workflows/integration/scvi_leiden

Description

Run scvi integration followed by neighbour calculations, 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'  
tiledb_s3_no_sign_request: [ false ]  
modality: [ "rna" ]  
sanitize_ensembl_ids: [ true ]  
output: "$id.$key.output.h5mu"  
output_model: "$id.$key.output_model.output_dir"  
output_tiledb: "$id.$key.output_tiledb"  
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" ]  
id: "run"  
publish_dir: "output/"  
EOM

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

Inputs

Name	Type & Properties	Description
--input	file	Path to the sample. Mutually exclusive with the 'input_uri' argument.
--tiledb_input_uri	string	A URI containing the TileDB-SOMA objects. Mutually exclusive with the 'input' argument.
--tiledb_s3_region	string	Region where the TileDB-SOMA database is hosted.
--tiledb_endpoint	string	Custom endpoint to use to connect to S3
--tiledb_s3_no_sign_request	boolean	Do not sign S3 requests. Credentials will not be loaded if this argument is provided.

Name

Type & Properties

--input

file

--tiledb_input_uri

string

--tiledb_s3_region

string

--tiledb_endpoint

string

--tiledb_s3_no_sign_request

boolean

Input slots

Name	Type & Properties	Description
--layer	string	use specified layer for expression values instead of the .X object from the modality.
--modality	string	Which modality to process.
--sanitize_ensembl_ids	boolean	Whether to sanitize ensembl ids by removing version numbers.

Name

Type & Properties

--layer

string

--modality

string

--sanitize_ensembl_ids

boolean

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.
--output_tiledb	file output	Output the TileDB database to the specified directory instead of adding it to the existing database.

Name

Type & Properties

--output

file

required

output

--output_model

file

required

output

--output_tiledb

file

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.
--obs_size_factor	string	Key in adata.obs for size factor information. Instead of using library size as a size factor, the provided size factor column will be used as offset in the mean of the likelihood. Assumed to be on linear scale.
--obs_categorical_covariate	string multiple	Keys in adata.obs that correspond to categorical data. These covariates can be added in addition to the batch covariate and are also treated as nuisance factors (i.e., the model tries to minimize their effects on the latent space). Thus, these should not be used for biologically-relevant factors that you do _not_ want to correct for.
--obs_continuous_covariate	string multiple	Keys in adata.obs that correspond to continuous data. These covariates can be added in addition to the batch covariate and are also treated as nuisance factors (i.e., the model tries to minimize their effects on the latent space). Thus, these should not be used for biologically-relevant factors that you do _not_ want to correct for.
--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

--obs_size_factor

string

--obs_categorical_covariate

string

multiple

--obs_continuous_covariate

string

multiple

--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