convert/from_h5mu_to_spatialdata

Description

Reads in an H5MU file and saves it as a SpatialData Zarr store. The selected
modality in the MuData is stored as the main table in the SpatialData object.
If a matching existing SpatialData is provided, it will be used to fill the
remaining SpatialData slots.

Type

python_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.zarr"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/convert/from_h5mu_to_spatialdata/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input H5MU file.
--input_spatialdata	file	An optional existing SpatialData Zarr store to fill remaining slots from.
--modality	string	The modality in the MuData to be used as the main table in the SpatialData object.
--output -o	file required output	The path to the output SpatialData Zarr store.

Name

Type & Properties

--input

-i

file

required

--input_spatialdata

file

--modality

string

--output

-o

file

required

output