Cell type annotation: scGPT integration/KNN workflow #875
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dorien-er
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DriesSchaumont
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Nov 15, 2024
src/workflows/annotation/scgpt_integration_knn/integration_test.sh
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src/workflows/annotation/scgpt_integration_knn/integration_test.sh
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| "input_var_key": "input_var_gene_names" | ||
| ], | ||
| args: [ | ||
| "output_var_key": "gene_symbols" |
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Question: what happens if this column already exists?
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Adjusted now: by default it will raise, but this behavior can be undone by enabling the --overwrite_existing_key param
| "input_obs_key": "reference_obs_batch_label", | ||
| ], | ||
| args: [ | ||
| "output_obs_key": "batch_label" |
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Question: what happens if this column already exists?
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By default it will raise, to be disabled with newly added flag "--overwrite_existing_key"
address review comments Co-authored-by: Dries Schaumont <[email protected]>
* update description concat component * Update src/dataflow/concatenate_h5mu/config.vsh.yaml Co-authored-by: Dries Schaumont <[email protected]> --------- Co-authored-by: Dries Schaumont <[email protected]>
Co-authored-by: Vladimir Shitov <[email protected]>
Co-authored-by: DriesSchaumont <[email protected]>
* Remove uses of auto: [publish: true] * Undo removal of publish component * Fix integration test
* add component to subset obsp * update changelog * update descriptions * fix tests * add comment
* update knn component * update changelog * update changelog * address pr comments * fix tests * fix tests
* update scanvi * typo * update changelog
#894) * Fix ingestion components not working when optional arguments are unset * update changelog * fix test
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Changelog
src/scgpt/embedding) and workflow (src/workflows/intgration/scgpt_leiden)Issue ticket number and link
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I have performed a self-review of my code
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Proposed changes are described in the CHANGELOG.md
CI tests succeed!