convert/from_h5mu_to_spatialexperiment

Description

Converts an h5mu file into a SpatialExperiment object.

Type

r_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.2.0 \  
  -main-script target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--modality	string required	Name of the modality to be converted.
--obsm_spatial_coordinates	string	Key in the .obsm field that contains the spatial coordinates. Will be mapped to spatialCoords in the SpatialExperiment object.
--output -o	file required output	Output SpatialExperiment file

Name

Type & Properties

--input

-i

file

required

--modality

string

required

--obsm_spatial_coordinates

string

--output

-o

file

required

output