2.1.0

New Features

• Add CellBender workflow for ambient RNA removal.
• CellRanger:
  • For ATAC-Seq data, add ARC-v1 chemistry keyword for analyzing only the ATAC part of 10x multiome data. See CellRanger scATAC-seq sample sheet section for details.
  • For antibody/hashing/citeseq/crispr data, add multiome chemistry keyword for the feature barcoding on 10x multiome data.
• STARsolo:
  • In workflow output, besides mtx format gene-count matrices, the workflow also generates matrices in 10x-compatible hdf5 format.

Improvements

• CellRanger: For antibody/hashing/citeseq/crispr data,
  • cumulus_feature_barcoding v0.9.0+ now supports multi-threading and faster gzip file I/O.
• Workflows check if output_directory is a valid Cloud URI based on the given backend value before execution. (Feature request #322 )

Updates

• Genome Reference:
  • Add Cellranger VDJ v7.0.0 genome references: GRCh38_vdj_v7.0.0 and GRCm38_vdj_v7.0.0 in CellRanger scIR-seq sample sheet section.
• Default version upgrade:
  • Update cellranger default to v7.0.0.
  • Update cellranger-atac default to v2.1.0.
  • Update cellranger-arc default to v2.0.1.
  • Update cumulus_feature_barcoding default to v0.10.0.
  • STARsolo workflow uses STAR v2.7.10a by default.