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@DriesSchaumont DriesSchaumont released this 15 May 06:20
· 1589 commits to main since this release
0.8.0
f7f65a4

openpipelines 0.8.0

BREAKING CHANGES

  • workflows/full_pipeline: Renamed inconsistencies in argument naming (#372):

    • rna_min_vars_per_cell was renamed to rna_min_genes_per_cell
    • rna_max_vars_per_cell was renamed to rna_max_genes_per_cell
    • prot_min_vars_per_cell was renamed to prot_min_proteins_per_cell
    • prot_max_vars_per_cell was renamed to prot_max_proteins_per_cell

  • velocity/scvelo: bump anndata from <0.8 to 0.9.

NEW FUNCTIONALITY

  • Added an extra label veryhighmem mostly for cellranger_multi with a large number of samples.

  • Added multiomics/prot_multisample pipeline.

  • Added clr functionality to prot_multisample pipeline.

  • Added interpret/lianapy: Enables the use of any combination of ligand-receptor methods and resources, and their consensus.

  • filter/filter_with_scrublet: Add --allow_automatic_threshold_detection_fail: when scrublet fails to detect doublets, the component will now put NA in the output columns.

  • workflows/full_pipeline: Allow not setting the sample ID to the .obs column of the MuData object.

  • workflows/rna_multisample: Add the ID of the sample to the .obs column of the MuData object.

  • correction/cellbender_remove_background: add obsm_latent_gene_encoding parameter to store the latent gene representation.

BUG FIXES

  • transform/clr: fix anndata object instead of matrix being stored as a layer in output MuData, resulting in NoneTypeError object after reading the .layers back in.

  • dataflow/concat and dataflow/merge: fixed a bug where boolean values were cast to their string representation.

  • workflows/full_pipeline: fix running pipeline with -stub.

  • Fixed an issue where passing a remote file URI (for example http:// or s3://) as param_list caused No such file errors.

  • workflows/full_pipeline: Fix incorrectly named filtering arguments (#372).

  • correction/cellbender_remove_background: add obsm_latent_gene_encoding parameter to store the latent gene representation.

MINOR CHANGES

  • integrate/scarches, integrate/scvi and correction/cellbender_remove_background: Update base container to nvcr.io/nvidia/pytorch:22.12-py3

  • integrate/scvi: add gpu label for nextflow platform.

  • integrate/scvi: use cuda enabled jax install.

  • convert/from_cellranger_multi_to_h5mu, dataflow/concat and dataflow/merge: update pandas to 2.0.0

  • dataflow/concat and dataflow/merge: Boolean and integer columns are now represented by the BooleanArray and IntegerArray dtypes in order to allow storing NA values.

  • interpret/lianapy: use the latest development release (commit 11156ddd0139a49dfebdd08ac230f0ebf008b7f8) of lianapy in order to fix compatibility with numpy 1.24.x.

  • filter/filter_with_hvg: Add error when specified input layer cannot be found in input data.

  • workflows/multiomics/full_pipeline: publish the output from sample merging to allow running different integrations.

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