metadata/add_id

Description

Add id of .obs. Also allows to make .obs_names (the .obs index) unique
by prefixing the values with an unique id per .h5mu file.

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'  
obs_output: [ "sample_id" ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.0 \  
  -main-script target/nextflow/metadata/add_id/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Path to the input .h5mu.
--input_id	string required	The input id.
--obs_output	string	Name of the .obs column where to store the id.
--output -o	file output	Name of output MuData file.
--make_observation_keys_unique	boolean_true	Join the id to the .obs index (.obs_names).
--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

--input_id

string

required

--obs_output

string

--output

-o

file

output

--make_observation_keys_unique

boolean_true

--output_compression

string