Track and resolve outstanding TODOs in workflows/spatialxe.nf

[an-altosian]

Overview

Tracking the three outstanding TODO comments in workflows/spatialxe.nf as of v1.0.0 release prep. These are real engineering work items that don't have current owners or scope; they should be picked up post-v1.0.0.

The remaining nf-core template-leftover TODOs (Group A — awsfulltest.yml, README.md, tests/nextflow.config, utils_nfcore_spatialxe_pipeline/main.nf:334,347,384) were already removed in upstream/dev commits 638ee81 and eb969f9.

Outstanding TODOs

workflows/spatialxe.nf:46

// TODO qc layer subworkflows

Severity: Medium. Suggests one or more QC subworkflows are pending wiring into the main workflow. Investigation needed: which QC subworkflows are referenced and what's missing? Likely candidates from the subworkflows/local/ tree: image_qc/, molecule_qc/, cell_type_separability/, ncvs/, etc.

Acceptance criteria:

• Identify the intended QC subworkflows
• Either wire them in or replace the TODO with a documented decision (e.g. "QC subworkflows ship in v1.1.0; tracked at #XXX")

workflows/spatialxe.nf:98

// TODO: Replace with params.test_data_mode for robustness

Severity: Low. Test-data branching logic uses a less-robust check (likely a string comparison or path check) when params.test_data_mode exists for this purpose.

Acceptance criteria:

• Replace the existing branching with a params.test_data_mode check
• Verify all tests/*_mode.nf.test profiles still pass

workflows/spatialxe.nf:639

// TODO collect all qc outs in a channel to be passed to multiqc

Severity: Medium. MultiQC wiring is incomplete — some QC outputs may not be reaching the report.

Acceptance criteria:

• Audit all QC subworkflow outputs against what's currently passed to MultiQC
• Gather missing outputs into a single channel
• Verify MultiQC report includes all expected sections

Related context

The full release-PR review-comment plan that produced this issue lives at docs/plans/2026-04-30_PLAN_release-pr-139-review-comments.md (internal-only, not committed to nf-core/spatialxe).

This issue is referenced in PR #148 (Address PR #139 review).