coproid

What problem does it solve?

Coproid automates the analysis of complex Illumina metagenomic samples to help identify the true host signal in paleofaeces and related microbiome-rich material, avoiding manual flag hunting and release-specific confusion.

Core Features & Use Cases

• Pinned pipeline execution: Runs the exact nf-core/coproid release bundled with the skill so results stay reproducible.
• Schema-validated inputs: Uses a samplesheet plus required genome, kraken2, and sourcepredict reference tables to enforce correct parameter usage.
• Provenance-aware workflows: Produces standardized outputs, MultiQC summaries, and run metadata for traceable downstream reporting.
• Use case: A researcher can provide sequencing reads and the required reference tables to process a faecal metagenomics study and obtain host-identification results without having to inspect upstream documentation.

Quick Start

Ask me to run the coproid pipeline on your samplesheet with the required genome, kraken2, and sourcepredict inputs, and I will launch the pinned release into your chosen output directory.