scpca-nf v0.9.0

What's Changed

• Support for processing additional 10x Genomics kits:
  • Flex Gene Expression, both single and multiplexed libraries
  • Chromium GEM-X single-cell 5' v3
  • Chromium GEM-X single-cell 3' v4
• Doublet detection is performed using scDblFinder. Results are stored in the filtered and processed objects.
• The --perform_celltyping flag now assigns cell types using SCimilarity in addition to the cell types from SingleR and CellAssign available in previous versions of the workflow.
  • Consensus cell types are now determined based on agreement between at least two of the three methods in an ontology-aware manner using the updated consensus reference in OpenScPCA-analysis v0.2.3. The resulting cell types are summarized in the QC and supplemental cell type reports.
• Cell types annotated as part of the OpenScPCA Project can be provided as input to the workflow. These annotations are added to the cell metadata of all objects and are summarized in the QC and cell type annotation reports.
• The --perform_cnv_inference flag can be used to perform CNV inference using a reference comprised of non-malignant cells, as determined by the consensus cell types. See the CNV inference documentation for more information.
• A new workflow, build-cellbrowser.nf, has been added and can be used to build an instance of the UCSC Cell Browser using output from the main scpca-nf workflow.
• Instructions for using the scpca-nf workflow with Cavatica have been added and can be found here.

New Contributors

• @jaclyn-taroni made their first contribution in #952

Full Changelog: v0.8.8...v0.9.0