task_batch_integration 2.0.0

A major update to the OpenProblems framework, switching from a Python-based framework to a Viash + Nextflow-based framework. This update features the same concepts as the previous version, but with a new implementation that is more flexible, scalable, and maintainable.

Migration

• Three subtasks (feature, embedding, graph) have been merged into one.

• Added expected input/output interfaces in src/api and document them in README.md.

• Store common resources used across tasks in a git submodule common.

• Methods, metrics, workflows and other components are implemented as Viash components with a per-component Docker image.

New functionality

• Switched to larger datasets derived from CELLxGENE.

• Added SCimilarity (PR #3).

• Added Geneformer (PR #6).

• Added UCE method (PR #7).

• Added scGPT zero shot (PR #8, #16).

• Added scPRINT (PR #13).

• Added scGPT fine-tuned (PR #17).

Major changes

• Prefilter batches in HVG overlap metric (PR #9).

• Precompute clustering for some metrics (PR #18).

Minor changes

• Add arguments for filtering methods in benchmarking workflow (PR #4).

• Update compute environment (PR #5).

• Adjust resources (PR #10).

• Update dependency components (PR #10).

• Update API formats (PR #21, #28, #31).

• Add support for zebrafish and C. elegans (PR #22).

• Bump scIB to v1.1.7 (PR #30).

• Update common submodule (PR #29).

Bug fixes

• Multiple fixes prior to release (PR #24, #25, #26, #27, #32, #34, #36, #37, #39, #41, #42, #43, #44).

Documentation

• Update documentation (PR #45).