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haniffalab / webatlas-pipeline

A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
MIT License
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Feat/multimodal #125

Closed dannda closed 11 months ago

dannda commented 1 year ago

Adds option in a multimodal yaml config file to define args for concatenating a matrix from cell2location. This enables defining a sample to use from the cell2location output file when it contains multiple samples, as well as a different prediction matrix. Also ensures observations from the AnnData object and cell2location match in order so concatenation is correct.

codecov-commenter commented 1 year ago

Codecov Report

Attention: 34 lines in your changes are missing coverage. Please review.

Comparison is base (f9e544a) 29.54% compared to head (5de458e) 28.78%. Report is 8 commits behind head on dev.

Files Patch % Lines
bin/integrate_anndata.py 0.00% 33 Missing :warning:
bin/process_h5ad.py 66.66% 1 Missing :warning:

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #125 +/- ## ========================================== - Coverage 29.54% 28.78% -0.76% ========================================== Files 16 16 Lines 914 945 +31 ========================================== + Hits 270 272 +2 - Misses 644 673 +29 ```

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