Update xenium ranger modules and subworkflows

[an-altosian]

This PR updates the xeniumranger version in its modules, and restructured the code to follow nf-core standard. Because xeniumranger is not on conda, I tested it using docker.

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 module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[khersameesh24]

Hi @an-altosian , left some comments. Would just need a small update, everything else looks good. Thanks for working on this again.

[Copilot]

Pull request overview

This PR updates the xeniumranger modules from version 3.0.1 to 4.0 and restructures the code to follow nf-core standards. The update includes changes to all xeniumranger modules (resegment, rename, relabel, and import-segmentation) with a new Docker container approach, refactored input/output patterns, and updated test files.

• Updated xeniumranger from version 3.0.1 to 4.0.0 with a new Dockerfile that downloads the tool directly instead of requiring a local tarball
• Restructured all modules to use the new nf-core version output pattern with eval() and topic: versions
• Simplified output structure to emit directories instead of glob patterns (**/outs/**)

Reviewed changes

Copilot reviewed 19 out of 24 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
modules/nf-core/xeniumranger/Dockerfile	Updated to xeniumranger 4.0.0 with wget-based download instead of COPY
modules/nf-core/xeniumranger/resegment/main.nf	Updated container version, simplified input/output patterns, removed parameter inputs
modules/nf-core/xeniumranger/resegment/meta.yml	Updated output documentation to reflect directory-based outputs
modules/nf-core/xeniumranger/resegment/tests/main.nf.test	Updated test inputs to use new data source and simplified assertions
modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap	Updated snapshots with new test data and version information
modules/nf-core/xeniumranger/rename/main.nf	Updated container version, consolidated input tuple, simplified output
modules/nf-core/xeniumranger/rename/meta.yml	Updated input/output documentation for new structure
modules/nf-core/xeniumranger/rename/tests/main.nf.test	Updated test inputs to match new input structure
modules/nf-core/xeniumranger/rename/tests/main.nf.test.snap	Updated snapshots with new test results
modules/nf-core/xeniumranger/relabel/main.nf	Updated container version, consolidated input tuple
modules/nf-core/xeniumranger/relabel/meta.yml	Updated documentation and renamed gene_panel to panel
modules/nf-core/xeniumranger/relabel/tests/main.nf.test	Simplified test assertions
modules/nf-core/xeniumranger/relabel/tests/main.nf.test.snap	Updated snapshots
modules/nf-core/xeniumranger/import-segmentation/main.nf	Updated container version, reordered inputs, added validation logic
modules/nf-core/xeniumranger/import-segmentation/meta.yml	Expanded documentation for image-based vs transcript-based modes
modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test	Significantly simplified tests, removed multiple test cases
modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap	Removed most snapshots, kept only stub test snapshot
modules/nf-core/xeniumranger/nextflow.config	Added new config file with commented-out settings
modules/nf-core/xeniumranger/README.md	Removed documentation about manual Docker updates

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[DongzeHE]

Hi @khersameesh24 , all addressed. Thank you for the comments and suggestions!

[khersameesh24]

LGTM