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.
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. |
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 v0.7.0 \
-main-script target/nextflow/convert/from_h5mu_to_spatialdata/main.nf \
-params-file params.yaml Relationships
Used by
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Current component
convert/from_h5mu_to_spatialdataopenpipeline_spatial v0.7.0
Uses
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