v2.0.0

What's Changed

• Version 2 Update by @chenv3 in #5
  • Flag updates
    • --version - renamed to --pipeline
    • --cellranger - added to select Cell Ranger version for GEX, CITE, VDJ, and MULTI pipelines
      • Handles version 7.1.0, 7.2.0, and 8.0.0
    • --genome - add additional options
      • Add 2024 genome release for GEX, CITE, and MULTI pipelines
      • Add custom json support for references not included as part of the pipeline
    • --rename added for GEX, VDJ, ATAC pipelines
      • Accepts a csv file to have Cell Ranger output a different name from FASTQ file name
      • Only runs the samples that are included in the rename file
  • Edit MULTI summary report to include sheet for FASTQ QC output
  • Add GEX QC Summary report
  • Edits to GEX QC analysis
    • Add silhouette analysis for GEX QC cluster resolutions
    • Add metadata parameter to add sample level metadata to Seurat object
    • Fix error to add back in cut-off line to pre-filter QC plots
  • Edit GEX QC report
    • Add support for silhouette analysis
    • Add explanation text for when adaptive thresholds are used
  • Edit multiconfig to be compatible with Cell Ranger 8.0.0

Breaking changes

Version flag - changed to pipeline flag

With the release of the newest version of Cell Ranger, a new flag was added to make it possible to select the version of Cell Ranger to run. It became clear that continued use of --version for selecting the version of the pipeline to run could lead to confusion about the two flags. As a result, the previously named --version is now is now named --pipeline.

In the future, please use --pipeline to select the version of the pipeline to run and --cellranger to select the version of Cell Ranger to use.

Full Changelog: v.1.1.1...v2.0.0