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openpipeline_composed x.x.x

NEW FUNCTIONALITY

  • workflows/single_cell/parallel_annotation: Add consensus voting based on per-method weighted probabilities via --run_consensus flag (default is true) (PR #22).

MINOR CHANGES

  • Migration of test resources to the package-specific s3://openpipelines-bio/openpipeline_composed/resources_test bucket (PR #24):

    • Add .info.test_resources to _viash.yaml to specify where test resources need to be synced from.
    • Test resources were regenerated via the scripts in resources_test_scripts/.

  • Bump openpipeline dependency version to v4.2.0 (PR #25).

openpipeline_composed 0.2.1

MINOR CHANGES

  • Bump openpipeline dependency version to v4.1.1 (PR #20).

openpipeline_composed 0.2.0

MAJOR CHANGES

  • Bump openpipeline dependency version to v4.1.0 and openpipeline_qc to v0.3.0, relevant updates include major changes to memory consumption and runtimes for and support for MuData encoded in Zarr format for calculate_qc_metrics, as well as updated defaults for annotation workflows (PR #17, PR #19).

NEW FUNCTIONALITY

  • workflows/single_cell/parallel_integration: Add a workflow that runs multiple integration methods (harmony, scvi, scanorama, bbknn) in parallel on a preprocessed h5mu and merges each method's annotations into a single output (PR #15).

  • workflows/single_cell/parallel_annotation: Add a workflow that runs multiple annotation methods (celltypist, harmony_knn, scanvi_scarches, scvi_knn, singler) in parallel on a preprocessed query h5mu and merges each method's predictions into a single output (PR #16, PR #19).

  • dataflow/move_anndata_slots: Add a component that moves selected slots (.obs, .var, .obsm, .varm, .obsp, .varp, .uns) from a modality in a source MuData file into a modality in a target MuData file (PR #15).

MINOR CHANGES

  • workflows/single_cell/process_integrate_annotate: Set scope to private (PR #6).

  • Bump openpipeline dependency version to v4.0.4 (PR #9).

  • Bump viash version to 0.9.7 (PR #10).

openpipeline_composed 0.1.1

MINOR CHANGES

  • Add a README (PR #4).

openpipeline_composed 0.1.0

Initial release containing a single-cell meta-workflow to process single cell omics samples, perform batch integration and/or label projection.