Module/scdblfinder#261

Merged

nictru merged 51 commits intonf-core:devfrom

KurayiChawatama:module/scdblfinder

Apr 10, 2026

Commits on Mar 17, 2026

Add scdblfinder module skeleton generated by nf-core tools
KurayiChawatama
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Fix scdblfinder: remove mockDoubletSCE and use real SCE object directly
KurayiChawatama
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Integrate scdblfinder into pipeline configuration and tests
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Fix scdblfinder module implementation and tests
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Update documentation to include scDblFinder
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added more documentation for scdblfinder
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added scdblfinder citation to citations md
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removed template comment from meta yml
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moved scdblfinder module to doublet detection dirtectory
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updated docs ouput to include scdblfinder
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[automated] Fix code linting

nf-core-bot
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KurayiChawatama
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Update modules/local/doublet_detection/scdblfinder/templates/scdblfinder.R

KurayiChawatama
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Copilot
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added https version of the singularity container link
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refactor(scDblFinder): optimize multiplet rate calculation using findInterval
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added explanation for column name change
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write updated SingleCellExperiment directly as h5ad without explicit conversion
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enhance h5ad writing with validation for cell barcodes and primary assay
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add scdblfinder to input methods in doublet detection subworkflow test
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streamline renaming of scDblFinder columns with less clumsy code
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removed explicit call of artifical doublet number in scdblfinder function
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updated test snapshot to match previous commit
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Enhance scDblFinder functionality and documentation
KurayiChawatama
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[automated] Fix code linting

nf-core-bot
authored and
KurayiChawatama
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change other doublet detection methods to use mix

KurayiChawatama
and
Copilot
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Remove redundant restoration of original cell barcodes in scDblFinder processing
KurayiChawatama
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Remove unnecessary comment about RNG seed parameter in scDblFinder script
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Refactor doublet rate handling in scDblFinder to streamline logic and improve readability
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Fix regex pattern for doublet detection tool options in nextflow_schema.json
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added intial batch processign steps code
KurayiChawatama
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Commits on Apr 6, 2026

Merge remote-tracking branch 'upstream/dev' into module/scdblfinder
KurayiChawatama
committed

Commits on Apr 9, 2026

Commits on Apr 10, 2026