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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).

  • workflows/single_cell/process_integrate_annotate: Expose the consensus voting step from parallel_annotation via --run_consensus (default is true) (PR #21).

  • workflows/single_cell/process_integrate_annotate: Perform integration and annotation with multiple methods in parallel rather than sequentially using the workflows/single_cell/parallel_annotation and workflows/single_cell/parallel_integration workflows (PR #21).

  • workflows/single_cell/parallel_subtyping: Add a workflow that subtypes each major cell type independently via reference-based label projection, splitting the reference by matching major cell type (--reference_obs_major_cell_type) so each type is subtyped against its own reference cells. Query cell types absent from the reference raise an error by default, or are passed through unannotated when --allow_missing_reference_cell_type is set. The subtype labels are combined into a single output h5mu (PR #23).

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

MAJOR CHANGES

  • workflows/single_cell/process_integrate_annotate: Replace the inlined integration and annotation steps with the single_cell/parallel_integration and single_cell/parallel_annotation sub-workflows, so the selected methods run in parallel. This exposes the full set of methods: integration now also supports scanorama and bbknn, and annotation now also supports harmony_knn, scvi_knn and singler. The trained scVI and scANVI/scArches models are now emitted as optional outputs (--output_scvi_model, --output_scanvi_model).

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.