cwl-commandlinetool-starter

## 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