Description

Module to use CellBender to remove ambient RNA from single-cell RNA-seq data

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

filtered{:bash}

:file

AnnData file containing filtered data (without empty droplets)

*.h5ad

unfiltered{:bash}

:file

AnnData file containing unfiltered data (with empty droplets)

*.h5ad

cellbender_h5{:bash}

:file

CellBender h5 file containing ambient RNA estimates

*.h5

Output

name:type
description
pattern

h5ad{:bash}

meta{:bash}

:file

AnnData file containing decontaminated counts as adata.X

*.h5ad

${prefix}.h5ad{:bash}

:file

AnnData file containing decontaminated counts as adata.X

*.h5ad

versions{:bash}

versions.yml{:bash}

:file

File containing software version

versions.yml

Tools

cellbender
BSD-3-Clause

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

cellbender.readthedocs.io/en/latest https://github.com/broadinstitute/CellBender
included in
scdownstream
maintainer
Github user nictru
get in touch
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