dataflow/split_modalities

Description

Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files.

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
input: [ "sample_path" ]  
output: "$id.$key.output./path/to/output"  
output_types: "$id.$key.output_types.csv"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.3 \  
  -main-script target/nextflow/dataflow/split_modalities/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Path to a single .h5mu file.
--output -o	file required output	Output directory containing multiple h5mu files.
--output_types	file required output	A csv containing the base filename and modality type per output file.
--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

required

output

--output_types

file

required

output

--output_compression

string