workflows/multiomics/neighbors_leiden_umap

Description

Performs neighborhood search, leiden clustering and run umap on an integrated embedding.

Type

nextflow_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.h5mu"  
leiden_resolution: [ 1 ]  
id: "run"  
publish_dir: "output/"  
EOM

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

Inputs

Name	Type & Properties	Description
--input	file required	Path to the sample.
--obsm_input	string required	The key of the embedding to use as input.
--modality	string	Which modality to process.

Name

Type & Properties

--input

file

required

--obsm_input

string

required

--modality

string

Outputs

Name	Type & Properties	Description
--output	file required output	Destination path to the output.

Name

Type & Properties

--output

file

required

output

Neighbour calculation

Name	Type & Properties	Description
--uns_neighbors	string required	In which .uns slot to store various neighbor output objects.
--obsp_neighbor_distances	string required	In which .obsp slot to store the distance matrix between the resulting neighbors.
--obsp_neighbor_connectivities	string required	In which .obsp slot to store the connectivities matrix between the resulting neighbors.

Name

Type & Properties

--uns_neighbors

string

required

--obsp_neighbor_distances

string

required

--obsp_neighbor_connectivities

string

required

Clustering options

Name	Type & Properties	Description
--obs_cluster	string	Prefix for the .obs keys under which to add the cluster labels. Newly created columns in .obs will be created from the specified value for '--obs_cluster' suffixed with an underscore and one of the resolutions resolutions specified in '--leiden_resolution'.
--leiden_resolution	double multiple	Control the coarseness of the clustering. Higher values lead to more clusters.

Name

Type & Properties

--obs_cluster

string

--leiden_resolution

double

multiple

Umap options

Name	Type & Properties	Description
--obsm_umap	string	In which .obsm slot to store the resulting UMAP embedding. When not specified, UMAP will not be executed.

Name

Type & Properties

--obsm_umap

string