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Support matrix.mtx.gz cellbender remove-background input#11565

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alecw:alecw_cellbender_matrix_mtx
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Support matrix.mtx.gz cellbender remove-background input#11565
alecw wants to merge 1 commit intonf-core:masterfrom
alecw:alecw_cellbender_matrix_mtx

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@alecw alecw commented May 7, 2026

cellbender remove-background can use as input the file triplet matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz. This change enables this input format via:

  • passing the 3 files in the h5ad input parameter;
  • and setting task.ext.input = '.', which tells remove-background to look for the 3 files in the working directory.

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cellbender remove-background can use as input the file triplet matrix.mtx.gz,
barcodes.tsv.gz, features.tsv.gz.  This change enables this input format via:
- passing the 3 files in the h5ad input parameter;
- and setting task.ext.input = '.', which tells remove-background to look for the
  3 files in the working directory.
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