cwl-validate-package

Validate CWL package syntax, structure, and Docker image accessibility before deployment.

30|6|Updated Mar 5, 2019
One-click install
npx skills add https://github.com/crim-ca/weaver --skill cwl-validate-package
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: cwl-validate-package
Source: https://github.com/crim-ca/weaver/tree/main/.agents/skills/cwl-validate-package
Command: npx skills add https://github.com/crim-ca/weaver --skill cwl-validate-package

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires cwltool, and includes scripts (resource) components.

What problem does it solve?

This Skill helps to validate the syntax and structure of Common Workflow Language (CWL) packages before deployment to Weaver, ensuring package quality and catching errors early.

Core Features & Use Cases

  • Syntax Validation: Checks for syntax errors, Docker requirements, input/output definitions, and CWL version compatibility.
  • Docker Validation: Verifies Docker images are accessible and properly formatted.
  • Workflow Validation: Ensures step names are unique, input/output connections are valid, and there are no circular dependencies.
  • Use Case: Before deploying a new process to Weaver, use this Skill to catch syntax errors and ensure the package is ready for deployment.

Quick Start

Run the 'cwl-validate-package' Skill on your CWL file 'process.cwl' to validate its syntax and structure.

Frequently Asked Questions about cwl-validate-package

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I validate CWL syntax before deploying a workflow?

To validate CWL syntax before deployment, run a validation check on your CWL file to catch syntax errors, Docker requirements, and version compatibility. This ensures your Common Workflow Language package is structurally sound and ready for Weaver deployment.

Can I check if Docker images are accessible in a CWL package?

Yes, you can check Docker image accessibility within a CWL package by running a Docker validation process. It verifies that required Docker images are properly formatted and accessible, ensuring workflow integrity before deployment.

Do I need cwltool to check Common Workflow Language structure?

Yes, you need cwltool installed to check Common Workflow Language structure. It is a required dependency for performing syntax validation and ensuring CWL package quality before deployment.

What is the best way to ensure bioinformatics workflow integrity before deployment?

The best way to ensure bioinformatics workflow integrity is to validate step names, input/output connections, and check for circular dependencies. This verifies the CWL package structure and Docker requirements before deployment.

Does CWL validation check for circular dependencies in workflows?

Yes, CWL validation checks for circular dependencies in workflows. It ensures step names are unique and input/output connections are valid, catching structural errors early before deploying the package.