Visium manual alignment and tissue detection

[ch99l]

No description provided.

[Copilot]

Pull request overview

Adds Loupe-based manual alignment and tissue detection for standard Visium workflows.

Changes:

• Generates spatial metadata and filters out-of-tissue barcodes.
• Preserves CB/UB tags during alignment and adjusts Visium barcode filtering.
• Adds validation, smoke-test configuration, and documentation.

Reviewed changes

Copilot reviewed 13 out of 15 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
subworkflows/prepare_input_visium_hd.nf	Uses the shared BAM filter.
subworkflows/prepare_input_standard.nf	Integrates Loupe-derived tissue positions.
README.md	Documents Visium alignment and metadata.
nextflow.config	Adds the Loupe parameter and version.
modules/preprocess_fastq.nf	Extends Visium barcode-rank searching.
modules/prepare_input/standard/extract_spatial_coordinates.nf	Supplies raw spatial coordinates.
modules/prepare_input/standard/create_visium_tissue_positions.nf	Adds the tissue-position process.
modules/prepare_input/shared/filter_barcoded_bam.nf	Shares and validates BAM filtering.
modules/alignment/align.nf	Preserves FASTQ comments as SAM tags.
main.nf	Filters standard Visium BAMs by tissue.
lib/Validation.groovy	Validates Loupe and Visium inputs.
conf/smoke_test.config	Configures Loupe smoke-test input.
CHANGELOG.md	Records release changes.
bin/visium_tissue_positions.py	Generates metadata and barcode lists.

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