Description

Module to subset AnnData object to cells with matching barcodes from the csv file

Input

name:type
description
pattern

meta{:bash}

:map

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

h5ad{:bash}

:file

Anndata object as H5AD file

*.h5ad

barcodes{:bash}

:file

CSV file containing barcodes. Barcodes are written in plain text. One column, no header

*.csv

Output

name:type
description
pattern

h5ad{:bash}

meta{:bash}

:map

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

*.h5ad

*.h5ad{:bash}

:file

AnnData file containing all cells with barcodes that match those in the input barcodes csv file

*.h5ad

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
scdownstreamscrnaseq
maintainers
Github user nictru
Github user LeonHafner
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