Release notes for OpenScPCA-nf

This document contains release notes for versioned releases of the OpenScPCA-nf workflow.

v0.1.2

Update scpcaTools images to v0.4.1 versions
Update simulations to match current (v0.8.5) scpca-nf output
- Change reduced dimension names in AnnData output (to X_pca and X_umap) and updated formatting to match scpca-nf v0.8.5
- Use new age columns
- Metadata for simulated data now includes project-specific fields
Centralized docker image definitions in config/containers.config
Added initial documentation about porting modules

Initial versioned release of the OpenScPCA-nf Nextflow workflow
Current modules:
- example: a very small test module for testing configuration parameters
- simulate_sce: creates simulated and permuted data for testing here and in OpenScPCA-analysis
- merge_sce: merges multiple datasets into a single SCE object and corresponding AnnData objects
- doublet_detection: runs scDblFinder to detect doublets in a dataset
The default workflow entrypoint currently runs the merge_sce and doublet_detection modules. Other workflow entrypoints are:
- test to run the example module
- simulate to run the simulate_sce module
Includes scripts for running the workflow on AWS batch through Code Deploy