create-workflow

name	create-workflow
description	INVOKE THIS SKILL IMMEDIATELY when user asks to: write/create/build a Nextflow pipeline or workflow, create any bioinformatics pipeline (RNA-seq, DNA-seq, variant calling, ChIP-seq, etc.), or compose/chain nf-core modules. This skill handles all Nextflow workflow creation tasks.
allowed-tools	Bash, Read, Edit, Write, Glob, Grep, Skill

Nextflow Workflow Writer

Create complete Nextflow workflows by composing validated nf-core modules.

Requires Nextflow 26.04.0 or later (for the nextflow module commands used during validation).

NEVER write a wrapper workflow just to run/test a single nf-core 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/info to discover and get proper inputs/parameters
• Runs modules directly via nextflow module run nf-core/<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 info <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 nf-core modules for each processing step
2. Use nextflow module info <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

Step 3: Validate Modules ONE BY ONE (MANDATORY)

NEVER skip this step. After user agreement:

1. Determine appropriate test data for validation
2. For EACH module in the plan, sequentially:
   • Install and run with test data: Invoke Skill(skill="run-module")
   • Verify outputs - confirm expected data is produced
   • Only proceed to next module after current one succeeds
3. Log ALL module run commands and their outputs to a debug file with the .modules-validation- prefix
4. If a command fails, stop and show the user the command used and the output generated before trying something else

Note: The run-module skill uses nextflow module commands for discovery, configuration, and execution — modules are installed on-the-fly.

DO NOT proceed to Step 4 until ALL modules have been individually validated.

Step 4: Compose Final Workflow

Only after ALL modules run successfully:

1. Configure nextflow.config with Wave + Conda:

   wave.enabled = true
   wave.strategy = 'conda,container'
   docker.enabled = true
   

2. Write the workflow script compositing all validated steps using Nextflow managed modules (no ./ prefix — Nextflow automatically downloads and installs them from the registry):

   include { MODULE_A } from 'nf-core/module_a'
   include { MODULE_B } from 'nf-core/module_b'
   
   workflow {
       MODULE_A(input_ch)
       MODULE_B(MODULE_A.out.results)
   }
   

3. Run the complete workflow using the same test data to validate end-to-end

Critical Guidelines

Command Execution

• Use -resume flag to leverage cached results when appropriate
• Use absolute paths, never relative paths

File Handling

• When specifying multiple files, separate with comma and wrap in double quotes: --input "file1.fq,file2.fq"
• ALWAYS expand wildcards/globs to comma-separated file lists before running
• Reference task IDs from stdout to locate output files in work directories

Module Include Syntax

• include { MOD } from 'nf-core/module' — Nextflow managed module (default). Nextflow automatically downloads and installs it from the registry. Always prefer this form.
• include { MOD } from './modules/nf-core/module/main.nf' — Local file path, resolved against the working directory. Only use when referencing locally modified modules.

Module Selection

• Prefer nf-core single-tool modules over sub-workflows
• Do not write wrapper workflows to test single modules - use Skill(skill="run-module") instead
• Use nextflow module search to find modules, then nextflow module info for details

Debugging Protocol

1. Check the task work directory using the task ID from stdout
2. Examine .command.log, .command.err, and .command.out files
3. Verify input files exist and are accessible
4. Check resource requirements (memory, CPUs) match available resources

Skill Delegation (IMPORTANT)

Delegate module-specific tasks to specialized skills using the Skill tool:

Task	Invoke Skill
Install/run/test a module	Skill(skill="run-module")

When to Delegate

• Step 3 (Validate Modules): Use run-module skill for each module validation

Example: Step 3 Validation

For each module in your plan:

1. Invoke: Skill(skill="run-module") → install, run with test data, and verify outputs
2. Only proceed to next module after success

These skills contain detailed instructions for their specific tasks and ensure consistent execution patterns.

Quick Reference

Step 1: Identify modules → Propose plan to user
Step 2: Wait for user agreement
Step 3: Validate ALL modules ONE BY ONE with test data
Step 4: Compose final workflow (only after Step 3 succeeds)