[Deployment]: create Code Ocean adapter and capsule for Limma Analysis #69

Goal

Create the first Code Ocean deployment adapter and Standard Capsule for canonical modules/OMIX-Limma-Analysis (currently module 0.1.0, interface 1). This is the downstream statistical-analysis capsule for declared continuous feature-by-sample matrices, including Seurat Pseudobulk donor means and GSVA enrichment scores.

Ownership

• Helix: canonical limma model and pseudobulk handoff review
• Compass: GSVA enrichment-score handoff review
• Harbor: initial adapter repository, App Panel, workflow discovery, and Code Ocean capsule
• Forge: pinned r-statistics runtime provenance
• Beacon: contract, source, parameter, handoff, and release-evidence parity

Required workflow inputs

• One continuous feature-by-sample matrix.
• Matching sample metadata.
• Optional Pseudobulk_Manifest.dcf when supplied by OMIX Seurat Pseudobulk.

The adapter should accept one unambiguous combined upstream result bundle and optional explicit file overrides. It must reject raw counts and direct users to OMIX DEG Analysis.

Required modes

1. Harmony donor means: input_kind=log2_expression, manifest-driven variance_model=ebayes.
2. SCTransform donor means: input_kind=log2_expression, manifest-driven variance_model=ebayes_trend.
3. GSVA output: input_kind=enrichment_score, with explicit contrasts and the appropriate declared variance model.
4. General declared continuous scores, without claiming support for untransformed proportions.

All public and advanced canonical parameters must be exposed, including ordered contrasts, covariates, optional donor blocking, input kind, variance model, and feature summarization. Platform output paths remain hidden.

Dependencies

• The Seurat Pseudobulk adapter issue provides end-to-end Harmony/SCT workflow fixtures and manifests.
• The GSVA adapter issue provides a representative enrichment-score workflow fixture.
• Canonical Limma Analysis must complete representative-data validation and any resulting compatible corrections before adapter release.

Acceptance evidence

• Adapter repository created from the standard template and registered in canonical module metadata after its URL exists.
• Canonical source export, commit, and hashes agree.
• CLI, schema, App Panel, source-parity, input-discovery, and failure-path tests pass.
• Representative Code Ocean runs validate Harmony, SCT, and GSVA score handoffs.
• Output tables, aligned metadata, run summary, design, contrast order, variance model, and donor-blocking provenance are inspected.
• Runtime image tag/digest and Code Ocean environment identity are recorded.
• Helix, Compass, Forge, and Beacon reviews pass. Release remains a separate explicit approval step.

Out of scope

• Raw-count normalization or voom; those remain in OMIX DEG Analysis.
• Re-running pseudobulk aggregation or GSVA inside this capsule.
• Changing the preserved Limma template behavior without a separate canonical scientific review.