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Can we make genes_metadata.tsv and cell_metadata.tsv optional?

Status: Open.

#61 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 28, 2025

Modify README

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#60 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 27, 2025

Use --input and --outdir as inputs and outputs parameters for the channel paths

Status: Open.

#57 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 26, 2025

Subsample test-data for droplet and plate as much as possible

Status: Open.

#48 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 25, 2025

Upgrade NF version used in nf-test GitHub actions for droplet and plate

Status: Open.

#47 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 25, 2025

Activate nf-core linting

Status: Open.

#38 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 24, 2025

[single-cell best practices] perform doublet detection from a majority vote from a number of tools

Status: Open.

#34 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 22, 2025

[single-cell best practices] add ambient RNA removal

Status: Open.

#33 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 22, 2025

Does any of our processes could be added as a new Module in nf-core?

Status: Open.

#32 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 21, 2025

Enable cloud compatibility

Status: Open.

#30 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 18, 2025

Add bundled documentation

Status: Open.

#19 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 18, 2025

Propose pipeline to nf-core

Status: Open.

#18 In ebi-gene-expression-group/scxa-tertiary-workflow;

· pmb59 opened on Mar 18, 2025