convert/from_xenium_to_spatialexperiment
Description
Creates a SpatialExperiment object from the downloaded unzipped Xenium Output Bundle directory
for 10x Genomics Xenium spatial gene expression data, and saves it as a SpatialExperiment object.
The constructor assumes the downloaded unzipped Xenium Output Bundle has the following structure:
Mandatory files
· | — cell_feature_matrix.h5
· | — cells.parquet
Optional files, by default added to the metadata() as a list of paths (will be converted to parquet):
· | — transcripts.parquet
· | — cell_boundaries.parquet
· | — nucleus_boundaries.parquet
· | — experiment.xenium
Arguments
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input Xenium Output Bundle |
--add_experiment_xenium | boolean | Whether to add xenium.experiment parameters to the metadata. |
--add_parquet_paths | boolean | Whether to add parquet paths to the metadata. If True, `transcripts.parquet`, `cell_boundaries.parquet`, `nucleus_boundaries.parquet` will be added to the metadata. |
--alternative_experiment_features | string multiple | Feature names containing these strings will be moved to altExps(sxe) slots as separate SpatialExperiment objects. |
--output -o | file required output | Output SpatialExperiment file |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
add_experiment_xenium: [ true ]
add_parquet_paths: [ true ]
alternative_experiment_features:
[
"NegControlProbe",
"UnassignedCodeword",
"NegControlCodeword",
"antisense",
"BLANK"
]
output: "$id.$key.output.rds"
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_xenium_to_spatialexperiment/main.nf \
-params-file params.yaml Relationships
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Current component
convert/from_xenium_to_spatialexperimentopenpipeline_spatial v0.7.0
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