workflows/integration/totalvi_leiden

Description

Run totalVI integration, followed by neighbour calculations, leiden clustering and UMAP.

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"  
rna_modality: [ "rna" ]  
prot_modality: [ "prot" ]  
obs_batch: [ "sample_id" ]  
output: "$id.$key.output.h5mu"  
output_model: "$id.$key.output_model"  
early_stopping: [ true ]  
obsm_integrated: [ "X_integrated_totalvi" ]  
obsm_normalized_rna_output: [ "X_totalvi_normalized_rna" ]  
obsm_normalized_protein_output: [ "X_totalvi_normalized_protein" ]  
uns_neighbors: [ "totalvi_integration_neighbors" ]  
obsp_neighbor_distances: [ "totalvi_integration_distances" ]  
obsp_neighbor_connectivities: [ "totalvi_integration_connectivities" ]  
obs_cluster: [ "totalvi_integration_leiden" ]  
leiden_resolution: [ 1 ]  
obsm_umap: [ "X_totalvi_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/totalvi_leiden/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input	file required	Input h5mu file to be integrated.
--rna_modality	string
--prot_modality	string	Name of the modality in the input (query) h5mu file containing protein data
--input_layer_rna	string	Input layer to use from the rna modality for gene counts. If None, X is used
--input_layer_protein	string	Input layer to use from the protein modality for protein counts. If None, X is used
--obs_batch	string	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.
--var_gene_names	string	.var column in the rna modality containing gene names. By default, use mod['rna'].var_names.
--var_protein_names	string	.var column in the protein modality containing protein names. By default, use mod['prot'].var_names.
--var_input	string	.var column containing highly variable genes. By default, do not subset genes.

Name

Type & Properties

--id

string

required

--input

file

required

--rna_modality

string

--prot_modality

string

--input_layer_rna

string

--input_layer_protein

string

--obs_batch

string

--obs_size_factor

string

--obs_categorical_covariate

string

multiple

--obs_continuous_covariate

string

multiple

--var_gene_names

string

--var_protein_names

string

--var_input

string

Outputs

Name	Type & Properties	Description
--output	file required output	Destination path to the output.
--output_model	file output	Directory where the trained reference model will be stored.

Name

Type & Properties

--output

file

required

output

--output_model

file

output

TotalVI Training Options

Name	Type & Properties	Description
--max_epochs	integer	Number of passes through the dataset, defaults to (20000 / number of cells) * 400 or 400; whichever is smallest.
--early_stopping	boolean	Whether to perform early stopping with respect to the validation set.

Name

Type & Properties

--max_epochs

integer

--early_stopping

boolean

TotalVI Integration Options

Name	Type & Properties	Description
--obsm_integrated	string	In which .obsm slot to store the resulting integrated embedding.
--obsm_normalized_rna_output	string	In which .obsm slot to store the normalized RNA data from TOTALVI.
--obsm_normalized_protein_output	string	In which .obsm slot to store the normalized protein data from TOTALVI.

Name

Type & Properties

--obsm_integrated

string

--obsm_normalized_rna_output

string

--obsm_normalized_protein_output

string

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

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