Nextflow Pipeline Overview

Nextflow Pipeline Overview Skill

When to Use This Skill

Use this skill when:

• Encountering an unfamiliar Nextflow pipeline for the first time
• Asked to explain what a pipeline does
• Needing to understand pipeline structure before making changes
• Investigating pipeline organization or complexity
• Preparing to debug or extend a Nextflow workflow

Available Tools

You have access to these specialized pipeline overview tools:

nf-workflow-overview_overview

Get a comprehensive overview including structure summary, workflows, processes count, and key parameters.

nf-workflow-overview_overview(directory?: string)

nf-workflow-overview_tree

Show directory tree of pipeline components (modules, subworkflows, workflows).

nf-workflow-overview_tree(directory?: string, depth?: string)

nf-workflow-overview_includes

Extract include statements showing dependencies between modules/subworkflows/workflows.

nf-workflow-overview_includes(directory?: string, file?: string)

nf-workflow-overview_config_params

Extract params block from nextflow.config with schema information.

nf-workflow-overview_config_params(directory?: string)

nf-workflow-overview_component_count

Quick count of processes, workflows, modules (local vs nf-core).

nf-workflow-overview_component_count(directory?: string)

Recommended Workflow

For New Pipelines

1. Start with overview to get high-level structure
2. Use tree to see directory organization
3. Check config_params to understand available parameters
4. Use includes to map dependency graph

For Large Pipelines

1. Use component_count first for quick complexity gauge
2. Follow with overview for structure summary
3. Use includes to understand modular organization
4. Read specific files identified as critical

For Debugging

1. Run overview to refresh on pipeline structure
2. Use includes to trace which modules are involved
3. Check config_params if issue is parameter-related

Key Principles

Progressive Disclosure: Start broad (overview), then drill down (specific files)

Token Efficiency: These tools extract only essential information, avoiding reading entire pipeline files

Context Building: Use multiple tools in sequence to build mental model before diving into code

ast-grep Integration: Tools use ast-grep for syntax-aware analysis when available

Example Usage

// When user asks: "What does this nf-core/rnaseq pipeline do?"
(await nf) - workflow - overview_overview({ directory: "/path/to/nf-core-rnaseq" });
(await nf) - workflow - overview_tree({ directory: "/path/to/nf-core-rnaseq", depth: "2" });

// When user asks: "How many processes does this pipeline have?"
(await nf) - workflow - overview_component_count({ directory: "/path/to/pipeline" });

// When user asks: "What parameters can I configure?"
(await nf) - workflow - overview_config_params({ directory: "/path/to/pipeline" });

Integration with Other Skills

This skill complements:

• nf-ast-grep tools: For finding specific code patterns
• nextflow-dev agent: For making changes after understanding structure
• nextflow-debug agent: For troubleshooting with structural context

Best Practices

1. Always overview first: Before making any changes, run overview to understand what you're working with
2. Use directory parameter: When working with multiple pipelines, always specify the directory
3. Combine tools: No single tool gives complete picture - use 2-3 in sequence
4. Check for schema: If nextflow_schema.json exists, run config_params for full parameter documentation
5. Respect token budget: These tools are designed to minimize context usage - trust their summaries

Common Patterns

Pattern 1: First-time exploration

overview → tree → includes → Read specific files

Pattern 2: Quick assessment

component_count → overview → Done (if sufficient)

Pattern 3: Parameter investigation

config_params → overview (if schema exists)
overview → config_params (if no schema)

Notes

• Tools default to current working directory if no directory specified
• All tools handle missing directories gracefully
• ast-grep features require ~/.local/share/opencode/ast-grep setup
• Tools are optimized for both nf-core and custom pipelines