modules/cellbender_merge

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

single-cellscRNA-seqambient RNA removal

https://github.com/nf-core/modules/[...]/modules/nf-core/cellbender/merge

Description

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

Input

name:type

description

pattern

`meta`
`:map`

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

`filtered`
`:file`

AnnData file containing filtered data (without empty droplets)

*.h5ad

`unfiltered`
`:file`

AnnData file containing unfiltered data (with empty droplets)

*.h5ad

`cellbender_h5`
`:file`

CellBender h5 file containing ambient RNA estimates

*.h5

Output

name:type

description

pattern

`h5ad`

`meta`
`:file`

AnnData file containing decontaminated counts as adata.X

*.h5ad

`${prefix}.h5ad`
`:file`

AnnData file containing decontaminated counts as adata.X

*.h5ad

`versions`

`versions.yml`
`: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

modules/cellbender_merge

Description

Input

`meta`
`:map`

`filtered`
`:file`

`unfiltered`
`:file`

`cellbender_h5`
`:file`

Output

`h5ad`

`meta`
`:file`

`${prefix}.h5ad`
`:file`

`versions`

`versions.yml`
`:file`

Tools

cellbender
BSD-3-Clause

included in

maintainer

get in touch

modules/cellbender_merge

Description

Input

meta:map

filtered:file

unfiltered:file

cellbender_h5:file

Output

h5ad

meta:file

${prefix}.h5ad:file

versions

versions.yml:file

Tools

cellbender BSD-3-Clause

included in

maintainer

get in touch

`meta`
`:map`

`filtered`
`:file`

`unfiltered`
`:file`

`cellbender_h5`
`:file`

`h5ad`

`meta`
`:file`

`${prefix}.h5ad`
`:file`

`versions`

`versions.yml`
`:file`

cellbender
BSD-3-Clause