Release openpipelines.bio v3.0.0 · openpipelines-bio/openpipeline

BREAKING CHANGES

transfer/publish: remove component after deprecating it in 2.1.0 (PR #1019).
Removed split_h5mu_train_test component (PR #1020).
tar_extract has been deprecated and will be removed in openpipeline 4.0 (PR #1014). Use vsh://toolbox/bgzip instead.
compress_h5mu: rename compression argument to output_compression (PR #1017, PR #1018).
delimit_fraction: remove unused layer argument (PR #1018).
download_file has been deprecated and will be removed in openpipeline 3.0 (PR #1015).
scarches: Loading of legacy models no longer asumes the model to based on SCANVI. An argument (reference_class) was added which need to be set in this case (PR #1035).
convert/from_h5mu_to_seurat has been deprecated and will be removed in openpipeline 4.0. Use convert/from_h5mu_or_h5ad_to_seurat instead (PR #1046).

liana: enabled jobs to be run in parallel and added two new arguments: consensus_opts, de_method (PR #1039)
from_h5mu_or_h5ad_to_seurat: converts an h5ad file or a single modality from an h5mu file to a seurat object (PR #1046).

Warning: These experimental features are subject to change in future releases.

Added from_h5mu_or_h5ad_to_tiledb component (PR #1034).
Added differential_expression/create_pseudobulk: Generation of pseudobulk samples from single-cell transcriptomics data,
to create bulk-like expression profiles suitable for differential expression analysis with methods designed for bulk differential expression analysis (PR #1042).
Added annotate/singler: Cell type annotation using SingleR (PR #1051).
Added tiledb/move_mudata_obsm_to_tiledb (PR #1065).

mapping/cellranger_*: Upgrade CellRanger to v9.0 (PR #992 and #1006).
leiden: bump base container to 3.13 (PR #1030).
scanvi, scarches, scvi and totalvi: bump scvi-tools to 1.3.1 and base image to nvcr.io/nvidia/pytorch:25.05-py3 (PR #1035).
lianapy: update liana to 1.5.0 (PR #1039)

velocyto: pin base container to python:3.10-slim-bookworm (PR #1063).
mapping/cellranger_multi: The output from Cell Ranger is now displayed as Cell Ranger is running (PR #1045).
Remove workflows directory (PR #993). The workflows which were at one point in this directory were all deprecated and moved to src/workflows.
Move output file compression argument for AnnData and MuData files to a base config file (src/base/h5_compression_argument.yaml) (PR #1017).
Add missing descriptions to components and arguments (PR #1018).
Add scope to component and workflow configurations (see https://viash.io/reference/config/scope.html) (PR #1013 and #1032).
workflows/multiomics/process_samples: Add optional --skip_scrublet_doublet_detection flag to bypass Scrublet doublet detection. Scrublet doublet detection runs by default and can now be optionally disabled (PR #1049).
Nextflow runner: use resourceLimits directive in the labels config to set a global limit on the memory (PR #1060).

cellranger_multi: Fix error when running Cell Ranger without any computational resources specified (PR #1056)
Bump viash to 0.9.4. This adds support for nextflow versions starting major version 25.01 and fixes an issue where an integer being passed to a argument with type: double resulted in an error (PR #1016).
Fix running neigbors_leiden_umap workflow with -stub enabled (PR #1026).
Add missing CUDA enabled jaxlib to components that use scvi-tools (scanvi, scarches, scvi and totalvi) (PR #1028)
leiden: fix issue where the logging system was shut down prematurely after the calculations were done (PR #1030)
Added missing gpu label to scarches component (PR #1027).
conversion/from_cellranger_multi_to_h5mu: fix conversion to MuData for experiments that combine probe barcodes with other feature barcodes (e.g. Antibody Capture and CIRSPR Guide Capture) (PR #1062).