v3.0.2

What's Changed

• Fix: add check of genome length to user provided genome by @rroutsong in #9
• Fix: add fix to integration
• Fix: handle situation where different integration methods succeed to integration summary report
• Fix: only pull out unique hashtags instead of all detected hashtags in cite QC

Full Changelog: v3.0.1...v3.0.2

v3.0.1

What's Changed

• feat: include resolution 0.1 in clustering and umaps by @rroutsong in #7

New Contributors

• @rroutsong made their first contribution in #7

Full Changelog: v3.0.0...v3.0.1

v3.0.0

What's Changed

• Version 3 Update by @chenv3 in #6
  • Added --forcecells flag which can be applied to the following pipelines
    • GEX
    • CITE
    • MULTI
    • ATAC
  • Added support for additional version to --cellranger flag for GEX, CITE, VDJ, and MULTi pielines
    • Also handles version 9.0.0
  • Added support for running pipeline on Cell Ranger output
  • Changed cellranger calls so optional flags are on the same line as the last required flag
  • Edits to GEX pipeline
    • Changed to running Seurat v5 using R4.4.0
    • Set an upper limit of 100 for mitochondrial filter threshold
    • Added in Seurat integration for normalization and SCTransform. Runs if more than one sample is processed
      • CCA
      • Joint PCA
      • RPCA
      • Harmony
    • Create a summary integration report
  • Edits to CITE pipeline
    • Add basic Seurat QC analysis
      • If hashtags are run with the name starting with “HTO-” or “HTO_‘, will try to run hashtag demultiplexing

Full Changelog: v2.0.1...v3.0.0

v2.0.1

What's Changed

• Editing rules to decrease the chance of accidental overwrite or deletion of existing runs
• GEX edit R rules to unset user R libs paths
• GEX put silhouette analysis within try to avoid QC failure if errors

Full Changelog: v2.0.0...v2.0.1

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

v.1.1.1

What's Changed

• Increase resources provided to cluster for rule aggregate
• Edit create_library_files script to better handle multiple paths matching due to overlapping sample names

Full Changelog: v1.1.0...v.1.1.1

v1.1.0

What's Changed

• Dev - GEX QC and Aggregate, BAM, and Clean-Up by @chenv3 in #2
  • GEX Initial QC with Seurat
  • GEX Initial QC Sample Report
  • Turn off automatic BAM creation
    • Add create-bam flag that can be used to create BAM file
    • Applies to:
      • GEX
      • CITE
      • MULTI
  • Add GEX aggregate flag
    • Choose between mapped and none for read depth normalization
  • Automatic clean-up of intermediate Cell Ranger folder for all pipelines
  • Edit summary report script to not check for intermediate folder and to keep 10x column header order for additional columns

Full Changelog: v1.0.0...v1.1.0

v1.0.0

What's Changed

• Establishment of Basic Pipeline by @chenv3 in #1
  • Cell Ranger analysis for different 10x technologies available via different options with version flag
    • GEX
    • VDJ
    • CITE-Seq
    • Multi
    • ATAC
    • Multiome
  • Creates summary excel file and copies of Cell Ranger web report in final report folder
  • Required flags are input, output, version, and genome
    • Genome currently only supports hg38 and mm10
• Patch to add json module by @skchronicles

Full Changelog: https://github.com/OpenOmics/cell-seek/commits/v1.0.0