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Tighten emptyDrops FDR from 0.01 to 0.001 - #14
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emptydrops.R called cells at FDR < 0.01; tighten to FDR < 0.001 so emptyDrops drops the low-UMI ambient barcodes it was rescuing. This stricter threshold is the one the downstream preprocessing-variant analysis was regenerated against (the 2026-10-04 "emptyDrops FDR tightened" update, reflected in all analysis reports). It was applied in the working tree but was not included in PR #13. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Tightening the emptyDrops FDR from 0.01 to 0.001 (665b78d) changes which barcodes pass cell calling, so the golden --run-workflow reference outputs on the emptyDrops arm no longer matched and the regression test failed. Regenerate them on testdata using the CI recipe (local executor, CellBender shim, pinned per-rule resources, cached conda envs) so the test passes against the new threshold. Only the emptyDrops lineage changed: the emptydrops filtered object and its filtered matrix, plus every soupx_emptydrops-derived object (soupx, scdblfinder, doubletfinder, post-hoc mad/threshold) and their marker tables. The CellRanger (soupx_tenx) and CellBender arms are unaffected and were left untouched -- their Seurat metadata is identical; only serialization timestamps differ, which the metadata comparator ignores. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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emptydrops.R called cells at FDR < 0.01; tighten to FDR < 0.001 so emptyDrops drops the low-UMI ambient barcodes it was rescuing. This stricter threshold is the one the downstream preprocessing-variant analysis was regenerated against (the 2026-10-04 "emptyDrops FDR tightened" update, reflected in all analysis reports). It was applied in the working tree but was not included in PR #13.