yascp - YASCP v2.0 — Flexible Inputs, Multi-modal Tweaks & Smarter Caching

Highlights

Way fewer reruns thanks to a fixed CellBender cache bug.

ATAC/PiP-seq friendlier execution: skip RNA-only steps automatically.

Derive CellSNP panel directly from BAM (works great for ATAC & Illumina PiP-seq).

Flexible inputs (opt-in): point YASCP at your MTX/BAM when you don’t have a ready .h5ad.

Regexable UMAP export for tidier screenshot/figure harvesting.

All Nextflow modules moved to local/ for stability and reproducibility.

Results tree cleaned up (consistent, greppable, and safe to rsync/archive).

- Python
Published by maxozo 7 months ago

yascp - YASCP v1.7 – Stable Release used for Cardinal Freezes

Highlights

This version was used for the majority of analyses in the Cardinal Freeze dataset. It represents a stable release for modular workflows across doublet detection, cell typing, clustering, and ambient RNA removal.

Added

• Support for running doublet detection on any AnnData (.h5ad) object, regardless of origin or upstream pipeline.
• Logging and memory optimizations added for large h5ad files.

Fixed

• Improved memory handling in the doublet module to better support large-scale inputs.
• Minor logging enhancements and CLI consistency improvements.

Dependencies

• Nextflow 22.04.4
• Singularity 3.11.4
• iRODS 4.2.7
• BCFtools 1.0
• Baton

Deprecated

• N/A

Note: This version was heavily used for production runs and tested extensively in HPC environments.

- Python
Published by maxozo 10 months ago

yascp - YASCP v1.9 – Unified Container & Simplified Inputs

Highlights

This release introduces major improvements in reproducibility, input consistency, and configuration hygiene.

Added

• Unified use of a single container across all modules with consistent software versions.
• The container is built independently of any paid Conda channels.
• Cleaned and annotated all config files.
• Standardized input format: all modules (e.g., doublet detection, celltype assignment) now expect .h5ad inputs only.
• Celltype assignment moved to the beginning of the pipeline for better modular reusability.

Fixed

• Removed inconsistency in input expectations across modules (.mtx vs .h5ad).
• Corrected result folder structure issues for partial pipeline runs.

Dependencies

• Nextflow 24.10.4
• Singularity 3.11.4
• Removed dependency on Conda-managed environments.

Deprecated

• .mtx input format is no longer supported in --doublets and --celltypes modules.

- Python
Published by maxozo 10 months ago

yascp - First YASCP release

This release is used to process Cardinal samples.

- Python
Published by maxozo over 2 years ago