Files

Build pipeline: test-vsh-ci-build-template-64dfm

Source commit: c94b21ffaf

Source message: update changelog

2025-12-08 15:54:34 +00:00

openpipeline_spatial x.x.x

MINOR CHANGES

Add scope to component and workflow configurations (PR #22).
Bump version of spatialdata-io to 0.3.0 and spatialdata to 0.5.0. Pin version of pyarrow to 18.0.0 for compatibility (PR #24).

convert/from_cosmx_to_h5mu: Fixed an issue where parent directories of the cosmx output bundle were duplicated when reading in data (PR #25).

convert: Updated multiple components to accept spatial output bundles in .zip format (for CosMx, Xenium and Aviti) as input (PR #19, PR #20).
convert/from_cosmx_to_h5mu: Updated component to handle CosMx output bundles generated with AtoMx SIP versions < v1.3.2 (PR #25).
nichecompass/gene_program_mask: Added a component to create a prior knowledge gene program mask for NicheComnpass analysis (PR #27).

filter/subset_cosmx: Added a component to subset COSMX data (PR #3, PR #9).
convert/from_cosmx_to_h5mu: Added converter component for COSMX data (PR #3, PR #9).
mapping/spaceranger_count: Added a spaceranger count component (PR #2).
convert/from_spatialdata_to_h5mu, convert/from_xenium_to_spatialdata, convert/from_xenium_to_h5mu: Added converter components for xenium data (PR #1, #10).
convert/from_xenium_to_spatialexperiment, convert/from_cosmx_to_spatialexperiment: Added converter components for Xenium or CosMx data to SpatialExperiment objects (PR #9).
convert/from_cells2stats_to_h5mu: Added a component to convert data resulting from Aviti Teton sequencers processed by Cells2Stats into an H5MU file (PR #15).
workflows/qc/qc: Added a pipeline for calculating qc metrics of spatial omics samples (PR #5).
workflows/multiomics/spatial_process_samples: Added a pipeline to pre-process multiple spatial omics samples (PR #7).
convert/from_h5mu_to_spatialexperiment: Added converter component for H5MU data to SpatialExperiment objects (PR #15).