Viash Hub

Description

Move a data matrix stored at the .layers or .X attributes in a MuData object to another layer.

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--modality	string	Which modality from the input MuData file to process.
--input_layer	string	Input layer to move to a new output location. If specified, will be used to select a key from .layers, otherwise .X is used.
--output -o	file required output	Output h5mu file.
--output_layer	string	Destination location for the layer. If not provided, .X will be used, Otherwise, will be the key for the .layers attribute in the output MuData 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

--modality

string

--input_layer

string

--output

-o

file

required

output

--output_layer

string

--output_compression

string

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.0 \  
  -main-script target/nextflow/transform/move_layer/main.nf \  
  -params-file params.yaml

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Current component

transform/move_layeropenpipeline v4.0.0

Uses

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