bacass

Run nf-core/bacass bacterial assembly and annotation pipelines with validated inputs and MultiQC reporting.

1|Updated Jun 19, 2026

Search Tags:#bioinformatics #nf-core #nextflow #genome annotation #samplesheet #bacterial assembly

Ready to run

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

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill helps you run the nf-core/bacass pipeline correctly without guessing release-specific flags, parameter names, or required inputs.

Core Features & Use Cases

Runs bacterial assembly and annotation workflows for short-read, long-read, and hybrid sequencing data.
Exposes the release-pinned input schema, parameter groups, defaults, and allowed values so agents can choose valid options.
Produces standard pipeline outputs, MultiQC reports, and provenance for reproducible reruns.
Use case: an analyst provides a samplesheet and desired profile, and the Skill guides a clean run for a bacterial isolate assembly project.

Quick Start

Use the bacass Skill to run the pipeline for your samplesheet and output directory, then add only the validated optional parameters needed for your sequencing data and environment.

Frequently Asked Questions about bacass

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

FAQPage Schema

How do I run bacterial genome assembly and annotation with nf-core and Nextflow?▼

Bacterial genome assembly and annotation uses the nf-core/bacass pipeline to process short-read, long-read, or hybrid sequencing data. It requires a tab-separated samplesheet and handles trimming, assembly, polishing, contamination screening, BUSCO evaluation, and annotation.

What format does the samplesheet need to be for the nf-core bacterial assembly pipeline?▼

The samplesheet must be a tab-separated file validated against the release-pinned input schema. This ensures correct sample metadata and sequencing data paths for the bacterial assembly pipeline.

Can I use the nf-core bacterial assembly workflow for both short-read and long-read sequencing data?▼

Yes, the bacterial assembly workflow supports short-read, long-read, and hybrid sequencing runs. It applies appropriate trimming, assembly, and polishing parameters based on your validated profile and input data.

How do I ensure reproducible outputs and provenance when running a bacterial assembly pipeline?▼

Reproducible bacterial assembly outputs and provenance are ensured by validating options against a pinned schema and generating standard MultiQC reports. This captures exact parameters and pipeline results for reruns.

Does the nf-core bacterial assembly pipeline include contamination screening and BUSCO evaluation?▼

Yes, bacterial assembly workflow includes contamination screening and BUSCO evaluation. These steps automatically assess assembly quality and detect potential contaminants during the pipeline run.

Why does my bacterial assembly pipeline fail when using incorrect release-specific parameters?▼

Bacterial assembly pipeline failures from incorrect parameters happen when flags do not match the pinned schema. Validating options against the release-specific input schema prevents these errors and ensures a clean run.