workflows/integration/scvi_leiden

Description

Run scvi integration followed by neighbour calculations, leiden clustering and run umap on the result.

Type

nextflow_script

Contributors

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"  
output_model: "$id.$key.output_model.output_dir"  
uns_neighbors: [ "scvi_integration_neighbors" ]  
obsp_neighbor_distances: [ "scvi_integration_distances" ]  
obsp_neighbor_connectivities: [ "scvi_integration_connectivities" ]  
obsm_output: [ "X_scvi_integrated" ]  
early_stopping_monitor: [ "elbo_validation" ]  
early_stopping_patience: [ 45 ]  
early_stopping_min_delta: [ 0 ]  
reduce_lr_on_plateau: [ true ]  
lr_factor: [ 0.6 ]  
lr_patience: [ 30 ]  
obs_cluster: [ "scvi_integration_leiden" ]  
leiden_resolution: [ 1 ]  
obsm_umap: [ "X_scvi_umap" ]  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.0 \  
  -main-script target/nextflow/workflows/integration/scvi_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.
--output_model	file required output	Folder where the state of the trained model will be saved to.

Name

Type & Properties

--output

file

required

output

--output_model

file

required

output

Neighbour calculation

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

Name

Type & Properties

--uns_neighbors

string

--obsp_neighbor_distances

string

--obsp_neighbor_connectivities

string

Scvi integration options

Name	Type & Properties	Description
--obs_batch	string required	Column name discriminating between your batches.
--obsm_output	string	In which .obsm slot to store the resulting integrated embedding.
--var_input	string	.var column containing highly variable genes. By default, do not subset genes.
--early_stopping	boolean	Whether to perform early stopping with respect to the validation set.
--early_stopping_monitor	string	Metric logged during validation set epoch.
--early_stopping_patience	integer	Number of validation epochs with no improvement after which training will be stopped.
--early_stopping_min_delta	double	Minimum change in the monitored quantity to qualify as an improvement, i.e. an absolute change of less than min_delta, will count as no improvement.
--max_epochs	integer	Number of passes through the dataset, defaults to (20000 / number of cells) * 400 or 400; whichever is smallest.
--reduce_lr_on_plateau	boolean	Whether to monitor validation loss and reduce learning rate when validation set `lr_scheduler_metric` plateaus.
--lr_factor	double	Factor to reduce learning rate.
--lr_patience	double	Number of epochs with no improvement after which learning rate will be reduced.

Name

Type & Properties

--obs_batch

string

required

--obsm_output

string

--var_input

string

--early_stopping

boolean

--early_stopping_monitor

string

--early_stopping_patience

integer

--early_stopping_min_delta

double

--max_epochs

integer

--reduce_lr_on_plateau

boolean

--lr_factor

double

--lr_patience

double

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