cellbender needs raw count matrix as input - Githubissues

nf-core / scdownstream

A single cell transcriptomics pipeline for QC, integration and making the data presentable

https://nf-co.re/scdownstream

MIT License

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cellbender needs raw count matrix as input #53

Closed fbnrst closed 1 day ago

fbnrst commented 3 days ago

Description of the bug

cellbender needs raw count matrix as input, see https://cellbender.readthedocs.io/en/latest/usage/index.html#use-case

However, right now, the h5ad channel is used as input, not raw: https://github.com/nf-core/scdownstream/blob/8d091c5240d42337174768e1ca7fb548e4e2ea03/subworkflows/local/ambient_rna_removal.nf#L21-L22

Command used and terminal output

No response

Relevant files

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System information

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