workflows/integration/bbknn_leiden

Description

Run bbknn followed by leiden clustering and run umap on the result.

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'  
id: "run"  
layer: [ "log_normalized" ]  
modality: [ "rna" ]  
output: "$id.$key.output.h5mu"  
obsm_input: [ "X_pca" ]  
obs_batch: [ "sample_id" ]  
uns_output: [ "bbknn_integration_neighbors" ]  
obsp_distances: [ "bbknn_integration_distances" ]  
obsp_connectivities: [ "bbknn_integration_connectivities" ]  
n_neighbors_within_batch: [ 3 ]  
n_pcs: [ 50 ]  
obs_cluster: [ "bbknn_integration_leiden" ]  
leiden_resolution: [ 1 ]  
obsm_umap: [ "X_leiden_bbknn_umap" ]  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/workflows/integration/bbknn_leiden/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input	file required	Path to the sample.
--layer	string	use specified layer for expression values instead of the .X object from the modality.
--modality	string	Which modality to process.

Name

Type & Properties

--id

string

required

--input

file

required

--layer

string

--modality

string

Outputs

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

Name

Type & Properties

--output

file

required

output

Bbknn

Name	Type & Properties	Description
--obsm_input	string	The dimensionality reduction in `.obsm` to use for neighbour detection. Defaults to X_pca.
--obs_batch	string	.obs column name discriminating between your batches.
--uns_output	string	Mandatory .uns slot to store various neighbor output objects.
--obsp_distances	string	In which .obsp slot to store the distance matrix between the resulting neighbors.
--obsp_connectivities	string	In which .obsp slot to store the connectivities matrix between the resulting neighbors.
--n_neighbors_within_batch	integer	How many top neighbours to report for each batch; total number of neighbours in the initial k-nearest-neighbours computation will be this number times the number of batches.
--n_pcs	integer	How many dimensions (in case of PCA, principal components) to use in the analysis.
--n_trim	integer	Trim the neighbours of each cell to these many top connectivities. May help with population independence and improve the tidiness of clustering. The lower the value the more independent the individual populations, at the cost of more conserved batch effect. If `None` (default), sets the parameter value automatically to 10 times `neighbors_within_batch` times the number of batches. Set to 0 to skip.

Name

Type & Properties

--obsm_input

string

--obs_batch

string

--uns_output

string

--obsp_distances

string

--obsp_connectivities

string

--n_neighbors_within_batch

integer

--n_pcs

integer

--n_trim

integer

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.

Name

Type & Properties

--obsm_umap

string