scpca-nf v0.6.3

What's Changed

• Make sure all RDS files are compressed
• Accommodate running multiple projects at once using the --project parameter

Full Changelog: v0.6.2...v0.6.3

scpca-nf v0.6.2

What's Changed

• Fixes a bug to make sure there's at least one gene or feature in the SingleCellExperiment object prior to converting to AnnData objects
• Temporarily remove cell type section from main qc report

Full Changelog: v0.6.1...v0.6.2

scpca-nf v0.6.1

What's Changed

• Fixes a bug when handling NA values in library metadata

Full Changelog: v0.6.0...v0.6.1

scpca-nf v0.6.0

What's Changed

• Add cluster assignments to processed SingleCellExperiment object
• Incorporate sample metadata into SingleCellExperiment objects
• Export all SingleCellExperiment objects as AnnData objects
• Added a workflow for generating references for cell type annotation
• Added CellAssign to cell type annotation
• Initial cell type report additions
• Allow for addition of submitter cell types
• Add style guide
• Account for failures in modeling gene variance and PCA

Full Changelog: v0.5.4...v0.6.0

scpca-nf v0.5.4

What's Changed

• Error handling for modeling gene variance, calculating PCA, and calculating UMAP

Full Changelog: v0.5.3...v0.5.4

scpca-nf v0.5.3

What's Changed

• Fixed intermittent ADT filtering bug
• Improved memory usage for QC report

Full Changelog: v0.5.2...v0.5.3

scpca-nf v0.5.2

What's Changed

• Added post-processing (filtering and normalization) for antibody-derived tag (ADT) data from CITE-seq experiments
• Added support for using additional organisms as references
• QC report updates
• Workflow development updates:
  • Improved behavior in limited resource environments
  • Added more workflow testing with stub blocks
• Experimental features added:
  • Integration of multiple samples
  • Cell-type annotation

Full Changelog: v0.5.1...v0.5.2

scpca-nf v0.5.1

What's Changed

• Make genetic demultiplexing optional

Full Changelog: v0.5.0...v0.5.1

scpca-nf v0.5.0

What's Changed

• Added support for processing libraries from multiple organisms
• Available references for mapping now include Human and Mouse Ensembl v104
• Option to skip feature mapping if already done
• Publish checkpoints for feature mapping

Full Changelog: v0.4.2...v0.5.0

scpca-nf v0.4.2

What's Changed

• Updated URL
• Ensure feature barcode files provided to salmon index contain the correct columns

Full Changelog: v0.4.1...v0.4.2