Cwl commandlinetool starter

Skill ma-compbio-lab/SkillFoundry/skills/reproducible-workflows/cwl-commandlinetool-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill cwl-commandlinetool-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

What its author says it does

Copied from the file, not written here

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.

SKILL.md

1.9 KB, 403 tokens by cl100k_base, as published. Nobody here has run it

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

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.
Inspect the raw_summary block and the materialized greeting.txt.
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.