modules/anndata_convert

Convert an AnnData H5AD file to Seurat and SingleCellExperiment RDS objects

single-cellanndataconversion

https://github.com/nf-core/modules/[...]/modules/nf-core/anndata/convert

Description

Convert an AnnData H5AD file to Seurat and SingleCellExperiment RDS objects

Input

name:type

description

pattern

`meta`
`:map`

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

`h5ad`
`:file`

Anndata object as H5AD file

*.h5ad

Output

name:type

description

pattern

`seurat`

`meta`
`:map`

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

`${prefix}.seurat.rds`
`:file`

Seurat object saved as an RDS file

*.seurat.rds

`sce`

`meta`
`:map`

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

`${prefix}.sce.rds`
`:file`

SingleCellExperiment object saved as an RDS file

*.sce.rds

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Topics

name:type

description

pattern

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

anndata
BSD-3-clause

An annotated data matrix.

anndata.readthedocs.io https://github.com/theislab/anndata 10.21105/joss.04371

modules/anndata_convert

Description

Input

`meta`
`:map`

`h5ad`
`:file`

Output

`seurat`

`meta`
`:map`

`${prefix}.seurat.rds`
`:file`

`sce`

`meta`
`:map`

`${prefix}.sce.rds`
`:file`

`versions`

`versions.yml`
`:file`

Topics

`versions`

`versions.yml`
`:file`

Tools

anndata
BSD-3-clause

maintainer

get in touch

modules/anndata_convert

Description

Input

meta :map

h5ad :file

Output

seurat

meta :map

${prefix}.seurat.rds :file

sce

meta :map

${prefix}.sce.rds :file

versions

versions.yml :file

Topics

versions

versions.yml :file

Tools

anndataBSD-3-clause

maintainer

get in touch

`meta`
`:map`

`h5ad`
`:file`

`seurat`

`meta`
`:map`

`${prefix}.seurat.rds`
`:file`

`sce`

`meta`
`:map`

`${prefix}.sce.rds`
`:file`

`versions`

`versions.yml`
`:file`

`versions`

`versions.yml`
`:file`

anndata
BSD-3-clause