classification tools can I build databases for using nf-core pipelines?▼

You can build databases for multiple classifier back ends including Kraken2, Centrifuge, DIAMOND, Kaiju, MALT, and sourmash. The pipeline processes your reference inputs to construct databases compatible with these taxonomic profiling workflows.

Does createtaxdb support both nucleotide and protein reference inputs for taxonomy profiling?▼

Yes, the pipeline supports both nucleotide and protein reference inputs for taxonomic profiling workflows. It processes these references from a structured samplesheet to build functional metagenomic classifier databases.

How do I ensure reproducible provenance when generating metagenomic databases?▼

To ensure reproducible provenance when generating metagenomic databases, the pipeline enforces release-specific execution of pinned pipeline versions. It tracks version, commit, and command data alongside standardized MultiQC reporting for full traceability.

What inputs do I need to prepare before running a database building pipeline for metagenomics?▼

Before running database building for metagenomics, you need a structured reference samplesheet containing your DNA and protein FASTAs, a designated output directory, and a specified database name to pass schema-validated parameters.

Why does my metagenomic database build fail due to missing required fields?▼

Metagenomic database builds fail when required output and database name fields are missing. The pipeline enforces schema-validated parameters to prevent errors, ensuring correct database inputs and required flags are provided before execution.