modules/scimap_mcmicro

SCIMAP is a suite of tools that enables spatial single-cell analyses

sortspatialsingle cell

https://github.com/nf-core/modules/[...]/modules/nf-core/scimap/mcmicro

Description

SCIMAP is a suite of tools that enables spatial single-cell analyses

Input

name:type

description

pattern

`meta`
`:map`

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

`cellbyfeature`
`:file`

CSV file with cell by feature table

*.{csv}

Output

name:type

description

pattern

`csv`

`meta`
`:map`

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

`*.csv`
`:file`

Sorted CSV file

*.{csv}

`h5ad`

`meta`
`:map`

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

`*.h5ad`
`:file`

Sorted H5AD file

*.{h5ad}

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

scimap
MIT License

Scimap is a scalable toolkit for analyzing spatial molecular data.

scimap.xyz scimap.xyz/All%20Functions/A.%20Pre%20Processing/sm.pp.mcmicro_to_scimap https://github.com/labsyspharm/scimap

modules/scimap_mcmicro

Description

Input

`meta`
`:map`

`cellbyfeature`
`:file`

Output

`csv`

`meta`
`:map`

`*.csv`
`:file`

`h5ad`

`meta`
`:map`

`*.h5ad`
`:file`

`versions`

`versions.yml`
`:file`

Tools

scimap
MIT License

included in

maintainer

get in touch

modules/scimap_mcmicro

Description

Input

meta:map

cellbyfeature:file

Output

csv

meta:map

*.csv:file

h5ad

meta:map

*.h5ad:file

versions

versions.yml:file

Tools

scimap MIT License

included in

maintainer

get in touch

`meta`
`:map`

`cellbyfeature`
`:file`

`csv`

`meta`
`:map`

`*.csv`
`:file`

`h5ad`

`meta`
`:map`

`*.h5ad`
`:file`

`versions`

`versions.yml`
`:file`

scimap
MIT License