Add gene efficiency correction as a separate pipeline stage#183
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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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* Register cellposev4 in benchmark run scripts 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> * fix anndata version mismatch with txsim * add segger to workflow (test) * duplicates when FOV stiching cleaned up * chunks issue atera * segger update image * claude fix for segger * atera version fix * wf for the custom rnaseq scripts * adjust the loader image name * adjust the memory * troubleshootig edges * segger update * cell type label correction * fix boundaries * OOM fixes * fix code * RCTD * segger to RAPIDS * fix rctd * segger debug (torchvision) * save the xenium version * add atera to datasets * Add gene efficiency correction as a separate pipeline stage (#183) 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> --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
dariarom94
added a commit
that referenced
this pull request
Jul 22, 2026
* Register cellposev4 in benchmark run scripts 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> * fix anndata version mismatch with txsim * add segger to workflow (test) * duplicates when FOV stiching cleaned up * chunks issue atera * segger update image * claude fix for segger * atera version fix * wf for the custom rnaseq scripts * adjust the loader image name * adjust the memory * troubleshootig edges * segger update * cell type label correction * fix boundaries * OOM fixes * fix code * RCTD * segger to RAPIDS * fix rctd * segger debug (torchvision) * save the xenium version * add atera to datasets * Add gene efficiency correction as a separate pipeline stage (#183) 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> * moscot to pca and segger troubleshooting --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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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.
Verified: viash config view, viash ns build (components + workflow, deps and alias resolve), and viash test on both new components (output spec-conformant).
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Proposed changes are described in the CHANGELOG.md
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