create-workflow

Nextflow Workflow Writer

Create complete Nextflow workflows by composing validated modules from the Nextflow Registry.

Modules are published under namespaces (e.g. nf-core/fastqc), and these skills compose modules from any of them.

Requires Nextflow 26.04 or later (for the nextflow module commands used during validation).

NEVER write a wrapper workflow just to run/test a single module.

❌ WRONG - Writing a workflow to run one module:

// DO NOT DO THIS - not even when a module run fails!
include { FASTQC } from 'nf-core/fastqc'
workflow { FASTQC(Channel.fromPath('data/*.fq.gz')) }

✅ CORRECT - Use the run-module skill:

Skill(skill="run-module")

The run-module skill:

• Uses nextflow module search/view to discover and get proper inputs/parameters
• Runs modules directly via nextflow module run <namespace>/<module>
• No wrapper workflow needed

⚠️ When a module run fails due to missing args:

• DO NOT write a wrapper workflow as a "fix"
• Instead: run nextflow module view <module> to get correct parameters
• Fix the command-line arguments and re-run directly

Only write a workflow in Step 4 when composing multiple validated modules together.

4-Step Workflow Creation Process

ALWAYS follow this structured process when creating a new workflow:

Step 1: Identify Modules and Propose Plan

1. Use nextflow module search <term> to find Registry modules for each processing step
2. Use nextflow module view <name> to understand inputs/outputs of each module
3. Present a plan to the user with:
   • List of identified modules
   • Processing sequence (which module runs first, second, etc.)
   • Data flow between modules (outputs → inputs)

STOP and wait for user approval before proceeding.

Step 2: User Agreement

• Wait for user to review and approve the proposed plan
• Address any questions or modifications requested
• Only proceed when user explicitly agrees