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Fix anndata concatenation #416

Merged
merged 12 commits into from
Jan 15, 2025
Merged

Fix anndata concatenation #416

merged 12 commits into from
Jan 15, 2025

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nictru
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@nictru nictru commented Jan 11, 2025

The way the concatenation was previously implemented, the tuple grouping in H5AD_CONVERSION grouped the anndata files by the entire meta map, which did not result in any actual grouping. Then, the "grouped" anndata object was saved as combined_<raw/filtered>.h5ad, which gives the impression that it should contain the raw/filtered data for all samples. In fact it always contained only one sample.

This PR fixes this behaviour and introduces the shared empty droplet calling subworkflow with scdownstream

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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LGTM

@nictru nictru merged commit 582c8a7 into nf-core:dev Jan 15, 2025
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@nictru nictru deleted the anndata-concatenation branch January 15, 2025 08:53
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3 participants