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Build branch fix-integration-tests with version fix-integration-tests (da62b4ff)

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Build pipeline: vsh-ci-dev-gckj5

Source commit: da62b4ffe3

Source message: Add labels to qc_test component
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2024-11-15 14:37:33 +00:00
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# openpipelines x.x.x
# openpipelines 2.x.x (Unreleased)
## BREAKING CHANGES
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- Store label probabilities instead of uncertainties
- Take `.h5mu` format as an input instead of `.h5ad`
* `labels_transfer/knn`: delete outdated component due to its functionality now implemented in `labels_transfer/pynndescent_knn`
* `reference/build_cellranger_arc_reference`: a default value of "output" is now specified for the argument `--genome`, inline with `reference/build_cellranger_reference` component. Additionally, providing a value for `--organism` is no longer required and its default value of `Homo Sapiens` has been removed (PR #864).
## NEW FUNCTIONALITY
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* `dataflow/split_h5mu` component: Added a component to split a single h5mu file into multiple h5mu files based on the values of an .obs column (PR #824).
* `labels_transfer/pynndescent_knn`: component: Added a component for KNN classification based on a PyNNDescent neighborhood graph (PR #830).
* `workflows/test_workflows/ingestion` components & `workflows/ingestion`: Added standalone components for integration testing of ingestion workflows (PR #801).
* `workflows/ingestion/make_reference`: Add additional arguments passed through to the STAR and BD Rhapsody reference components (PR #846).
@@ -103,7 +99,7 @@
* `dimred/densmap` component: Added a densMAP dimensionality reduction component (PR #748).
* `annotete/scanvi` component: Added a component to annotate cells using scANVI (PR #833).
* `annotate/scanvi` component: Added a component to annotate cells using scANVI (PR #833).
* `transform/bpcells_regress_out` component: Added a component to regress out effects of confounding variables in the count matrix using BPCells (PR #863).
@@ -129,6 +125,10 @@
* `metadata/duplicate_var` component: Added a component to make a copy from one .var field or index to another .var field within the same MuData object (PR #877).
* `filter/subset_obsp` component: Added a component to subset an .obsp matrix by column based on the value of an .obs field. The resulting subset is moved to an .obsm field (PR #888).
* `labels_transfer/knn` component: Enable using additional distance functions for KNN classification (PR #830) and allow to perform KNN classification based on a pre-calculated neighborhood graph (PR #890).
## MINOR CHANGES
* `resources_test_scripts/cellranger_atac_tiny_bcl.sh` script: generate counts from fastq files using CellRanger atac count (PR #726).
@@ -142,8 +142,6 @@
* Bump scvelo to `0.3.2` (PR #828).
* Bump viash to `0.8.6` (PR #815).
* Pin numpy<2 for several components (PR #815).
* Added `resources_test_scripts/cellranger_atac_tiny_bcl.sh` script: download tiny bcl file with an ATAC experiment, download a motifs file, demultiplex bcl files to reads in fastq format (PR #726).
@@ -162,23 +160,38 @@
## BUG FIXES
* `dataflow/concatenate_h5mu`: fix writing out multidimensional annotation dataframes (e.g. `.varm`) that had their
data dtype (dtype) changed as a result of adding more observations after concatenation, causing `TypeError`.
One notable example of this happening is when one of the samples does not have a multimodal annotation dataframe
which is present in another sample; causing the values being filled with `NA` (PR #837).
* `qc/calculate_qc_metrics`: increase total counts accuracy with low precision floating dtypes as input layer (PR #852).
* Fix failing tests for `ingestion/cellranger_postprocessing`, `ingestion/conversion` and `multiomics/process_batches` (PR #869).
* `convert/from_10xh5_to_h5mu`: add .uns slot to mdata root when metrics file is provided (PR #887).
* Use `params.resources_test` in test workflows in order to point to an alternative location (e.g. a cache).
* Fix ingestion components not working when optional arguments are unset (PR #894).
## DOCUMENTATION
* Update authorship of components (PR #835).
# openpipelines 1.0.3
## BUG FIXES
* `qc/calculate_qc_metrics`: increase total counts accuracy with low precision floating dtypes as input layer (PR # , backported from PR #852).
# openpipelines 1.0.2
## BUG FIXES
* `dataflow/concatenate_h5mu`: fix writing out multidimensional annotation dataframes (e.g. `.varm`) that had their
data dtype (dtype) changed as a result of adding more observations after concatenation, causing `TypeError`.
One notable example of this happening is when one of the samples does not have a multimodal annotation dataframe
which is present in another sample; causing the values being filled with `NA` (PR #842, backported from PR #837).
# openpipelines 1.0.1
## BUG FIXES
* Bump viash to `0.8.6` (PR #816, backported from #815). This changes the at-runtime generated nextflow process from an in-memory to an on-disk temporary file, which should cause less issues with Nextflow Fusion.
# openpipelines 1.0.0-rc6
## BUG FIXES