cwl-validate-package

name	cwl-validate-package
description	Validate CWL package syntax and structure before deployment to Weaver. Check for syntax errors, Docker requirements, input/output definitions, and CWL version compatibility. Use to catch errors early and ensure package quality before deployment.
license	Apache-2.0
compatibility	Requires cwltool installed locally. Supports CWL v1.0, v1.1, v1.2.
metadata	{"author":"fmigneault"}

Validate CWL Package

Validate CWL package syntax and structure before deploying to Weaver.

When to Use

• Before deploying a new process to catch errors early
• When creating or modifying CWL packages
• To verify Docker requirements are properly specified
• When troubleshooting package deployment failures
• To ensure CWL version compatibility

Parameters

Required

• package_file (path): CWL file to validate (.cwl or .yaml)

Optional

• strict (boolean): Enable strict validation mode
• check_docker (boolean): Verify Docker images are accessible

CLI Usage

# Basic validation
cwltool --validate process.cwl

# Validate with strict mode
cwltool --validate --strict process.cwl

# Validate and check requirements
cwltool --print-pre --validate process.cwl

# Validate workflow with dependencies
cwltool --validate workflow.cwl

Validation Checks

Syntax Validation

• CWL version compatibility
• YAML/JSON structure
• Required fields present
• Type definitions correct

Semantic Validation

• Input/output types match
• Command line bindings valid
• File paths resolvable
• Expressions syntax correct

Docker Validation

• DockerRequirement properly formatted
• Image names valid
• Tags specified (recommended)

Workflow Validation

• Step names unique
• Input/output connections valid
• No circular dependencies
• All required inputs provided

Common Issues and Fixes

Issue: "Unknown field 'xyz'"

# ❌ Wrong - typo in field name
DockerRequirment:  # Missing 'e'
  dockerPull: image

# ✅ Correct
DockerRequirement:
  dockerPull: image

Issue: "Type mismatch"

# ❌ Wrong - string where File expected
inputs:
  input_file: string

# ✅ Correct
inputs:
  input_file: File

Issue: "Missing required field"

# ❌ Wrong - missing class
cwlVersion: v1.2

# ✅ Correct
cwlVersion: v1.2
class: CommandLineTool

Issue: "Invalid expression"

# ❌ Wrong - incorrect JavaScript syntax
arguments: ["$(runtime.outdir"]  # Missing closing )

# ✅ Correct
arguments: ["$(runtime.outdir)"]

Example: Valid CWL Package

cwlVersion: v1.2
class: CommandLineTool
baseCommand: [echo]

requirements:
  DockerRequirement:
    dockerPull: debian:stable-slim

inputs:
  message:
    type: string
    inputBinding:
      position: 1

outputs:
  output:
    type: stdout

stdout: output.txt

Validation Output

Success

process.cwl is valid CWL

Errors

ERROR process.cwl:5:1: Unknown field `DockerRequirment`
  Did you mean `DockerRequirement`?

Advanced Validation

Check Docker Images

# Verify Docker image exists
docker pull $(grep dockerPull process.cwl | cut -d: -f2-)

Test Locally

# Run with sample inputs
cwltool process.cwl inputs.json

Validate Against Schema

# Use CWL schema validator
schema-salad-tool --print-jsonld-context process.cwl

Integration with Weaver

After validation, deploy to Weaver:

# 1. Validate locally
cwltool --validate process.cwl

# 2. Test with sample data
cwltool process.cwl test-inputs.json

# 3. Deploy to Weaver
weaver deploy -u $WEAVER_URL -p my-process -b process.cwl

Related Skills

• process-deploy - Deploy validated package
• cwl-debug-package - Debug validation failures
• cwl-understand-docker - Docker requirements
• job-exceptions - Debug deployment errors

Documentation

• CWL Application Packages
• CWL Specification
• CWL User Guide
• Process Deployment

Tools

• cwltool: Reference CWL implementation
• schema-salad: CWL schema validator
• Docker: For testing Docker-based packages

Best Practices

1. Always validate before deploying to Weaver
2. Use specific Docker tags (not latest)
3. Test locally with sample data
4. Document inputs/outputs with descriptions
5. Pin CWL version explicitly (v1.0, v1.1, v1.2)