What is the recommended way to start exploring a new pipeline?

The best practice is to start with the 'overview' tool for a high-level summary, followed by 'tree' for organization and 'config_params' for configuration options.

Does this skill work with custom Nextflow pipelines or only nf-core?

It is designed to work with both standard nf-core pipelines and custom Nextflow implementations by analyzing common DSL2 patterns and directory structures.

Can I use this to map dependencies between modules?

Yes, the includes tool specifically extracts dependency relationships to show how modules, subworkflows, and workflows are interconnected.

How does this help with token efficiency in Claude?

Instead of reading entire .nf files, these tools extract only the essential structural metadata and include statements, significantly reducing context usage.

Nextflow Pipeline Overview

Name: Nextflow Pipeline Overview
Author: edmundmiller

byedmundmiller

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Data Science & ML

Analyzes and summarizes Nextflow pipelines to provide immediate structural insights and dependency maps.

About

The Nextflow Pipeline Overview skill enables Claude to rapidly deconstruct and explain complex Nextflow workflows without consuming excessive context. By utilizing specialized tools for structural summaries, directory trees, and parameter extraction, it allows developers to grasp the architecture of unfamiliar pipelines, track component dependencies, and identify configuration schemas. This skill is particularly valuable for bioinformatics engineers and data scientists who need to audit, debug, or extend large-scale nf-core or custom pipelines while maintaining token efficiency through syntax-aware analysis.

Key Features

40 GitHub stars
Automated dependency mapping via include statement extraction
Visual directory tree of pipeline components (modules, subworkflows)
Configuration and parameter block parsing with schema support
High-level workflow structure summaries and process counts
Token-efficient analysis using ast-grep for syntax-aware extraction

Use Cases

Quickly auditing pipeline complexity and available configuration parameters
Mapping complex workflow dependencies before making code changes
Onboarding and exploring unfamiliar nf-core or custom pipelines

About

Key Features

40 GitHub stars
Automated dependency mapping via include statement extraction
Visual directory tree of pipeline components (modules, subworkflows)
Configuration and parameter block parsing with schema support
High-level workflow structure summaries and process counts
Token-efficient analysis using ast-grep for syntax-aware extraction

Use Cases

Quickly auditing pipeline complexity and available configuration parameters
Mapping complex workflow dependencies before making code changes
Onboarding and exploring unfamiliar nf-core or custom pipelines