Wdl task starter

Skill ma-compbio-lab/SkillFoundry/skills/reproducible-workflows/wdl-task-starter

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

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill wdl-task-starter

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What its author says it does

Copied from the file, not written here

Use this skill to author and run a minimal WDL task and workflow with miniwdl. Do not use it for Cromwell-specific backends or large imported workflow graphs.

SKILL.md

2.0 KB, 460 tokens by cl100k_base, as published. Nobody here has run it

Purpose

Run a local WDL task end to end and use it as a starter for task and workflow authoring.

When to use

You need a verified OpenWDL-style local example.
You want a small WDL task or workflow starter with JSON inputs.

When not to use

You need cloud backends or Cromwell execution.
You need advanced imports or large workflow graphs.

Inputs

A WDL document
A Cromwell-style JSON input object
Optional run directory and summary path

Outputs

A JSON run summary with the output JSON emitted by miniwdl
The rendered greeting.txt file inside the run directory

Requirements

slurm/envs/workflow-languages
miniwdl
udocker inside the same prefix for daemonless local execution

Procedure

Run python3 skills/reproducible-workflows/wdl-task-starter/scripts/run_wdl_hello.py --name Ada --workspace scratch/wdl/workspace --summary-out scratch/wdl/summary.json.
Inspect the WDL outputs JSON and the materialized greeting.txt; the wrapper configures a daemonless local miniwdl execution path for this toy task.
Use examples/hello.wdl and examples/hello-inputs.json as the base for new tasks or workflows.

Validation

miniwdl run exits successfully.
The output JSON includes greeting text and a file output.

Failure modes and fixes

Missing runtime: verify slurm/envs/workflow-languages exists and python -m WDL --version works.
Missing daemonless backend: verify slurm/envs/workflow-languages/bin/udocker --version works.
Input mismatch: run miniwdl run --json to inspect the required input object shape.

Safety and limits

This skill runs a local toy workflow only.
Extend runtime blocks carefully before using external containers or large file inputs.