integrate/scanorama

Description

Use Scanorama to integrate different experiments.

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'  
modality: [ "rna" ]  
output: "$id.$key.output"  
obs_batch: [ "batch" ]  
obsm_input: [ "X_pca" ]  
obsm_output: [ "X_scanorama" ]  
knn: [ 20 ]  
batch_size: [ 5000 ]  
sigma: [ 15 ]  
approx: [ true ]  
alpha: [ 0.1 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.2 \  
  -main-script target/nextflow/integrate/scanorama/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--modality	string	Which modality from the input MuData file to process.
--output -o	file required output	Output .h5mu file
--obs_batch	string	Column name discriminating between your batches.
--obsm_input	string	Basis obsm slot to run scanorama on.
--obsm_output	string	The name of the field in adata.obsm where the integrated embeddings will be stored after running this function. Defaults to X_scanorama.
--knn	integer	Number of nearest neighbors to use for matching.
--batch_size	integer	The batch size used in the alignment vector computation. Useful when integrating very large (>100k samples) datasets. Set to large value that runs within available memory.
--sigma	double	Correction smoothing parameter on Gaussian kernel.
--approx	boolean	Use approximate nearest neighbors with Python annoy; greatly speeds up matching runtime.
--alpha	double	Alignment score minimum cutoff
--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

--output

-o

file

required

output

--obs_batch

string

--obsm_input

string

--obsm_output

string

--knn

integer

--batch_size

integer

--sigma

double

--approx

boolean

--alpha

double

--output_compression

string