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CELLTYPES_SINGLER slows down the pipeline by using single CPU

bugSomething isn't workingSomething isn't working

Status: Open.

#260 In nf-core/scdownstream;

· kim-fehl opened on Mar 11, 2026

nf-core pipelines download fails with strict v2 syntax parser: includeConfig error

bugSomething isn't workingSomething isn't working

Status: Open.

#259 In nf-core/scdownstream;

· kim-fehl opened on Mar 11, 2026

Add CyteType cell type annotation

enhancementNew feature or requestNew feature or request

Status: Open.

#257 In nf-core/scdownstream;

· nictru opened on Mar 11, 2026

Remove duplication on cellbender for preprocessing data

enhancementNew feature or requestNew feature or request

Status: Open.

#249 In nf-core/scdownstream;

· nttg8100 opened on Jan 28, 2026

Add ExpiMap integration method

enhancementNew feature or requestNew feature or request

Status: Open.

#246 In nf-core/scdownstream;

· nictru opened on Jan 27, 2026

Add symphony integration method

enhancementNew feature or requestNew feature or request

Status: Open.

#245 In nf-core/scdownstream;

· nictru opened on Jan 27, 2026

Process NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:FINALIZE:ADATA_TORDS (merged) terminated with an error exit status

bugSomething isn't workingSomething isn't working

Status: Open.

#240 In nf-core/scdownstream;

· royfrancis opened on Jan 15, 2026

Add support for local/custom celltypist models

enhancementNew feature or requestNew feature or request

Status: Open.

#213 In nf-core/scdownstream;

· nictru opened on Aug 9, 2025

Allow processing data with PCA instead of actual integration

enhancementNew feature or requestNew feature or request

Status: Open.

#179 In nf-core/scdownstream;

· nictru opened on May 21, 2025

Implement dynamic QC filtering

enhancementNew feature or requestNew feature or request

NBIS

Status: Open.

#174 In nf-core/scdownstream;

· nictru opened on May 18, 2025

Implement gene annotation

enhancementNew feature or requestNew feature or request

NBIS

Status: Open.

#173 In nf-core/scdownstream;

· nictru opened on May 18, 2025

Implement batch effect quantification

enhancementNew feature or requestNew feature or request

NBIS

Status: Open.

#172 In nf-core/scdownstream;

· nictru opened on May 18, 2025