Viash Hub

Description

Converts an h5ad file or a single modality of an h5mu file into a Seurat file.

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5ad or h5mu file
--modality	string	Modality to be converted if the input file is an h5mu file.
--assay	string	Name of the assay to be created.
--output -o	file required output	Output Seurat file

Name

Type & Properties

--input

-i

file

required

--modality

string

--assay

string

--output

-o

file

required

output

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
assay: [ "RNA" ]  
output: "$id.$key.output.rds"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.0 \  
  -main-script target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf \  
  -params-file params.yaml

Relationships

Used by

0 relationships

No components use this component.

Current component

convert/from_h5mu_or_h5ad_to_seuratopenpipeline v3.0.0

Uses

0 relationships

No component dependencies found.