OpenOmics/cell-seek

What's Changed

• Version 2 Update by @chenv3 in https://github.com/OpenOmics/cell-seek/pull/5
  • Flag updates
    • Version flag - changed to pipeline flag
    • Cellranger flag - 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 flag - 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 flag 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 the version flag for selecting the version of the pipeline to run could lead to confusion about the two flags. As a result, the previously named version flag 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: https://github.com/OpenOmics/cell-seek/compare/v.1.1.1...v2.0.0