implement matthias recom, update to snaptshots and version bump.

[heylf]

This commit finalizes the 1.0.1 release and implements a review recommendation from Matthias regarding the --expansion-distance XeniumRanger parameter.

Release finalization (1.0.1)

• nextflow.config: pipeline version bumped from 1.1.0dev to 1.0.1.
• assets/multiqc_config.yml: report links updated from the dev branch/docs to the 1.0.1 release tag/docs.
• ro-crate-metadata.json: creativeWorkStatus changed from InProgress to Stable, version set to 1.0.1, and the pipeline URL updated to https://nf-co.re/spatialaxe/1.0.1/.
• CHANGELOG.md: added a new 1.0.1dev section header and finalized the 1.0.1 - [date] section.

New expansion_distance parameter (Matthias's recommendation)

Previously, --expansion-distance was appended to XeniumRanger's arguments via a static ext.args closure in conf/modules.config, gated only on nuclei and params.expansion_distance. This commit removes that closure and instead threads expansion_distance as an explicit process/subworkflow input:

• modules/nf-core/xeniumranger/import-segmentation/main.nf: added expansion_distance as a tuple input; the module now only emits --expansion-distance=<value> when a nuclei segmentation is being imported (XeniumRanger rejects the flag for transcript-assignment or cells-only imports).
• The new parameter was propagated through the call chain in 10 local subworkflows:
  • baysor_run_prior_segmentation_mask
  • baysor_run_transcripts_parquet
  • baysor_run_transcripts_parquet_tiled
  • cellpose_baysor_import_segmentation
  • cellpose_resolift_morphology_ome_tif
  • proseg_preset_proseg2baysor
  • proseg_preset_proseg2baysor_tiled
  • segger_create_train_predict
  • stardist_resolift_morphology_ome_tif
  • xeniumranger_import_segmentation_redefine_bundle
  • xeniumranger_resegment_morphology_ome_tif
• workflows/spatialaxe.nf: the top-level workflow now passes expansion_distance into each of the above subworkflow calls.

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!
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

[heylf]

I will update the module as well in a moment.