integrate/harmonypy

Description

Performs Harmony integration based as described in https://github.com/immunogenomics/harmony. Based on an implementation in python from https://github.com/slowkow/harmonypy

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'  
output: "$id.$key.output"  
modality: [ "rna" ]  
obsm_input: [ "X_pca" ]  
obsm_output: [ "X_pca_integrated" ]  
theta: [ 2 ]  
id: "run"  
publish_dir: "output/"  
EOM

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

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--output -o	file required output	Output h5mu file.
--modality	string	Which modality from the input MuData file to process.
--obsm_input	string	Which .obsm slot to use as a starting PCA embedding.
--obsm_output	string	In which .obsm slot to store the resulting integrated embedding.
--theta	double multiple	Diversity clustering penalty parameter. Can be set as a single value for all batch observations or as multiple values, one for each observation in the batches defined by --obs_covariates. theta=0 does not encourage any diversity. Larger values of theta result in more diverse clusters.
--obs_covariates	string required multiple	The .obs field(s) that define the covariate(s) to regress out.
--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

--modality

string

--obsm_input

string

--obsm_output

string

--theta

double

multiple

--obs_covariates

string

required

multiple

--output_compression

string