Module to use CellBender to remove ambient RNA from single-cell RNA-seq data
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
filtered
:file
AnnData file containing filtered data (without empty droplets)
*.h5ad
unfiltered
AnnData file containing unfiltered data (with empty droplets)
cellbender_h5
CellBender h5 file containing ambient RNA estimates
*.h5
output_layer_name
:string
The name of the layer to store counts
h5ad
AnnData file containing decontaminated counts as adata.X
adata.X
${prefix}.h5ad
versions_cellbender
versions.yml
File containing software version
versions
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
