Add SCS support for issue #126

[katwre]

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 of changes

Refs #126

This draft PR starts SCS integration for spatialxe by wiring the Xenium-to-SCS input preparation path for --mode image --method scs.

Implemented in this PR

• pass experiment.xenium through the workflow so pixel size metadata can be used
• convert Xenium transcript coordinates from microns to pixel space for SCS
• generate SCS-ready outputs:
  • scs_input_bgi.tsv
  • morph2d.tif
  • xenium2scs_metrics.tsv
• publish only the files needed for SCS from this preparation step
• relax bundle validation for the SCS preparation path

Validation

• Nextflow SCS preparation path runs successfully
• The generated outputs were successfully used with SCS outside the pipeline
• SCS outside the pipeline completed successfully and produced output files

Remaining work

• integrate actual SCS execution into the pipeline
• connect SCS outputs into downstream pipeline results
• add tests and documentation updates