Draft: Add scPortrait feature for issue #26

[TPbiocode]

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).

PR Description

Refs #26

This draft PR starts scPortrait feature integration in the spatialxe pipeline by adding an image-mode segmentation path for the method 'scportrait'.

Implemented in this PR

• Added scportrait to allowed methods in config and schema.
• Added a new local scportrait image segmentation module.
• Added template-based Python segmentation script for the module.
• Added a scportrait image subworkflow that feeds masks into xeniumranger import-segmentation.
• Wired scportrait method routing in the main workflow.
• Added publishDir config for scportrait outputs.

Changes

• Initial implementation of scPortrait feature
• Added related workflow and module components
• Updated pipeline configuration for scPortrait method selection

Notes

This work is in progress

Further updates will follow as development continues, including testing, documentation updates, and linting