convert/from_xenium_to_h5mu

Description

Converts the output from Xenium to a single .h5mu file, where the count matrix is written to the rna modality.
The following files are expected to be present in the Xenium output bundle:
├── cell_feature_matrix.h5
├── cells.parquet
├── experiment.xenium
└── metrics_summary.csv

Type

python_script

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.h5mu"  
obsm_coordinates: [ "spatial" ]  
uns_experiment: [ "xenium_experiment" ]  
uns_metrics: [ "xenium_metrics" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.1.1 \  
  -main-script target/nextflow/convert/from_xenium_to_h5mu/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input folder. Must contain the output from a Xenium run.
--output -o	file output	Output .h5mu file.
--obsm_coordinates	string	Name of the .obsm slot under which to store the cell centroid coordinates.
--uns_experiment	string	Name of the .uns slot under which to store the Xenium experiment specifications.
--uns_metrics	string	Name of the .uns slot under which to store the summary QC metrics.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--input

-i

file

required

--output

-o

file

output

--obsm_coordinates

string

--uns_experiment

string

--uns_metrics

string

--output_compression

string