scpca-nf v0.8.1

What's Changed

• Output HDF5 files now have the .h5ad extension instead of .hdf5
• Bug fixes:
  • Skip running CellAssign if a processed object only has 1 cell
  • No cell type reports are created if processed objects only have 1 cell
  • Make sure to account for no genetic demultiplexing when estimating sample cell counts for metadata.json
  • Skip any downstream processing if no cells are left after filtering out empty droplets

Full Changelog: v0.8.0...v0.8.1

scpca-nf v0.8.0

What's Changed

• Addition of merge.nf used to create merged SingleCellExperiment and AnnData objects
  • The merged workflow takes as input a list of projects and creates a single merged object for each project
  • Also includes a report, summarizing the contents of the merged object
• Some minor aesthetic fixes to cell type report
• Use bz2 compression to reduce file sizes for SingleCellExperiment objects
• Add nextflow_schema.json to repo

Full Changelog: v0.7.3...v0.8.0

scpca-nf v0.7.3

What's Changed

• Skip any additional processing (clustering, cell type assignment) for processed objects with 0 cells
• Use new max_mem label for CellAssign classification, which uses params.max_memory after the first failure.

Full Changelog: v0.7.2...v0.7.3

scpca-nf v0.7.2

What's Changed

• Skip CellAssign if too few cells
• Small bug fixes for running multiplexed samples through cell typing
• Skip cell typing for cell line samples
• Small adjustments to UMAPs in the cell typing report
• Account for missing input files

Full Changelog: v0.7.1...v0.7.2

scpca-nf v0.7.1

What's Changed

• Update memory and CPU requests for running CellAssign
• Set max retries after AWS instance failure to 2
• Use On Demand instances on 3rd retry
• Create faceted UMAPs in cell type report

Full Changelog: v0.7.0...v0.7.1

scpca-nf v0.7.0

What's Changed

• Addition of cell type annotation to the main workflow, including:
  • Annotation with either SingleR or CellAssign
  • New output that includes a processed SingleCellExperiment and AnnData objects with cell type annotations and a cell type summary report
  • Documentation for adding cell type annotations
• By default, cell type annotation is turned off. To run the workflow with cell type annotation, use the --perform_celltyping flag.
• By default, if cell typing results already exist, previous results are used. The --repeat_celltyping flag can be used to repeat previous cell type annotation.
• Addition of pre-commit to the repo

Full Changelog: v0.6.3...v0.7.0

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