convert/from_h5mu_to_seurat

Description

Converts an h5mu file into a Seurat file.

Restrictions:

Only the intersection of cells is currently loaded into the Seurat object due to the object structure limitation.
Multimodal embeddings (global .obsm slot) are loaded with the assay.used field set to the default assay.
Embeddings names are changed in order to comply with R & Seurat requirements and conventions.
Feature names with underscores ('_') are automatically replaced with dashes ('-')
Seurat does not support global variables metadata /var.

Type

r_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.rds"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.2 \  
  -main-script target/nextflow/convert/from_h5mu_to_seurat/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--output -o	file required output	Output Seurat file

Name

Type & Properties

--input

-i

file

required

--output

-o

file

required

output