cellbender output saved in additional layer

[magochab]

Cellbender output (new count matrix) is save as a new layer named 'cellbender_corrected', and the default layer X is not changed. To use the corrected data user need to manually change value in layer X.
Will be possibility to add option, that user can specify where cellbender output is saved?

[DriesSchaumont]

As a reference for when we will be adressing this issue:

openpipeline/src/workflows/ingestion/cellranger_postprocessing/main.nf

Line 48 in 27e74d9

state + [input: output.output, layer: "cellbender_corrected"]

[DriesSchaumont]

Just a note: this has become less of a problem because we now support the rna_layer argument in the process_samples pipeline.