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@cakirb cakirb released this 27 Feb 09:45
· 145 commits to main since this release
v0.2
2c98cb3
  • Improvements in python scripts
    • Changed output filenames in all scripts
    • gather_matrices.py
      • added support for Cellbender v3 outputs
    • qc.py
      • moved sampleID annotation step from pool_all.py
    • pool_all.py
      • added support for resume functionality of nextflow
      • removed sampleID annotation step (moved to qc.py)
    • add_scrublet_meta.py
      • added an extra step to remove empty columns in input metadata
    • integration.py
      • added support to specify batch key and categorical covariate keys (default: sampleID for batch key, empty for covariates)
  • Improvements in main.py
    • fixed output generation problem
    • modified find_doublets process so it only runs for good QC samples
    • added batch_key parameter to specify the column from cell metadata for scVI integration (default: sampleID)
    • added covar_keys parameter to specify the columns from cell metadata for scVI integration (no default)
  • Updated workflow figure in README.md

Full Changelog: v0.1...v0.2

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