cwl-commandlinetool-starter

name	cwl-commandlinetool-starter
description	Use this skill to author and run a minimal Common Workflow Language CommandLineTool and one-step workflow with cwltool. Do not use it for containerized production execution or complex scatter/gather workflows.

Purpose

Run a small local CWL example end to end and use it as a starter for command-line tool wrapping.

When to use

• You need a verified local CWL example.
• You want a starter for wrapping a simple command-line tool in CWL.

When not to use

• You need cluster scheduling or production orchestration.
• You need Docker-only workflows.

Inputs

• A CWL workflow or command-line tool file
• A YAML or JSON job input file
• Optional output directory and summary path

Outputs

• The workflow output file
• A JSON run summary with the parsed CWL outputs and the rendered greeting text

Requirements

• slurm/envs/workflow-languages
• cwltool

Procedure

1. Run python3 skills/reproducible-workflows/cwl-commandlinetool-starter/scripts/run_cwl_hello.py --message "hello from cwl" --workspace scratch/cwl/workspace --summary-out scratch/cwl/summary.json.
2. Inspect the raw_summary block and the materialized greeting.txt.
3. Use examples/hello.cwl and examples/hello-job.yml as the base for a new local CommandLineTool.

Validation

• cwltool validates and runs successfully.
• The summary records a greeting text and an output file named greeting.txt.

Failure modes and fixes

• Missing runtime: verify slurm/envs/workflow-languages exists and contains cwltool.
• Validation failure: run python -m cwltool --validate on the CWL file before debugging execution.

Safety and limits

• This skill disables containers and runs a local toy example only.
• Extend carefully before wrapping destructive commands or large data paths.

Provenance

• https://www.commonwl.org/user_guide/
• https://github.com/common-workflow-language/cwl-v1.2