Viash Hub

Description

Converts a single layer h5ad file into a single MuData object

Arguments

Name	Type & Properties	Description
--input -i	file required multiple	Input h5ad files
--modality	string multiple	List of names to use for the modalities. Will be used as the keys in the .mod attribute in the output MuData object The number of items provided for this argument equal the number of input files (--input) and their order should match.
--output -o	file output	Output MuData file.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata H5 files. By default no compression is applied.

Name

Type & Properties

--input

-i

file

required

multiple

--modality

string

multiple

--output

-o

file

output

--output_compression

string

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
input: [ "input.h5ad" ]  
modality: [ "rna" ]  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/convert/from_h5ad_to_h5mu/main.nf \  
  -params-file params.yaml

Relationships

Used by

1 relationships

workflows/ingestion/conversionopenpipeline v4.2.0

Current component

convert/from_h5ad_to_h5muopenpipeline v4.2.0

Uses

0 relationships

No component dependencies found.