1.4.0

• On cellranger workflow
  • Add support for multiomics analysis using linked samples. cellranger-arc count, cellranger multi and cellranger count will be automatically triggered based on the sample sheet
  • Add support for cellranger version 6.0.1 and 6.0.0
  • Add support for cellranger-arc version 2.0.0, 1.0.1, 1.0.0
  • Add support for cellranger-atac version 2.0.0
  • Add support for cumulus_feature_barcoding version 0.6.0, which handles CellPlex CMO tags
  • Add GRCh38-2020-A_arc_v2.0.0, mm10-2020-A_arc_v2.0.0, GRCh38-2020-A_arc_v1.0.0 and mm10-2020-A_arc_v1.0.0 references for cellranger-arc.
  • Fixed bugs in cellranger_atac_create_reference
  • Add delete undetermined FASTQs option for mkfastq
• On demultiplexing workflow
  • Replace demuxlet with popscle, which includes both demuxlet and freemuxlet
• On cumulus workflow
  • Fix bug that remap_singlets and subset_singlets don't work when input is in sample sheet format.
• Modified workflows to remove trailing spaces and support spaces within output_directory