feat: add portable WDL module skill

[claymcleod]

Description

A creating-wdl-modules agent skill was added as a repository-local skill discoverable by Claude Code, GitHub Copilot, and OpenAI Codex. It codified license-first review, digest-pinned BioContainers images by default, WDL 1.4 task conventions, documented fixture provenance, and native sprocket dev test coverage. Strict Sprocket configuration and pinned CI gates for skill discovery, formatting, linting, and root-level module testing were also added.

The fq module was implemented as the first concrete application of the skill, wrapping fq 0.12.0 across four tasks: fq_filter, fq_generate, fq_lint, and fq_subsample. Every public CLI option from the pinned upstream was typed as a WDL input; the hidden verbose flag was excluded. Finite choice sets are represented as WDL enums with values matching the pinned CLI tokens, and redundant same-name enum values are inferred. The synthetic FASTQ fixtures are generated deterministically with fq generate --seed 7 --record-count 4 --read-length 8. Wrapper-level guards were added for cross-input constraints that upstream silently accepts—empty source arrays, mismatched source/destination lengths, mutually exclusive filter modes, and unpaired read-two arguments; upstream fq validates probability bounds directly. All 20 native tests pass against the digest-pinned BioContainers image.

Tools referenced

Tool	Version	License	SPDX	License file	Needs review?
fq	0.12.0	MIT License	MIT	Link	☐

Checklist

• My contribution contains only original workflow logic. It does not include third-party source code, binaries, container images, or copied third-party scripts or similar materials.
• I have identified every external tool my module invokes and listed its license in the table above.
• Every tool listed uses a license from the approved list, or I have flagged it for review in the table above.
• No tool uses a license from the prohibited list or any other license that imposes obligations triggered by network interaction, SaaS deployment, or similar use-based mechanisms.
• If this is a version bump, I have re-verified that the tool's license has not changed in a way that is incompatible with this repository's policies.
• I have the right to license my contribution under the terms of this repository (MIT or Apache-2.0).

Maintainer checklist

• I have verified that every tool listed in the tools table carries a license from the approved list, or have reviewed and approved any license flagged for review.
• No tool uses a license from the prohibited list or any other license that imposes obligations triggered by network interaction, SaaS deployment, or similar use-based mechanisms.