metadata/duplicate_var

Description

Make a copy of an existing .var field or index to another .var field within the same mudata object.

Type

python_script

Links

Repository

Contributors

Launch

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 2.0.0 \  
  -main-script target/nextflow/metadata/duplicate_var/main.nf \  
  -params-file params.yaml

MuData Input

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--modality	string
--input_var_key	string	.var field to be copied. If no key is provided, the .var index will be copied.

Name

Type & Properties

--input

-i

file

required

--modality

string

--input_var_key

string

Arguments

Name	Type & Properties	Description
--overwrite_existing_key	boolean_true	If set to true and the --output_obs_key already exists in the input file, the .obs field will be overwritten.

Name

Type & Properties

--overwrite_existing_key

boolean_true

MuData Output

Name	Type & Properties	Description
--output -o	file required output	Output h5mu file.
--output_var_key	string required	.var field where the copied --input_var_key will be stored.
--output_compression	string	The compression format to be used on the output h5mu object.

Name

Type & Properties

--output

-o

file

required

output

--output_var_key

string

required

--output_compression

string