Fixes: segger and fastreseg#186
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The cellposev4 segmentation component exists but was not listed in any run script, so it never ran. Add it to segmentation_methods alongside cellpose (active in the seqeracloud scripts, commented in the local/test scripts, matching the existing convention). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Promote gene_efficiency_correction from an expression-correction method to its own stage (methods_gene_efficiency_correction) that runs after expression correction, offering two options: no_correction (pass-through) and gene_efficiency_correction. - New API src/api/comp_method_gene_efficiency_correction.yaml (input and output on file_spatial_corrected_counts). - New components under methods_gene_efficiency_correction/; the moved gene_efficiency_correction now reads --input and preserves an upstream normalized_uncorrected layer. - Remove gene_efficiency_correction from methods_expression_correction. - run_benchmark: insert the gene_eff stage between expression correction and aggregate_spatial_data; it overwrites the output_correction state key so aggregate_spatial_data and the similarity metric need no rewiring and controls keep working. Add --gene_efficiency_correction_methods and alias the colliding no_correction dependency (gene_eff_no_correction). - Update run scripts' method lists for the new stage. Verified: viash config view, viash ns build (components + workflow, deps and alias resolve), and viash test on both new components (output spec-conformant). Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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