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Fix anndata concatenation #416
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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. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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LGTM
The way the concatenation was previously implemented, the tuple grouping in
H5AD_CONVERSION
grouped the anndata files by the entiremeta
map, which did not result in any actual grouping. Then, the "grouped" anndata object was saved ascombined_<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