[BIG] Adding spoQC to spatialaxe and many other changes

[heylf]

1. Adding spoQC

• Added the entire spoQC quality-control subworkflow: subworkflows/local/spoqc/main.nf plus 31 new local modules under modules/local/spoQC/ (ambient, analysis_category, analysis_cluster, analysis_overview, annotation, bubble, cell, cellcycle, combine_masks, doublet, finalreport, general, hqcr_celltype, hqcr_ident, hqpr_bounding_box, hqpr_celltype, hqpr_clustering, hqpr_metrices, hqpr_refinement, hqtr_ac, hqtr_bounding_box, hqtr_celltype, hqtr_clustering, hqtr_metrices, hqtr_qv, hqtr_refinement, marker, model, transcript, void, whole_slide), each with its own main.nf, meta.yml, and nf-test suite (tests/main.nf.test + snapshot).
• Wired spoQC into workflows/spatialaxe.nf.
• Added bin/spatialdata_write.py support for spoQC's SpatialData output.
• New test configs: conf/tests/test_spoqc.config, conf/tests/test_full_spoqc.config

Comment

Note

The tool will be released soon. It comes with proper documentation and spatialaxe will reference this documentation.

2. spatialaxe resource-label rework

• conf/base.config: single process_high/process_low-style labels with a combinatorial label system; process_{tiny,low,mid,high,xl}_cpus, _mem, and _time labels, each scaling with task.attempt.

3. nf-schema plugin upgrade (2.5.1 → 2.7.2)

• nextflow.config: bumped the plugin version.
• subworkflows/nf-core/utils_nfschema_plugin/main.nf: added a cli_typecast input, renamed parametersSchema → parameters_schema across option maps, fixed --help text resolution.
• subworkflows/nf-core/utils_nextflow_pipeline/main.nf: rewrote dumpParametersToJSON to use groovy.json.JsonGenerator with converters for Path/Duration/MemoryUnit/VersionNumber, replacing the old JsonOutput/FilesEx approach.
• subworkflows/local/utils_nfcore_spatialaxe_pipeline/main.nf: passes the new cli_typecast argument through.
• nextflow_schema.json: cleanup — removed redundant "default": false entries, added "default": true for cell_segmentation_only, added numeric defaults for max_x/max_y, normalized float defaults, unicode-escaped µm.
• modules.json / ro-crate-metadata.json: regenerated to match.

4. Bigger test-data support

• Added nf-core/unzip module usage so the pipeline can unpack the larger test dataset.
• Added assets/samplesheet_full.csv, conf/test_full.config

5. Samplesheet redefintion

• sample,bundle,image,annotation,stainings: samplesheet allows for two additional optional columns annotation,stainings that are useful for the QC subworkflow.

6. Rework of subworkflow and pipeline for proper qc mode

• spatialdata_write_meta_merge/main.nf: Change to subworkflow to account for proper qc mode.
• Change to bin/spatialdata_write.py: Adding an all mode to set all available features to True, which is important for QC.
• Added bin/spatialdata_write.py support for spoQC's SpatialData output.

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
• 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]

Finally 😅 all tests pass @kubranarci could you please check again

[kubranarci]

LGTM!