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Cellbender fails in some samples when we calculated --expected-cells

Status: Open.

#51 In joechanlab/nf-scrnaseq;

· aelhossiny opened on Feb 19, 2026

possibly use a hard threshold on background_fraction

Status: Open.

#41 In joechanlab/nf-scrnaseq;

· lm687 opened on Oct 18, 2024

Cellbender demultiplexing

enhancementNew feature or requestNew feature or request

Status: Open.

#33 In joechanlab/nf-scrnaseq;

· Mamie opened on Aug 2, 2024

Integrate rapids-singlecell

enhancementNew feature or requestNew feature or request

Status: Open.

#29 In joechanlab/nf-scrnaseq;

· Mamie opened on Jul 20, 2024

Output optional Seurat RDS

enhancementNew feature or requestNew feature or request

Status: Open.

#28 In joechanlab/nf-scrnaseq;

· Mamie opened on Jul 19, 2024

Leiden parameter search

enhancementNew feature or requestNew feature or request

Status: Open.

#15 In joechanlab/nf-scrnaseq;

· jpintar opened on Jul 5, 2024

Use of Cell Ranger filtered H5 files to get --expected-cells

Status: Open.

#11 In joechanlab/nf-scrnaseq;

· jpintar opened on Jul 1, 2024