Fix meta_fb never defined in CELLRANGER_MULTI (#9798)

[SZhengP]

PR checklist

Closes #9798

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[Copilot]

Pull request overview

This pull request fixes a bug where an undefined variable meta_fb was referenced in the CELLRANGER_MULTI module, replacing it with the correct variable fb_options.

Changes:

• Fixed undefined variable reference by changing meta_fb.options to fb_options.options on lines 126-127

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[Copilot]

While this PR correctly fixes the immediate issue (undefined variable meta_fb), there appears to be a related bug on line 95 (outside the scope of this PR) that prevents fb_options_use from ever being truthy.

On line 95, fb_options is assigned the value of meta_ab.options or meta_crispr.options (the options map itself), but on line 105, the code checks fb_options?.options, which would be looking for a nested options property. Since fb_options is a map (e.g., ["r1-length": "26"]), not a meta object, fb_options?.options will always be null, making fb_options_use null, and these lines 126-127 will never execute.

Line 95 should likely be: fb_options = meta_ab?.options ? meta_ab : (meta_crispr?.options ? meta_crispr : [:]) to assign the entire meta object rather than just the options map. This would make it consistent with how meta_vdj and meta_gex are used in lines 123-124 and 107-117 respectively.

This issue should be addressed in a follow-up PR to make the feature barcode options functional.

Suggested change

	fb_options_r1_length = fb_options_use && fb_options.options.containsKey("r1-length") ? "r1-length,${fb_options.options["r1-length"]}" : ''
	fb_options_r2_length = fb_options_use && fb_options.options.containsKey("r2-length") ? "r2-length,${fb_options.options["r2-length"]}" : ''
	// Normalize feature-barcode options: support both meta objects (with `.options`) and raw option maps
	def fb_options_map = fb_options?.options ?: fb_options ?: [:]
	fb_options_r1_length = fb_options_use && fb_options_map.containsKey("r1-length") ? "r1-length,${fb_options_map["r1-length"]}" : ''
	fb_options_r2_length = fb_options_use && fb_options_map.containsKey("r2-length") ? "r2-length,${fb_options_map["r2-length"]}" : ''

[tgelafr-pfzr]

Ditto to what copilot said, but more fundamentally we need a new test for this use case, the two bugs reveal a lack of coverage.

[SZhengP]

Ditto to what copilot said, but more fundamentally we need a new test for this use case, the two bugs reveal a lack of coverage.

Yeah. I saw that and I am working on it.

[SZhengP]

Please keep this PR open as it is not done. Currently, the logic in this module is not contained but highly dependent on the local align_cellrangermulti subworkflow in scrnaseq pipeline. Some logic needs to be re-written.