feat: add SegTraQ QC module

[priyalT]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/spatialxe branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

Description

Adds SegTraQ (Segmentation and Transcript Assignment QC) as a quality control module for spatial omics segmentation results.

What is SegTraQ?

A Python toolkit for quantitative and visual QC of segmentation and transcript assignment in spatial omics data, developed at EMBL.

Changes

New files:

• modules/local/segtraq/Dockerfile — Container with segtraq==0.0.3
• modules/local/segtraq/baseline/main.nf — SEGTRAQ_BASELINE process
• modules/local/segtraq/baseline/templates/baseline.py — Python script for baseline QC
• modules/local/segtraq/baseline/meta.yml — Module metadata
• subworkflows/local/segtraq_qc/main.nf — SEGTRAQ_QC subworkflow
• subworkflows/local/segtraq_qc/meta.yml — Subworkflow metadata
  Modified files:
• nextflow.config — Added run_segtraq, segtraq_centroid_x_key, segtraq_centroid_y_key
• nextflow_schema.json — Schema entries for new params
• conf/modules.config — publishDir for SEGTRAQ_BASELINE
• workflows/spatialxe.nf — Wired SEGTRAQ_QC after SPATIALDATA_WRITE_META_MERGE

[heylf]

Looks at first glance fine. I will dig deeper now.

[jfy133]

As I'm talking to @priyalT on Zoom, I did a quick generic review:

1. Run nf-core pipelines lint --fix ro_crate (I can't remember the exact command
2. Include the --run_segtraq_qc in at least one of the test profiles, and update the relevant snapshot
3. Add yourself to the nextflow.config contributors
4. Add a changelog entry (if being updated for the first release)

[heylf]

Linter issue might fix itself if we merge PR #123

[heylf]

look good

[heylf]

Just write template clustering_stability.py

[heylf]

volumne module LGTM

[heylf]

LGTM.

Could be merged. Then probably it needs a bit honing and testing to see how it works with the pipeline.