Changelog

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.

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

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).

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

Provide feedback