v0.5.0

• New workflow: only_qc
  • It is now easier to run the pipeline until the pooling step.
  • This can be used to process different sets of samples in different times, then all the outputs from this workflow can be used together with after_qc mode.
• Improvements and changes in scripts:
  • It is now possible to run the pipeline without Cellbender output, STARsolo output is used only in this case.
  • Removing metadata columns in integration.py was reverted back
  • New RESUME scripts have been added
  • after_qc workflow can now use the samples in the sample list only rather than all the objects in the folder.
  • Reports folder is now named similar to the results folder.
  • Outputting plots in run_qc step now works as expected.
• Updates in README
  • The workflow diagram has been recreated.
  • The workflow modes have been described with a new figure.
  • Outputs from each step have been described in detail.
  • Text in some steps were revised.

v0.4.0

• Added support for single-nuc samples
• Improvements in scripts
  • integration.py now removes the columns which were created in previous steps
  • RESUME scripts have been reorganised

Full Changelog: v0.3.0...v0.4.0

v0.3.0

• New workflow: after_qc
  • It is now easier to work with the samples which has been processed with scAutoQC pipeline before.
• Improvements in nextflow pipeline and python scripts
  • Created new RESUME script for afterqc workflow.
  • integration.py should now work more efficiently.
  • ss_matrix and covar_keys parameters have been removed (they will be considered for the future releases).

Full Changelog: v0.3.0...v0.2.2

v0.2.2

• Bug fixes

v0.2.1

• Fix typos in README and qc.py

v0.2.0

• 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

v0.1.0

First version