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implement annotation subtyping workflow #23

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Merged
dorien-er merged 9 commits into from
Jul 14, 2026
Merged

implement annotation subtyping workflow #23

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c45ada4
add subtyping workflow
dorien-er Jul 1, 2026
e22eb24
add reference split
dorien-er Jul 1, 2026
437fc84
update tests
dorien-er Jul 2, 2026
af21c62
Merge remote-tracking branch 'origin/main' into subtyping
dorien-er Jul 13, 2026
72e9e25
merge origin/main
dorien-er Jul 13, 2026
3a9465d
Merge remote-tracking branch 'origin/main' into subtyping
dorien-er Jul 13, 2026
b14e9f5
expand test cases
dorien-er Jul 14, 2026
a64bc71
Merge remote-tracking branch 'origin/main' into subtyping
dorien-er Jul 14, 2026
89cc7d1
Update src/single_cell/parallel_subtyping/config.vsh.yaml
dorien-er Jul 14, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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* `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):
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