https://github.com/cellgeni/nf-scautoqc - 25-101

This release includes important bug fixes and enhancements to ensure smoother pipeline execution:

• qc.py adjustments: Now correctly applies QC metrics based on the presence of spliced/unspliced layers.
• Robust metadata handling: The add_metadata step no longer fails when metadata input is absent.
• Improved resumability: The addmetadatabasic process now fully supports resume functionality for interrupted runs.

- Python
Published by cakirb about 1 year ago

https://github.com/cellgeni/nf-scautoqc - 25-091

This update introduces a new workflow and multiple enhancements based on user feedback:

• Added a new workflow:
  • subset workflow: Enables running the pipeline by subsetting objects using predefined cutoffs instead of the automatic QC workflow (steps 2a-3-4-5a). More details are available in the README.
• Added support for Cell Ranger outputs in addition to STARsolo.
• Improvements in nextflow pipeline:
  • Updated the Singularity image for better compatibility.
  • Renamed certain output files for clarity.
  • Optimised the RESUME functionality to improve reliability.
  • Introduced smart memory allocation for the pool_all and add_metadata steps based on input size.
  • Optimised resource allocation for other processes.
  • Enabled the pipeline to work seamlessly with symbolic links in the input.
• Optimisations in scripts:
  • Removed unused lines, characters, and packages for cleaner code.
  • Fixed hardcoded paths to improve flexibility.
  • Optimised memory usage in the pool_all process.

Full Changelog: https://github.com/cellgeni/nf-scautoqc/compare/v0.5.0...v0.6.0

- Python
Published by cakirb about 1 year ago

https://github.com/cellgeni/nf-scautoqc - 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.

- Python
Published by cakirb about 2 years ago

https://github.com/cellgeni/nf-scautoqc - 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: https://github.com/cellgeni/nf-scautoqc/compare/v0.3.0...v0.4.0

- Python
Published by cakirb about 2 years ago

https://github.com/cellgeni/nf-scautoqc - 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.
  • ssmatrix and covarkeys parameters have been removed (they will be considered for the future releases).

Full Changelog: https://github.com/cellgeni/nf-scautoqc/compare/v0.3.0...v0.2.2

- Python
Published by cakirb over 2 years ago

https://github.com/cellgeni/nf-scautoqc - v0.2.2

• Bug fixes

- Python
Published by cakirb over 2 years ago

https://github.com/cellgeni/nf-scautoqc -

• Fix typos in README and qc.py

- Python
Published by cakirb over 2 years ago

https://github.com/cellgeni/nf-scautoqc - 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)
  • addscrubletmeta.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: https://github.com/cellgeni/nf-scautoqc/compare/v0.1...v0.2

- Python
Published by cakirb over 2 years ago

https://github.com/cellgeni/nf-scautoqc - v0.1.0

First version

- Python
Published by cakirb over 2 years ago